Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling
The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional c...
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Published in | BMC genomics Vol. 12; no. 1; p. 441 |
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Main Authors | , , , , , , , , , , , , , , , |
Format | Journal Article |
Language | English |
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BioMed Central Ltd
05.09.2011
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Abstract | The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models.
To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs.
The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events. |
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AbstractList | Abstract Background: The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results: To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion: The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events. The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events. The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events. BACKGROUNDThe developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. RESULTSTo address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. CONCLUSIONThe resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events. Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated for gene expression profiling combined with systematic in situ screening. These studies, however, fall short of capturing the transcriptional complexity arising from each locus due to the limited scope of microarray-based technology, which is largely based on "gene-centric" models. Results To address this, the polyadenylated RNA and microRNA transcriptomes of the 15.5 dpc mouse kidney were profiled using strand-specific RNA-sequencing (RNA-Seq) to a depth sufficient to complement spatial maps from pre-existing microarray datasets. The transcriptional complexity of RNAs arising from mouse RefSeq loci was catalogued; including 3568 alternatively spliced transcripts and 532 uncharacterized alternate 3' UTRs. Antisense expressions for 60% of RefSeq genes was also detected including uncharacterized non-coding transcripts overlapping kidney progenitor markers, Six2 and Sall1, and were validated by section in situ hybridization. Analysis of genes known to be involved in kidney development, particularly during mesenchymal-to-epithelial transition, showed an enrichment of non-coding antisense transcripts extended along protein-coding RNAs. Conclusion The resulting resource further refines the transcriptomic cartography of kidney organogenesis by integrating deep RNA sequencing data with locus-based information from previously published expression atlases. The added resolution of RNA-Seq has provided the basis for a transition from classical gene-centric models of kidney development towards more accurate and detailed "transcript-centric" representations, which highlights the extent of transcriptional complexity of genes that direct complex development events. |
ArticleNumber | 441 |
Audience | Academic |
Author | Mercer, Tim R Little, Melissa H Tang, Dave Kolle, Gabriel Cloonan, Nicole Nourbakhsh, Ehsan Mattick, John S Krishnan, Keerthana Rumballe, Bree A Steen, Jason A Thiagarajan, Rathi D Gardiner, Brooke B Georgas, Kylie M Grimmond, Sean M Wani, Shivangi Chiu, Han S |
