|
| Status |
Public on Oct 31, 2017 |
| Title |
HDAC2 15-1 |
| Sample type |
SRA |
| |
|
| Source name |
293FT HEK cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: 293FT
|
| Treatment protocol |
293FT cells were transfected with guide RNA expressing plasmids targeting the first ATG of the HDAC2 gene, followed by puromycin selection to obtain clonal lines of HDAC2-null cells.
|
| Growth protocol |
Cells were grown using standard cell culture techniquesin DMEM supplemented with 10% FBS and 1% L-glutamine
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from cells at 60-70% confluence utilizing the Nucleospin RNA kit (Macherey-Nagel, Ref #740955.5)
KAPA mRNA stranded kit (KK8401, Roche Catalog07962169001) for library preparation with poly-A enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
WT_L15_EdgeR.txt
|
| Data processing |
illumina bclfastq 2.16.0 version for pipeline
TopHat v2.0.14, library-type fr-firststrand
Reads were counted and organized into a matrix using bioconductor package "summarizeOverlaps"
EdgeR (edgeR_3.14.0) was used to perform differential expression analysis
Genome_build: hg19
Supplementary_files_format_and_content: Text files with differentially expressed genes, log fold change, p-value, and FDR
|
| |
|
| Submission date |
Feb 15, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Paul Knoepfler |
| E-mail(s) |
knoepfler@ucdavis.edu
|
| Organization name |
UC Davis School of Medicine
|
| Department |
Cell Biology and Human Anatomy
|
| Lab |
Knoepfler
|
| Street address |
1 Shields Ave
|
| City |
Davis |
| State/province |
CA |
| ZIP/Postal code |
95616 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (1) |
| GSE94947 |
RNA-seq of HDAC2-disrupted 293FT cells by CRISPR-Cas9 |
|
| Relations |
| BioSample |
SAMN06339416 |
| SRA |
SRX2564620 |
