|
| Status |
Public on Nov 09, 2016 |
| Title |
TAPCt_N2_RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
HCN cells in TAP or proliferative growth condition
|
| Organism |
Rattus norvegicus |
| Characteristics |
cell line: hippocampal neural stem (HCN) cells derived from the adult rat brain
passages: multiple
growth condition: TAP
treatment: electroporated with empty vector
|
| Treatment protocol |
HCN cells were either non-electroporated or electroporated with empty vector or REST knock-down shRNA vector
|
| Growth protocol |
HCN cells were grown in quiescence (FGF2+BMP4+) or proliferation (FGF+ only) conditions on adherent plates as monolayer (typically 2–3 × 106 cells per 10cm plate) in DMEM:F12 (Omega Scientific Inc.) media supplemented with N2, glutamate and PSF.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using miRNAeasy kit Qiagen 217004. Ribosomal RNA was removed using RiboZero kit Epicenter. Libraries were prepared using standard Illumina protocol and sequenced on Illumina HiSeq 2500.
RNA libraries were prepared for sequencing using standard Illumina protocols, and sequenced on Illumina platform, Illumina HiSeq 2500
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
RiboZero cleaned, total RNA
Cuffdiff_TAPCtrlvsTAPRESTkd.xls
|
| Data processing |
Reads were mapped on rn4 genome using Tophat2 and differential gene expression was determined by Cufflink and Cuffdiff.
Genome_build: rn4 (RGSC_v3.4)
Supplementary_files_format_and_content: excel file of Cuffdiff output to test differentially expressed genes for two or four replicates of each treatment
|
| |
|
| Submission date |
May 09, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Jenny Hsieh |
| E-mail(s) |
[email protected]
|
| Phone |
12146456262
|
| Organization name |
UT Southwestern Medical Center
|
| Street address |
6001 Forest Park Road, NA6.514AA
|
| City |
Dallas |
| State/province |
Texas |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (2) |
| GSE70696 |
Genome wide transcriptome analysis (RNA-seq) of adult hippocampal neural stem cells in vitro a.k.a. HCN cells in quiescent and proliferative conditions in non-electroporated or electroporated with control empty vector or REST knock-down shRNA vector |
| GSE70698 |
REST regulation of gene networks in adult neural stem cells |
|
| Relations |
| BioSample |
SAMN04961792 |
| SRA |
SRX1748284 |
