|
| Status |
Public on Mar 29, 2017 |
| Title |
Control shRNA.rep2_ChIP-seq |
| Sample type |
SRA |
| |
|
| Source name |
K562_Control shRNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
cell type: myeloid leukemia cell line
shRNA: control shRNA
chip-antibody: CUX1 sc-6327 Santa Cruz
|
| Treatment protocol |
For RNA-seq experiments, cells were treated with 2 ug/mL of doxycycline for four days.
|
| Growth protocol |
K562 cells were grown in RPMI with 10% fetal bovine serum and penicillin/streptomycin.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
RNA was isolated using Trizol. Genomic DNA was isolated follwing the Myers Lab ChIP-seq Protocol v042211.2 (www.encodeproject.org),
Barcoded RNA-seq libraries were generated using the standard Illumina TruSEQ kit. Barcoded ChIP-seq libraries were made with Ovation Ultralow Library kit (NuGEN).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
processed data file:
DiffBindResults.txt
|
| Data processing |
RNA-seq reads were aligned to hg19 with Tophat .2.10 using default parameters. Reads with quality scores >30 were counted using HTseq-tools and analyzed with EdgeR
ChIP-seq reads were aligned to hg19 using bwa (version 0.7.5) and peaks called using Q.
Genome_build: Hg19
Supplementary_files_format_and_content: RNA-seq text file contains EdgeR results for Gene ID, log fold change, log counts per million, p value and q values for control versus knockdown. ChIP-seq text file contains DiffBind results for peak location, mean occupancy in the control, mean ocupancy in the knockdown, fold change in occupancy, p value, and FDR for control versus knockdown.
|
| |
|
| Submission date |
Dec 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Megan E. McNerney |
| E-mail(s) |
megan.mcnerney@uchospitals.edu
|
| Phone |
7738348896
|
| Organization name |
The University of Chicago
|
| Department |
Pathology
|
| Lab |
Megan McNerney
|
| Street address |
900 East 57th Street, KCBD 5128
|
| City |
Chicago |
| State/province |
Illinois |
| ZIP/Postal code |
60637 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE92882 |
Functional genomic analysis of the haploinsufficient tumor suppressor, CUX1 |
|
| Relations |
| BioSample |
SAMN06179740 |
| SRA |
SRX2442524 |