AuthorAffiliation | 1 Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia |
AuthorAffiliation_xml | – name: 1 Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia |
Author_xml | – sequence: 1 givenname: Rathi D surname: Thiagarajan fullname: Thiagarajan, Rathi D email: rathi@scripps.edu organization: Institute for Molecular Bioscience, The University of Queensland, St, Lucia QLD 4072, Australia. rathi@scripps.edu – sequence: 2 givenname: Nicole surname: Cloonan fullname: Cloonan, Nicole – sequence: 3 givenname: Brooke B surname: Gardiner fullname: Gardiner, Brooke B – sequence: 4 givenname: Tim R surname: Mercer fullname: Mercer, Tim R – sequence: 5 givenname: Gabriel surname: Kolle fullname: Kolle, Gabriel – sequence: 6 givenname: Ehsan surname: Nourbakhsh fullname: Nourbakhsh, Ehsan – sequence: 7 givenname: Shivangi surname: Wani fullname: Wani, Shivangi – sequence: 8 givenname: Dave surname: Tang fullname: Tang, Dave – sequence: 9 givenname: Keerthana surname: Krishnan fullname: Krishnan, Keerthana – sequence: 10 givenname: Kylie M surname: Georgas fullname: Georgas, Kylie M – sequence: 11 givenname: Bree A surname: Rumballe fullname: Rumballe, Bree A – sequence: 12 givenname: Han S surname: Chiu fullname: Chiu, Han S – sequence: 13 givenname: Jason A surname: Steen fullname: Steen, Jason A – sequence: 14 givenname: John S surname: Mattick fullname: Mattick, John S – sequence: 15 givenname: Melissa H surname: Little fullname: Little, Melissa H – sequence: 16 givenname: Sean M surname: Grimmond fullname: Grimmond, Sean M |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/21888672$$D View this record in MEDLINE/PubMed |
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Cites_doi | 10.1073/pnas.091110798 10.1186/1471-2164-9-564 10.1038/nmeth.1315 10.1038/ng0794-440 10.1093/nar/gkm952 10.1016/j.devcel.2010.04.008 10.1016/S0378-1119(00)00016-0 10.1016/j.devcel.2006.09.009 10.1016/j.stem.2008.05.020 10.1038/ncb1722 10.1038/ki.2010.385 10.1126/science.1163853 10.1242/dev.037432 10.1093/bioinformatics/btp692 10.1101/gr.084129.108 10.1186/gb-2008-9-9-234 10.1038/sj.emboj.7601381 10.1093/bioinformatics/btp459 10.1007/s003359900870 10.1261/rna.7240905 10.1681/ASN.2004121127 10.1074/jbc.M609578200 10.1016/j.ydbio.2003.11.002 10.1016/S0305-0491(98)00053-4 10.1016/j.devcel.2008.09.007 10.1186/1471-2105-7-328 10.1093/hmg/ddi084 10.1101/gad.205001 10.1016/j.ydbio.2009.05.578 10.1101/gad.1640608 10.1073/pnas.88.21.9618 10.1681/ASN.2008020233 10.1038/nature05874 10.1101/gr.079558.108 10.1261/rna.562907 10.1016/j.ydbio.2008.10.009 10.1016/S0888-7543(02)00023-X 10.1038/ncb1373 10.1242/dev.01858 10.1073/pnas.96.14.7962 10.1093/bioinformatics/btl429 10.1242/dev.129.22.5301 10.1242/dev.119.3.711 10.1242/dev.121.11.3603 10.1038/nrg2484 10.1038/271501a0 10.1097/01.ASN.0000043081.65110.C4 10.1038/nrm2738 10.1016/j.molcel.2009.08.008 10.1016/j.ydbio.2007.08.007 10.1186/1471-2164-11-205 10.1038/nprot.2009.236 10.1186/gb-2010-11-8-r86 10.1093/nar/gkl782 10.1681/ASN.2009070718 10.1016/j.molcel.2009.09.008 10.1002/dvdy.21787 10.1186/gb-2002-3-9-research0044 10.1006/bbrc.1997.6545 10.1093/hmg/2.11.1967 10.1186/gb-2010-11-5-r56 10.1152/physiolgenomics.00043.2005 10.1038/nmeth.1223 10.1016/S0092-8674(04)00045-5 10.1093/hmg/6.13.2247 10.1126/science.1112009 10.1002/(SICI)1096-9896(199808)185:4<352::AID-PATH119>3.0.CO;2-# 10.1038/ng1953 10.1016/j.ygeno.2005.02.001 10.1242/dev.128.16.3105 10.1038/nmeth.1226 |
