High accuracy, high-resolution prevalence measurement for the majority of locally expressed regulatory genes in early sea urchin development.
Accurate measurements of transcript abundance are a prerequisite to understand gene activity in development. Using the NanoString nCounter, an RNA counting device, we measured the prevalence of 172 transcription factors and signaling molecules in early sea urchin development. These measurements show high fidelity over more than five orders of magnitude down to a few transcripts per embryo. Most of the genes included are locally restricted in their spatial expression, and contribute to the divergent regulatory states of cells in the developing embryo. In order to obtain high-resolution expression profiles from fertilization to late gastrulation samples were collected at hourly intervals. The measured time courses agree well with, and substantially extend, prior relative abundance measurements obtained by quantitative PCR. High temporal resolution permits sequences of successively activated genes to be precisely delineated providing an ancillary tool for assembling maps of gene regulatory networks. The data are available via an interactive website for quick plotting of selected time courses.
Materna
Stefan C
SC
Division of Biology 156-29, California Institute of Technology, Pasadena, CA 91125, USA. materna@caltech.edu
Nam
Jongmin
J
Davidson
Eric H
EH
D000818:Animals; D020869:Gene Expression Profiling; D005809:Genes, Regulator; D012617:Sea Urchins / Q000235:genetics* / Q000254:growth & development
Dev Biol. 2008 Aug 1;320(1):49-59
18582858
Science. 2006 Nov 10;314(5801):941-52
17095691
Dev Biol. 2006 Dec 1;300(1):49-62
17081512
Dev Biol. 2010 Apr 15;340(2):249-55
20122918
Development. 2007 Oct;134(20):3649-64
17855430
Dev Biol. 2009 Jan 15;325(2):317-28
19028486
Dev Biol. 2006 Dec 1;300(1):108-20
16997293
Dev Biol. 2010 Apr 15;340(2):188-99
19895806
Dev Biol. 2006 Dec 1;300(1):35-48
16997294
Proc Natl Acad Sci U S A. 2007 Jul 24;104(30):12383-8
17636127
Dev Biol. 2010 Apr 15;340(2):170-8
19523466
Nat Protoc. 2008;3(12):1876-87
19008874
Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9371-6
12883007
Dev Biol. 2006 Sep 15;297(2):587-602
16925988
Dev Biol. 2006 Dec 1;300(1):74-89
17055477
Biotechniques. 2005 Jul;39(1):75-85
16060372
Dev Biol. 2009 May 15;329(2):410-21
19268450
Development. 1995 Apr;121(4):1111-22
7743924
Dev Biol. 1991 Jun;145(2):255-65
1645680
Dev Biol. 2007 Jun 15;306(2):860-9
17451671
Dev Biol. 2006 Dec 1;300(1):90-107
17054934
Nat Biotechnol. 2008 Mar;26(3):317-25
18278033
Proc Natl Acad Sci U S A. 2008 Dec 23;105(51):20089-94
19104065
Proc Natl Acad Sci U S A. 2008 Apr 22;105(16):5955-62
18413610