|
| Status |
Public on Apr 25, 2018 |
| Title |
TFAP2C-/- Line 2 2i+LIF Replicate 2 RNA [RNA-Seq] |
| Sample type |
SRA |
| |
|
| Source name |
TFAP2C deficient mESCs cultured for seven passages in 2i+LIF media
|
| Organism |
Mus musculus |
| Characteristics |
cell type: TFAP2C deficient mESCs cultured for seven passages in 2i+LIF media
passage number: p38+p7
library type: Ovation RNASeq System V2
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini Kit (Qiagen) and quantified using the Qubit RNA HS Assay kit (Thermo Scientific)
5ng to 50ng total RNA input was used to generate sequencing libraries using the Ovation Ultralow Library System V2 (Nugen) and then Ovation Rapid Library System (Nugen) protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
RNA (polyA enriched)
|
| Data processing |
RNA-seq: RNA-seq reads were first aligned to the mm9 or hg19 gene annotation using Tophat, and reads that did not map to the gene annotation were mapped to the genome as a whole. Default parameters were used, except that the --no-coverage-search parameter was used. Readcounts for each gene were calculated using HTseq with default parameters, mapping to the UCSC hg19 (human) or mm9 Ensembl (mouse) annotations.
Genome_build: hg19 (human); mm9 (mouse)
|
| |
|
| Submission date |
Jul 10, 2017 |
| Last update date |
Apr 26, 2018 |
| Contact name |
William Abraham Pastor |
| E-mail(s) |
william.pastor@mcgill.ca
|
| Phone |
514-618-3348
|
| Organization name |
McGill University
|
| Department |
Biochemistry
|
| Lab |
Pastor
|
| Street address |
3655 Promenade Sir William Osler
|
| City |
Montreal |
| State/province |
QC |
| ZIP/Postal code |
H3G 1Y6 |
| Country |
USA |
| |
|
| Platform ID |
GPL21103 |
| Series (1) |
| GSE101074 |
TFAP2C regulates transcription in human naive pluripotency by opening enhancers |
|
| Relations |
| BioSample |
SAMN07339195 |
| SRA |
SRX2993539 |
