|
| Status |
Public on Jul 01, 2012 |
| Title |
K562 siGATA2 RNA-seq |
| Sample type |
SRA |
| |
|
| Source name |
K562 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
knockdown: GATA2
|
| Treatment protocol |
K562 cells (3 x 106) were transfected with 240 pmol of SMART pool siRNA targeting human GATA-1, GATA-2, or siGenome nontargeting siRNA pool (Dharmacon/ Fisher Scientific) with the Nucleofector II (Lonza). Cells were harvested 48 h post-transfection.
|
| Growth protocol |
K562 cells were cultured in IMEM (Mediatech Inc) containing 10% FBS, 25 ïg/ml Gentamicin, 100 U/ml Penicillin, and 100 ïg/ml Streptomycin. After siRNA transfection, the cells were cultured with IMEM containing 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA libraries were prepared in accordance with the Illumina TruSeq⢠RNA Sample Prep Kit protocol. Briefly, mRNAs were fragmented at elevated temperature using divalent cations and transcribed into cDNA thereby generating a library of cDNA fragments. Barcoded RNA-Seq adapters provided with the Illumina kit were then ligated to the blunt ends of the cDNA fragments. The libraries of cDNA fragments were subjected to PCR amplification using universal primer sites present at the end of the ligated adapters. The libraries were then subjected to quality control steps such as verification of fragment size using the High Sensitivity DNA kit (Agilent Technologies) on an Agilent 2100 Bioanalyzer and concentration was determined by a KAPA Library Quantification Kit utilizing real-time PCR with standards suitable for Illumina sequencing libraries.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Illumina TruSeq RNA Sample Prep Kit
|
| Data processing |
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) (hg18) genomes using the Bowtie. All reads mapping with two or fewer mismatches were retained.
Expression: FPKM value generated with Cufflinks software were used as gene expression value.
|
| |
|
| Submission date |
Sep 19, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Xun Lan |
| E-mail(s) |
xlan@stanford.edu
|
| Phone |
7738345917
|
| Organization name |
Stanford University
|
| Department |
Genetics
|
| Lab |
Pritchard's Lab
|
| Street address |
318 Campus Dr. Room S240
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE32213 |
Integration of Hi-C and ChIP-seq data reveals distinct types of chromatin hubs |
|
| Relations |
| SRA |
SRX098080 |
| BioSample |
SAMN00722458 |
