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| Status |
Public on May 18, 2015 |
| Title |
Comparative transcriptomic analysis of self-organized, in vitro generated optic tissues |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Embryonic stem (ES) cells have a remarkable capacity to self-organize complex, multi-layered optic cups in vitro via a culture technique called SFEBq. During both SFEBq and in vivo optic cup development, Rax (Rx) expressing neural retina epithelial (NRE) tissues utilize Fgf and Wnt/β-catenin signalling pathways to differentiate into neural retina (NR) and retinal-pigmented epithelial (RPE) tissues, respectively. How these signaling pathways affect gene expression during optic tissue formation has remained largely unknown, especially at the transcriptome scale.
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| Overall design |
We generated Day 10 Rx+ optic tissue using SFEBq, exposed these tissues to either Fgf or Wnt/β-catenin stimulation, and assayed their gene expression at Days 12 and 15 using RNA-Seq. We measured gene expression in these 5 sample groups in biological triplicate using RNA-seq (Illumina HiSeq) .
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| Contributor(s) |
Andrabi M, Kuraku S, Takata N, Sasai Y, Love NR |
| Citation(s) |
26110066 |
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| Submission date |
Oct 16, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Munazah Andrabi |
| E-mail(s) |
munazah@cdb.riken.jp
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| Organization name |
RIKEN:Center for Developmental Biology
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| Lab |
Genome Resource and Analysis Unit
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| Street address |
2-2-3 Minatojima-minamimachi
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| City |
Chuo-ku |
| State/province |
Kobe |
| ZIP/Postal code |
650-0047 |
| Country |
Japan |
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| Platforms (1) |
| GPL18480 |
Illumina HiSeq 1500 (Mus musculus) |
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| Samples (15)
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| GSM1526922 |
Day 12 +Fgf, replicate1 |
| GSM1526923 |
Day 12 +Fgf, replicate2 |
| GSM1526924 |
Day 12 +Fgf, replicate3 |
| GSM1526925 |
Day 12 +Wnt, replicate1 |
| GSM1526926 |
Day 12 +Wnt, replicate2 |
| GSM1526927 |
Day 12 +Wnt, replicate3 |
| GSM1526928 |
Day 15 +Fgf, replicate1 |
| GSM1526929 |
Day 15 +Fgf, replicate2 |
| GSM1526930 |
Day 15 +Fgf, replicate3 |
| GSM1526931 |
Day 15 +Wnt, replicate1 |
| GSM1526932 |
Day 15 +Wnt, replicate2 |
| GSM1526933 |
Day 15 +Wnt, replicate3 |
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| Relations |
| BioProject |
PRJNA264087 |
| SRA |
SRP048990 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE62432_Expression_Values_All_Samples.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
| GSE62432_RAW.tar |
5.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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