|
| Status |
Public on Jul 26, 2016 |
| Title |
hg19_shMLL1_H3K4me3_150727_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
HCT116
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Human colorectal tumor
passages: Low passages (6-10)
cell line: HCT116
chip antibody: H3K4me3 (homemade)
|
| Treatment protocol |
Treatment with GSK126[5uM] or DMSO was administrated at 0- and 48-hour; harvesting cells at 96-hours.
|
| Growth protocol |
Cell medium was composed as follow: DMEM 1X (Thermo Fisher), 10% serum (Corning), 1X glutamine (Life Technologies), 1X penicillin/streptomycin (Life Technologies), cells were grown in a CO2 incubator (5% CO2) at 37˚C
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA after ChIP protocol was isolated using QIAGEN PCR purification kit.
ChIP-sequencing libraries were prepared using the KAPA HTP Library Preparation Kit complemented with NEXTflex DNA Barcodes from Bioo Scientific. 10 ng of DNA was used as starting material for input and ip samples. Libraries were amplified using 13 cycles on the thermocycler. Post amplification libraries were size selected at 250- 450bp in length using Agencourt AMPure XP beads from Beckman Coulter. Libraries were validated using the Agilent High Sensitivity DNA Kit.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Cells lentiviral infected with MLL1 specific shRNA vector
|
| Data processing |
Basecalls were performed using Casava v1.8 and bcl2fastq v2.17 for Illumina HiSeq and NextSeq output,respectively.
Both ChIP-seq and RNA-seq reads were trimmed from 3' end until the final base had a quality score > 30, using Trimmomatic v0.33, discarding reads left with < 20 bp
ChIP-seq reads were aligned to UCSC hg19 and dm3 using Bowtie version 0.12.9. Only uniquely mapping reads with at most two mismatches were retained.
To create ChIP-seq coverage plots, the locations of the mapped ChIP-seq reads were extended to 150 bp to represent sequenced fragments, renormalized (to reads per million, rpm) and reformatted in the bigWig file format.
genome build: hg19
processed data files format and content: bigWig files were generated using the genomicRanges R package. Score represents the normalized coverage of RNA or DNA fragments at a given genomic coordinate.
|
| |
|
| Submission date |
May 23, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Ali Shilatifard |
| E-mail(s) |
[email protected]
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Department |
Department of Biochemistry and Molecular Genetics
|
| Lab |
Shilatifard Lab
|
| Street address |
320 E Superior St
|
| City |
Chicago |
| State/province |
IL |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE81795 |
An epigenetic mark of polycomb response elements implemented by Trx/MLL/COMPASS |
|
| Relations |
| BioSample |
SAMN05164206 |
| SRA |
SRX1794295 |