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References | 19906860 - Development. 2009 Dec;136(23):3927-36 7920666 - Nat Genet. 1994 Jul;7(3):440-7 18376396 - Nat Cell Biol. 2008 May;10(5):593-601 20493806 - Dev Cell. 2010 May 18;18(5):698-712 15013809 - Dev Biol. 2004 Mar 15;267(2):505-16 9745033 - Mamm Genome. 1998 Oct;9(10):799-806 19000842 - Dev Cell. 2008 Nov;15(5):781-91 19015660 - Nat Rev Genet. 2009 Jan;10(1):57-63 9168922 - Biochem Biophys Res Commun. 1997 Apr 28;233(3):723-8 18992736 - Dev Biol. 2009 Jan 1;325(1):179-88 1658787 - Proc Natl Acad Sci U S A. 1991 Nov 1;88(21):9618-22 15998744 - Physiol Genomics. 2005 Oct 17;23(2):159-71 622185 - Nature. 1978 Feb 9;271(5645):501 20738864 - Genome Biol. 2010;11(8):R86 17277314 - J Biol Chem. 2007 Apr 6;282(14):10553-60 19088304 - Genome Res. 2009 Mar;19(3):481-90 16895931 - Bioinformatics. 2006 Oct 15;22(20):2475-9 20507594 - Genome Biol. 2010;11(5):R56 18828881 - Genome Biol. 2008;9(9):234 20944551 - Kidney Int. 2011 Feb;79(3):317-30 16489342 - Nat Cell Biol. 2006 Mar;8(3):278-84 18516045 - Nat Methods. 2008 Jul;5(7):621-8 20360310 - J Am Soc Nephrol. 2010 May;21(5):756-61 20436464 - Nat Biotechnol. 2010 May;28(5):511-5 11688560 - Development. 2001 Aug;128(16):3105-15 19056939 - Science. 2008 Dec 19;322(5909):1855-7 17011485 - Dev Cell. 2006 Oct;11(4):441-50 17036046 - EMBO J. 2006 Nov 1;25(21):5214-28 10717475 - Gene. 2000 Mar 21;245(2):245-51 19648138 - Bioinformatics. 2009 Oct 1;25(19):2615-6 12538735 - J Am Soc Nephrol. 2003 Feb;14(2):352-8 15701730 - RNA. 2005 Mar;11(3):241-7 18985749 - Dev Dyn. 2008 Dec;237(12):3738-48 14744438 - Cell. 2004 Jan 23;116(2):281-97 10393930 - Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):7962-7 12225583 - Genome Biol. 2002 Aug 22;3(9):RESEARCH0044 12573261 - Genomics. 2003 Jan;81(1):58-66 9361030 - Hum Mol Genet. 1997 Dec;6(13):2247-55 19038026 - BMC Genomics. 2008;9:564 19818710 - Mol Cell. 2009 Oct 9;36(1):61-74 12399320 - Development. 2002 Nov;129(22):5301-12 17237358 - RNA. 2007 Mar;13(3):313-6 17765889 - Dev Biol. 2007 Oct 15;310(2):442-53 19638999 - Nat Rev Mol Cell Biol. 2009 Sep;10(9):637-43 8281163 - Hum Mol Genet. 1993 Nov;2(11):1967-8 17940140 - RNA. 2007 Dec;13(12):2287-99 18682239 - Cell Stem Cell. 2008 Aug 7;3(2):169-81 15703187 - Hum Mol Genet. 2005 Apr 1;14(7):913-23 20346121 - BMC Genomics. 2010;11:205 17991681 - Nucleic Acids Res. 2008 Jan;36(Database issue):D154-8 19782023 - Mol Cell. 2009 Sep 24;35(6):737-8 20203668 - Nat Protoc. 2010 Mar;5(3):516-35 15930111 - Development. 2005 Jun;132(12):2809-23 16817968 - BMC Bioinformatics. 2006;7:328 20022975 - Bioinformatics. 2010 Feb 15;26(4):493-500 17082204 - Nucleic Acids Res. 2007 Jan;35(Database issue):D156-61 18776121 - J Am Soc Nephrol. 2008 Nov;19(11):2150-8 9787767 - Comp Biochem Physiol B Biochem Mol Biol. 1998 Apr;119(4):761-7 11562352 - Genes Dev. 2001 Sep 15;15(18):2433-44 8582274 - Development. 1995 Nov;121(11):3603-13 18381893 - Genes Dev. 2008 Apr 1;22(7):894-907 16141073 - Science. 2005 Sep 2;309(5740):1564-6 19501082 - Dev Biol. 2009 Aug 15;332(2):273-86 15885504 - Genomics. 