|
| Status |
Public on Oct 20, 2020 |
| Title |
Control_OPC_C |
| Sample type |
SRA |
| |
|
| Source name |
Oligodendrocyte precursor cells (OPCs)
|
| Organism |
Mus musculus |
| Characteristics |
cell type: epiblast stem cell derived OPCs
drug treatment: none
|
| Treatment protocol |
CRISPR-Control and CRISPR-Vhl OPCs were grown and then lysed for RNA. For drug treated samples, CRISPR-Control OPCs and CRISPR-Vhl OPCs were grown for a day and then media was switched to media containing either DMSO or 300nM AZD8330 for 14hrs and then lysed for RNA.
|
| Growth protocol |
OPCs were grown in DMEM F12 supplemented with N2max and B27 and Fgf2 and Pdgfa.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Phenol-chloroform with TRIzol.
Submitted RNA to Novogene for library construction and sequencing.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
CRISPR-Control OPCs
Control_Vhl_tpm_table.csv
|
| Data processing |
Raw RNA sequencing reads were analyzed with salmon 0.14.1 (Patro et al. Nature Methods 2017) to quantify transcript abundance in transcripts per million (TPM) for the Gencode M22 release.
Transcripts were summarized as gene-level TPM abundances with tximport (Soneson et al. F1000Research 2015)
Genome_build: mm10
Supplementary_files_format_and_content: Comma-separated values file of raw TPM expression values
|
| |
|
| Submission date |
Jan 10, 2020 |
| Last update date |
Oct 20, 2020 |
| Contact name |
Paul Tesar |
| E-mail(s) |
paul.tesar@case.edu
|
| Organization name |
Case Western Reserve University
|
| Department |
Genetics & Genome Sciences
|
| Street address |
10900 Euclid Ave.
|
| City |
Cleveland |
| State/province |
Ohio |
| ZIP/Postal code |
44106 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE143473 |
Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function [RNA-Seq] |
| GSE143474 |
Non-Canonical Targets of HIF1a Impair Oligodendrocyte Progenitor Cell Function |
|
| Relations |
| BioSample |
SAMN13826232 |
| SRA |
SRX7541955 |
