|
| Status |
Public on Feb 01, 2016 |
| Title |
Mock_ChIP |
| Sample type |
SRA |
| |
|
| Source name |
cell line purchased from Invitrogen
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Jurkat cells_T-ALL
antibody: IgG control
|
| Treatment protocol |
no treatment
|
| Growth protocol |
cultured in RPMI 1640 supplemented with 10% FBS and 100 U/ml penicillin and 100 mg/ml streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Binding of UTX transcription factor was measured using a ChIP protocol as previously described (Palii, 2011). Chromatin from 1x10^8 cells was fragmented to a size range of 100-300 bases with a Bioruptor (Diagenode) at 4 degrees C. Solubilized chromatin was immunoprecipitated with an antibody against UTX (home made 9838P mixed with A302-374A) or an isotype IgG control. Antibody-chromatin complexes were pulled-down using Dynabeads-Protein A, washed and eluted. After cross-link reversal and proteinase K treatment, immunoprecipitated DNA was extracted with phenol-chloroform.
ChIPed DNA was amplified using the Illumina protocol with modifications described in (Palii, 2011).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Mock ChIP
|
| Data processing |
Basecalling was performed with Illumina RTA 1.12.4.2
ChIP-Seq reads were aligned to the hg19 genome assembly using BWA (version 0.6.2)
Reads mapping to more than 2 locations on the genome were removed with Samtools (version 0.1.18)
Reads mapping to the same genomic location more than once, or duplicated reads, were removed with Samtools (version 0.1.18)
MACS (version 2.0.10) was used to detect tag enrichment of ChIP-Seq experiment, using default values and using a p-value cutoff of 10^-10
Genome_build: hg19
Supplementary_files_format_and_content: WIG files represent the read coverage of the ChIP-Seq over the genome. The files were generated from unique reads without duplicates from the alignment with BWA using the UCSC genome browser standalone tools for Unix. BED files represent the genomic location of ChIP-Seq enrichment peaks as determined by MACS.
|
| |
|
| Submission date |
Jan 09, 2015 |
| Last update date |
May 15, 2019 |
| Organization |
Ottawa Hospital Research Institute |
| Phone |
(613) 737-8899 -73255
|
| Department |
Cellular and Molecular Medicine
|
| Lab |
Ottawa Bioinformatics Core Facility
|
| Street address |
501 Smyth Rd.
|
| City |
Ottawa |
| State/province |
ON |
| ZIP/Postal code |
K1H 8L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE64832 |
UTX inhibition as selective epigenetic therapy against TAL1-driven T cell acute lymphoblastic leukemia |
| GSE72300 |
T-cell ALL in response to TAL1-KD, UTX-KD, and GSKJ4 treatment |
|
| Relations |
| BioSample |
SAMN03280486 |
| SRA |
SRX835578 |