2005 Jun;85(6):782-9 17220889 - Nat Genet. 2007 Feb;39(2):259-63 18516046 - Nat Methods. 2008 Jul;5(7):613-9 9828833 - J Pathol. 1998 Aug;185(4):352-9 19349980 - Nat Methods. 2009 May;6(5):377-82 20691850 - Curr Top Dev Biol. 2010;90:193-229 17571346 - Nature. 2007 Jun 14;447(7146):799-816 8187639 - Development. 1993 Nov;119(3):711-20 20436462 - Nat Biotechnol. 2010 May;28(5):503-10 11331749 - Proc Natl Acad Sci U S A. 2001 May 8;98(10):5649-54 15917337 - J Am Soc Nephrol. 2005 Jul;16(7):1993-2002 18550803 - Genome Res. 2008 Sep;18(9):1509-17 DA Haber (3594_CR32) 1991; 88 S Baskerville (3594_CR50) 2005; 11 J Shendure (3594_CR58) 2002; 3 Q Wei (3594_CR45) 2010; 21 Y Lu (3594_CR54) 2007; 310 N Cloonan (3594_CR11) 2008; 5 K Georgas (3594_CR26) 2009; 332 UW Rothenpieler (3594_CR40) 1993; 119 3594_CR78 3594_CR79 F Tang (3594_CR17) 2009; 6 HK Saini (3594_CR51) 2008; 9 C Trapnell (3594_CR14) 2010 EW Brunskill (3594_CR5) 2008; 15 KM Schmidt-Ott (3594_CR3) 2005; 16 T Watanabe (3594_CR55) 2008; 237 G Holmes (3594_CR71) 1997; 233 PA Gregory (3594_CR48) 2008; 10 D Wilhelm (3594_CR81) 2007; 282 S Katayama (3594_CR60) 2005; 309 SR Patel (3594_CR41) 2004; 267 AR Dallosso (3594_CR63) 2007; 13 A Konlg (3594_CR33) 1993; 2 MA Faghihi (3594_CR59) 2010; 11 N Klüver (3594_CR35) 2009; 325 Y Zhang (3594_CR64) 2007; 35 DA Loebel (3594_CR56) 2005; 85 VA Gennarino (3594_CR49) 2009; 19 X Ge (3594_CR73) 2006; 22 G Alfano (3594_CR65) 2005; 14 VK Nagalakshmi (3594_CR46) 2011; 79 3594_CR80 G Challen (3594_CR4) 2005; 23 F Costantini (3594_CR1) 2010; 18 AS Flynt (3594_CR76) 2007; 39 Z Wang (3594_CR7) 2009; 10 B Li (3594_CR21) 2010; 26 M Wang (3594_CR22) 2006; 7 O Beltcheva (3594_CR37) 2003; 14 MA Faghihi (3594_CR74) 2009; 10 F Tang (3594_CR16) 2010; 5 Y Nakatsuru (3594_CR36) 2000; 245 L Thorrez (3594_CR10) 2010; 11 N Cloonan (3594_CR30) 2009; 25 V Ruotsalainen (3594_CR38) 1999; 96 RO Stuart (3594_CR6) 2001; 98 DP Bartel (3594_CR43) 2004; 116 Y He (3594_CR72) 2008; 322 MA Faghihi (3594_CR57) 2009; 10 M Self (3594_CR20) 2006; 25 SS Potter (3594_CR61) 1998; 9 J Yu (3594_CR77) 2002; 129 JC Marioni (3594_CR13) 2008; 18 A Kobayashi (3594_CR19) 2008; 3 W Gilbert (3594_CR29) 1978; 271 S Abdelhak (3594_CR68) 1997; 6 I Naguibneva (3594_CR69) 2006; 8 SJ Harvey (3594_CR44) 2008; 19 T Moulton (3594_CR52) 1994; 7 R Nishinakamura (3594_CR39) 2001; 128 N Cloonan (3594_CR8) 2008; 9 S-M Park (3594_CR47) 2008; 22 3594_CR23 K Moorwood (3594_CR62) 1998; 185 E Birney (3594_CR9) 2007; 447 A Kobayashi (3594_CR25) 2005; 132 3594_CR27 CA MacArthur (3594_CR67) 1995; 121 LD Spotila (3594_CR34) 1998; 119 LK Mathew (3594_CR70) 2009; 35 X Cai (3594_CR53) 2007 FC Noonan (3594_CR66) 2003; 81 S Griffiths-Jones (3594_CR18) 2008; 36 J Goecks (3594_CR24) 2010; 11 AH Juan (3594_CR75) 2009; 36 M Guttman (3594_CR15) 2010 E de Graaff (3594_CR31) 2001; 15 WP Kloosterman (3594_CR42) 2006; 11 M Little (3594_CR2) 2010 A Mortazavi (3594_CR12) 2008; 5 R Agrawal (3594_CR28) 2009; 136 |
