|
Status |
Public on Jul 16, 2012 |
Title |
Z - KD 1 |
Sample type |
SRA |
|
|
Source name |
H2A.Z KD
|
Organism |
Homo sapiens |
Characteristics |
cell line: HeLa treatment: H2A.Z KD lentiviral construct: TRC72585
|
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.Z 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 |
SRX154880 |
BioSample |
SAMN01055126 |