|
| Status |
Public on May 30, 2018 |
| Title |
shRNA.ctr-RCH-ACV-C |
| Sample type |
SRA |
| |
|
| Source name |
RCH-ACV E2A-PBX1+ human cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: E2A-PBX1+ B-ALL cell line
shRNA knockdown: shRNA-E2A-PBX1
|
| Growth protocol |
RPMI R10
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol for total RNA
Manufacture prototol for RNAseq library; customized protocol for ChIP-seq (Wong et al., 2015, Cancer Cell)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Data processing |
RNA-seq libraries were constructed using Illumina’s TruSeq Stranded mRNA LT Kit and sequenced at Centrillion Genomics Technologies (http://www.centrilliontech.com). RAW fastq files were mapped by bowtie2 to the human hg19 genome assembly. Mapped files (BAM) were subjected to read counting using R-bioconductor package (GenomicAlignments: summarizeOverlaps function). Expression matrix (prior normalization) was then used for differential expression calculations and statistical modeling using R-bioconductor package (DESeq2).
ChIP-seq samples were analyzed as follows: i) Reads mapped by BWA to human genome assembly hg19; ii) Peaks called and differential peaks analyzed by MAC2; iii) peaks were viewed by genome browser IGV; iv) density plot and heatmap were generated using the program ngsplot.
Genome_build: hg19
|
| |
|
| Submission date |
Aug 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Stephen HK WONG |
| E-mail(s) |
honkit@stanford.edu
|
| Phone |
6507235340
|
| Organization name |
Stanford University
|
| Department |
Pathology
|
| Lab |
Dr. Michael Cleary
|
| Street address |
G2035 SIM1 Bldg
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL21290 |
| Series (2) |
| GSE102947 |
SETDB2 links E2A-PBX1 to cell cycle dysregulation in acute leukemia through CDKN2C repression [sequencing] |
| GSE125334 |
SETDB2 links E2A-PBX1 to cell cycle dysregulation in acute leukemia through CDKN2C repression |
|
| Relations |
| BioSample |
SAMN07537174 |
| SRA |
SRX3114674 |