References_xml | – volume: 98 start-page: 5649 year: 2001 ident: 3594_CR6 publication-title: Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.091110798 contributor: fullname: RO Stuart – volume: 9 start-page: 564 year: 2008 ident: 3594_CR51 publication-title: BMC genomics doi: 10.1186/1471-2164-9-564 contributor: fullname: HK Saini – volume: 6 start-page: 377 year: 2009 ident: 3594_CR17 publication-title: Nat Meth doi: 10.1038/nmeth.1315 contributor: fullname: F Tang – volume: 7 start-page: 440 year: 1994 ident: 3594_CR52 publication-title: Nat Genet doi: 10.1038/ng0794-440 contributor: fullname: T Moulton – volume: 36 start-page: D154 year: 2008 ident: 3594_CR18 publication-title: Nucleic Acids Res doi: 10.1093/nar/gkm952 contributor: fullname: S Griffiths-Jones – volume: 18 start-page: 698 year: 2010 ident: 3594_CR1 publication-title: Developmental cell doi: 10.1016/j.devcel.2010.04.008 contributor: fullname: F Costantini – volume: 245 start-page: 245 year: 2000 ident: 3594_CR36 publication-title: Gene doi: 10.1016/S0378-1119(00)00016-0 contributor: fullname: Y Nakatsuru – volume: 11 start-page: 441 year: 2006 ident: 3594_CR42 publication-title: Developmental cell doi: 10.1016/j.devcel.2006.09.009 contributor: fullname: WP Kloosterman – volume: 3 start-page: 169 year: 2008 ident: 3594_CR19 publication-title: Cell Stem Cell doi: 10.1016/j.stem.2008.05.020 contributor: fullname: A Kobayashi – volume: 10 start-page: 593 year: 2008 ident: 3594_CR48 publication-title: Nature cell biology doi: 10.1038/ncb1722 contributor: fullname: PA Gregory – volume: 79 start-page: 317 year: 2011 ident: 3594_CR46 publication-title: Kidney Int doi: 10.1038/ki.2010.385 contributor: fullname: VK Nagalakshmi – volume: 322 start-page: 1855 year: 2008 ident: 3594_CR72 publication-title: Science doi: 10.1126/science.1163853 contributor: fullname: Y He – volume: 136 start-page: 3927 year: 2009 ident: 3594_CR28 publication-title: Development doi: 10.1242/dev.037432 contributor: fullname: R Agrawal – volume: 26 start-page: 493 year: 2010 ident: 3594_CR21 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp692 contributor: fullname: B Li – volume: 19 start-page: 481 year: 2009 ident: 3594_CR49 publication-title: Genome Research doi: 10.1101/gr.084129.108 contributor: fullname: VA Gennarino – volume: 9 start-page: 234 year: 2008 ident: 3594_CR8 publication-title: Genome biology doi: 10.1186/gb-2008-9-9-234 contributor: fullname: N Cloonan – volume: 25 start-page: 5214 year: 2006 ident: 3594_CR20 publication-title: Embo J doi: 10.1038/sj.emboj.7601381 contributor: fullname: M Self – volume: 25 start-page: 2615 year: 2009 ident: 3594_CR30 publication-title: Bioinformatics (Oxford, England) doi: 10.1093/bioinformatics/btp459 contributor: fullname: N Cloonan – ident: 3594_CR27 – volume: 9 start-page: 799 year: 1998 ident: 3594_CR61 publication-title: Mammalian Genome doi: 10.1007/s003359900870 contributor: fullname: SS Potter – volume: 11 start-page: 241 year: 2005 ident: 3594_CR50 publication-title: RNA doi: 10.1261/rna.7240905 contributor: fullname: S Baskerville – volume: 16 start-page: 1993 year: 2005 ident: 3594_CR3 publication-title: Journal of the American Society of Nephrology: JASN doi: 10.1681/ASN.2004121127 contributor: fullname: KM Schmidt-Ott – volume: 282 start-page: 10553 year: 2007 ident: 3594_CR81 publication-title: Journal of Biological Chemistry doi: 10.1074/jbc.M609578200 contributor: fullname: D Wilhelm – volume: 267 start-page: 505 year: 2004 ident: 3594_CR41 publication-title: Developmental Biology doi: 10.1016/j.ydbio.2003.11.002 contributor: fullname: SR