|
| Status |
Public on Sep 26, 2017 |
| Title |
43-12 ATRA (exon-level) |
| Sample type |
RNA |
| |
|
| Source name |
fetal testis, ATRA
|
| Organism |
Rattus norvegicus |
| Characteristics |
tissue: fetal testis
strain: SAS SD (Charles River #400)
treatment: 10^-6 M all-trans retinoic acid
individual (pairing): 43-12
|
| Treatment protocol |
Samples were treated by addition of 10^-6 M ATRA in 1:4000 DMSO vehicle or vehicle only to the culture media. Treatment design was paired so that each fetus (individual) had one testis cultured in treatment media and one in vehicle.
|
| Growth protocol |
Gestational day (GD) 15 fetal rat testes were cultured in supplemented DMEM/F-12 media on Millicell CM cell culture inserts for 24 h.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from fetal testes after 24 h of culture, using the Qiagen AllPrep DNA/RNA Micro Kit, per manufacturer's instructions, including the on-column DNase digestion.
|
| Label |
biotin
|
| Label protocol |
Labeling was performed using GeneChip WT Terminal Labeling reagents (Agilent). 100 ng input RNA was converted to cDNA and amplified by in vitro transcription (IVT) over night. 15 ug purified IVT cRNA was reverse transcribed and labeled with dUTP. 5.5 ug purified cDNA was fragmented and 5.15 ug cDNA were end-labeled with biotin. All steps were done according to the manufacturer's protocol.
|
| |
|
| Hybridization protocol |
5.15 ug fragmented and end-labeled sample was hybridized for 16 hr at 45 C and 60 rpm to Rat Transcriptome Array (RTA) 1.0 microarrays (Affymetrix) and scanned at the Brown University Genomics Core.
|
| Scan protocol |
Microarrays were scanned using the Affymetrix 3000 7G Scanner.
|
| Description |
Sample name: 251-263
Alt-Splice analysis in Transcriptome Analysis Console
|
| Data processing |
Raw data were processed in Affymetrix Gene Chip Command Console software to produce .cel files and Affymtrix Expresion Console for .chp files for alt-splice analysis.
affymetrix-algorithm-name = sst-rma-alt-splice : sst-dabg
affymetrix-algorithm-version = 1.0
|
| |
|
| Submission date |
Jul 19, 2017 |
| Last update date |
Jan 23, 2018 |
| Contact name |
Daniel James Spade |
| E-mail(s) |
daniel_spade@brown.edu
|
| Phone |
4018635726
|
| Organization name |
Brown University
|
| Department |
Pathology and Laboratory Medicine
|
| Street address |
Box G-E5
|
| City |
Providence |
| State/province |
RI |
| ZIP/Postal code |
02912 |
| Country |
USA |
| |
|
| Platform ID |
GPL23629 |
| Series (1) |
| GSE101634 |
Short-term in vitro culture of rat fetal testes with all-trans retinoic acid |
|
| Relations |
| Reanalyzed by |
GSM2747659 |
