|
| Status |
Public on Dec 31, 2012 |
| Title |
C17_2b_12h_un |
| Sample type |
SRA |
| |
|
| Source name |
C17.2b neural progenitor cells, untreated, 12h
|
| Organism |
Mus musculus |
| Characteristics |
cell line: C17.2b
cell type: C17.2 neural progenitor cells stably expressing tagged thyroid hormone receptor beta
treatment: none
treatment duration: 12h
|
| Treatment protocol |
Cells were treated with 10-7M T3 or left untreated for 6, 12 or 24h.
|
| Growth protocol |
C17.2 cells were passed every four days and grown in DMEM medium containing 12% FBS and 2 mM Glutamine and Penicillin / Streptomycin. Cells were grown for 24h in serum-free medium before treatment.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were lysed and total RNA was extracted using a commercial kit. PolyA RNA were then reverse-transcribed into cDNA.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
AB SOLiD System 3.0 |
| |
|
| Description |
PolyA RNA
|
| Data processing |
Basecalls were done with applied solid.sage.v106.
Reads were aligned on a library of 28 nt fragments of the RefSeq release from 07/20/2011 digested by NaeIII with applied solid.sage.v106. Alignment was done assuming one mismatch maximum, dividing the number of reads matching with several transcripts equally between transcript and grouping all different transcripts for a same gene under a unique gene symbol. This file is linked to the Series record as a supplementary file.
Reads number were normalized between samples by the total number of reads to obtain read frequencies (reads per million).
Genome_build: mm9
Supplementary_files_format_and_content: DGE_processed_data.txt is a matrix presenting for each gene and each sample the normalized (reads per million) number of reads for every gene, assuming one mismatch maximum, dividing the number of reads matching with several transcripts equally between transcript and grouping all different transcripts for a same gene under a unique gene symbol. This file is linked to the Series record as a supplementary file.
|
| |
|
| Submission date |
Jun 06, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Fabrice Chatonnet |
| E-mail(s) |
fabrice.chatonnet@ens-lyon.org
|
| Phone |
+33 2 99 28 99 39
|
| Organization name |
University Hospital of Rennes
|
| Lab |
Inserm U1236 MICMAC
|
| Street address |
2 rue Henri le Guilloux
|
| City |
Rennes |
| ZIP/Postal code |
35033 |
| Country |
France |
| |
|
| Platform ID |
GPL9318 |
| Series (2) |
| GSE38539 |
Digital Gene Expression (DGE) of thyroid hormone (T3)-responsive genes in C17.2 cells stably transfected with thyroid hormone receptors alpha and beta |
| GSE41727 |
Genome-wide analysis of thyroid hormone receptors' shared and specific functions in neural cells |
|
| Relations |
| SRA |
SRX151809 |
| BioSample |
SAMN01041076 |