Patel – volume: 119 start-page: 761 year: 1998 ident: 3594_CR34 publication-title: Comparative Biochemistry and Physiology Part B: Biochemistry and Molecular Biology doi: 10.1016/S0305-0491(98)00053-4 contributor: fullname: LD Spotila – volume: 15 start-page: 781 year: 2008 ident: 3594_CR5 publication-title: Developmental Cell doi: 10.1016/j.devcel.2008.09.007 contributor: fullname: EW Brunskill – volume: 7 start-page: 328 year: 2006 ident: 3594_CR22 publication-title: BMC Bioinformatics doi: 10.1186/1471-2105-7-328 contributor: fullname: M Wang – volume: 14 start-page: 913 year: 2005 ident: 3594_CR65 publication-title: Human Molecular Genetics doi: 10.1093/hmg/ddi084 contributor: fullname: G Alfano – volume: 15 start-page: 2433 year: 2001 ident: 3594_CR31 publication-title: Genes & Development doi: 10.1101/gad.205001 contributor: fullname: E de Graaff – volume: 332 start-page: 273 year: 2009 ident: 3594_CR26 publication-title: Dev Biol doi: 10.1016/j.ydbio.2009.05.578 contributor: fullname: K Georgas – volume: 22 start-page: 894 year: 2008 ident: 3594_CR47 publication-title: Genes & Development doi: 10.1101/gad.1640608 contributor: fullname: S-M Park – volume: 88 start-page: 9618 year: 1991 ident: 3594_CR32 publication-title: Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.88.21.9618 contributor: fullname: DA Haber – volume: 19 start-page: 2150 year: 2008 ident: 3594_CR44 publication-title: Journal of the American Society of Nephrology: JASN doi: 10.1681/ASN.2008020233 contributor: fullname: SJ Harvey – volume: 447 start-page: 799 year: 2007 ident: 3594_CR9 publication-title: Nature doi: 10.1038/nature05874 contributor: fullname: E Birney – volume: 18 start-page: 1509 year: 2008 ident: 3594_CR13 publication-title: Genome research doi: 10.1101/gr.079558.108 contributor: fullname: JC Marioni – volume: 13 start-page: 2287 year: 2007 ident: 3594_CR63 publication-title: RNA doi: 10.1261/rna.562907 contributor: fullname: AR Dallosso – volume: 325 start-page: 179 year: 2009 ident: 3594_CR35 publication-title: Developmental Biology doi: 10.1016/j.ydbio.2008.10.009 contributor: fullname: N Klüver – ident: 3594_CR80 – ident: 3594_CR78 – start-page: 193 volume-title: Current Topics in Developmental Biology year: 2010 ident: 3594_CR2 contributor: fullname: M Little – volume: 81 start-page: 58 year: 2003 ident: 3594_CR66 publication-title: Genomics doi: 10.1016/S0888-7543(02)00023-X contributor: fullname: FC Noonan – volume: 8 start-page: 278 year: 2006 ident: 3594_CR69 publication-title: Nat Cell Biol doi: 10.1038/ncb1373 contributor: fullname: I Naguibneva – volume-title: Nature biotechnology year: 2010 ident: 3594_CR15 contributor: fullname: M Guttman – volume: 132 start-page: 2809 year: 2005 ident: 3594_CR25 publication-title: Development doi: 10.1242/dev.01858 contributor: fullname: A Kobayashi – volume: 96 start-page: 7962 year: 1999 ident: 3594_CR38 publication-title: Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.96.14.7962 contributor: fullname: V Ruotsalainen – volume: 22 start-page: 2475 year: 2006 ident: 3594_CR73 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl429 contributor: fullname: X Ge – volume: 129 start-page: 5301 year: 2002 ident: 3594_CR77 publication-title: Development doi: 10.1242/dev.129.22.5301 contributor: fullname: J