|
| Status |
Public on Jul 16, 2012 |
| Title |
Bbd - KD 1 |
| Sample type |
SRA |
| |
|
| Source name |
H2A.Bbd KD
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HeLa
treatment: H2A.Bbd KD
lentiviral construct: TRC106827
|
| Treatment protocol |
RNA-seq experiments were done from trizol purified toRNA from nuclei isolated as described in Pandya-Jones & Black (RNA 15:1896, 2009).
|
| Growth protocol |
HeLa cells were grown in DMEM with 10% calf serum
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For RNA-seq experiments, toRNA from nuclei were depleted of rRNA (Epizyme kit) and libraries were cloned using the truSeq RNAseq kit from Illumina.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
H2A.Bbd knock-down, replicate 1
|
| Data processing |
Paired-end RNA-seq tags were mapped using Tophat software package. Transcript annotations were taken from UCSC RefSeq track.
Tag pairs that had less than 50-bp separation between the mates were filtered out.
RNA-seq coverage was estimated as a number of paired-end fragments spanning over each interrogated genomic position. Coverage was normalized by total number of fragments.
Genome_build: hg18
|
| |
|
| Submission date |
Jun 18, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Peter J Park |
| E-mail(s) |
peter_park@harvard.edu
|
| Phone |
617-432-7373
|
| Organization name |
Harvard Medical School
|
| Department |
Center for Biomedical Informatics
|
| Street address |
10 Shattuck St
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE38770 |
Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [RNA-Seq] |
| GSE38771 |
Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells |
|
| Relations |
| SRA |
SRX154878 |
| BioSample |
SAMN01055124 |