Yu – volume: 119 start-page: 711 year: 1993 ident: 3594_CR40 publication-title: Development (Cambridge, England) doi: 10.1242/dev.119.3.711 contributor: fullname: UW Rothenpieler – volume: 121 start-page: 3603 year: 1995 ident: 3594_CR67 publication-title: Development doi: 10.1242/dev.121.11.3603 contributor: fullname: CA MacArthur – volume: 10 start-page: 57 year: 2009 ident: 3594_CR7 publication-title: Nat Rev Genet doi: 10.1038/nrg2484 contributor: fullname: Z Wang – volume: 271 start-page: 501 year: 1978 ident: 3594_CR29 publication-title: Nature doi: 10.1038/271501a0 contributor: fullname: W Gilbert – volume: 14 start-page: 352 year: 2003 ident: 3594_CR37 publication-title: J Am Soc Nephrol doi: 10.1097/01.ASN.0000043081.65110.C4 contributor: fullname: O Beltcheva – volume: 10 start-page: 637 year: 2009 ident: 3594_CR74 publication-title: Nat Rev Mol Cell Biol doi: 10.1038/nrm2738 contributor: fullname: MA Faghihi – volume: 36 start-page: 61 year: 2009 ident: 3594_CR75 publication-title: Molecular cell doi: 10.1016/j.molcel.2009.08.008 contributor: fullname: AH Juan – volume: 310 start-page: 442 year: 2007 ident: 3594_CR54 publication-title: Developmental Biology doi: 10.1016/j.ydbio.2007.08.007 contributor: fullname: Y Lu – volume: 11 start-page: 205 year: 2010 ident: 3594_CR10 publication-title: BMC genomics doi: 10.1186/1471-2164-11-205 contributor: fullname: L Thorrez – volume: 5 start-page: 516 year: 2010 ident: 3594_CR16 publication-title: Nat Protocols doi: 10.1038/nprot.2009.236 contributor: fullname: F Tang – ident: 3594_CR23 – volume: 11 start-page: R86 year: 2010 ident: 3594_CR24 publication-title: Genome Biology doi: 10.1186/gb-2010-11-8-r86 contributor: fullname: J Goecks – volume: 35 start-page: D156 year: 2007 ident: 3594_CR64 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkl782 contributor: fullname: Y Zhang – ident: 3594_CR79 – volume: 21 start-page: 756 year: 2010 ident: 3594_CR45 publication-title: Journal of the American Society of Nephrology: JASN doi: 10.1681/ASN.2009070718 contributor: fullname: Q Wei – volume: 35 start-page: 737 year: 2009 ident: 3594_CR70 publication-title: Molecular cell doi: 10.1016/j.molcel.2009.09.008 contributor: fullname: LK Mathew – volume: 237 start-page: 3738 year: 2008 ident: 3594_CR55 publication-title: Developmental dynamics: an official publication of the American Association of Anatomists doi: 10.1002/dvdy.21787 contributor: fullname: T Watanabe – volume: 3 start-page: RESEARCH0044 year: 2002 ident: 3594_CR58 publication-title: Genome biology doi: 10.1186/gb-2002-3-9-research0044 contributor: fullname: J Shendure – volume: 233 start-page: 723 year: 1997 ident: 3594_CR71 publication-title: Biochemical and Biophysical Research Communications doi: 10.1006/bbrc.1997.6545 contributor: fullname: G Holmes – volume: 2 start-page: 1967 year: 1993 ident: 3594_CR33 publication-title: Human Molecular Genetics doi: 10.1093/hmg/2.11.1967 contributor: fullname: A Konlg – volume: 11 start-page: R56 year: 2010 ident: 3594_CR59 publication-title: Genome biology doi: 10.1186/gb-2010-11-5-r56 contributor: fullname: MA Faghihi – volume: 23 start-page: 159 year: 2005 ident: 3594_CR4 publication-title: Physiological Genomics doi: 10.1152/physiolgenomics.00043.2005 contributor: fullname: G Challen – volume: 5 start-page: 613 year: 2008 ident: 3594_CR11 publication-title: Nature methods doi: 10.1038/nmeth.1223 contributor: fullname: N Cloonan – volume: 10 start-page: 637 year: 2009 ident: 3594_CR57 publication-title: Nature reviews Molecular cell biology doi: 10.1038/nrm2738 contributor: fullname: MA Faghihi – volume: 116 start-page: 281 year: 2004 ident: 3594_CR43 publication-title: Cell doi: 10.1016/S0092-8674(04)00045-5 contributor: fullname: DP Bartel – volume: 6 start-page: 2247 year: 1997 ident: 3594_CR68 publication-title: Human molecular genetics doi: 10.1093/hmg/6.13.2247 contributor: fullname: S Abdelhak – volume: 309 start-page: 1564 year: 2005 ident: 3594_CR60 publication-title: Science (New York, NY) doi: 10.1126/science.1112009 contributor: fullname: S Katayama – volume: 185 start-page: 352 year: 1998 ident: 3594_CR62 publication-title: The Journal of pathology doi: 10.1002/(SICI)1096-9896(199808)185:4<352::AID-PATH119>3.0.CO;2-# contributor: fullname: K Moorwood – volume: 39 start-page: 259 year: 2007 ident: 3594_CR76 publication-title: Nature genetics doi: 10.1038/ng1953 contributor: fullname: AS Flynt – volume-title: RNA year: 2007 ident: 3594_CR53 contributor: fullname: X Cai – volume: 85 start-page: 782 year: 2005 ident: 3594_CR56 publication-title: Genomics doi: 10.1016/j.ygeno.2005.02.001 contributor: fullname: DA Loebel – volume: 128 start-page: 3105 year: 2001 ident: 3594_CR39 publication-title: Development (Cambridge, England) doi: 10.1242/dev.128.16.3105 contributor: fullname: R Nishinakamura – volume: 5 start-page: 621 year: 2008 ident: 3594_CR12 publication-title: Nature methods doi: 10.1038/nmeth.1226 contributor: fullname: A Mortazavi – volume-title: Nature biotechnology year: 2010 ident: 3594_CR14 contributor: fullname: C Trapnell |
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Snippet | The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been generated... Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been... Abstract Background: The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps... BACKGROUNDThe developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been... BACKGROUND: The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps have been... Abstract Background The developing mouse kidney is currently the best-characterized model of organogenesis at a transcriptional level. Detailed spatial maps... |
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StartPage | 441 |
SubjectTerms | Alternative Splicing Animals Binding sites Colleges & universities Embryonic development Exons Gene expression Genomes Genomics High-Throughput Nucleotide Sequencing - methods Hybridization Kidney - embryology Kidney - metabolism kidney development Kidneys mesenchymal-epithelial transition Mice microarray MicroRNAs - genetics miR-214, microRNA Organogenesis Physiological aspects Polymerase chain reaction RNA RNA, Antisense - genetics RNA, Messenger - genetics RNA-Seq sense-antisense transcripts Sequence Analysis, RNA - methods Six2, Wt1 Transcription, Genetic Transcriptome |
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Title | Refining transcriptional programs in kidney development by integration of deep RNA-sequencing and array-based spatial profiling |
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