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Sample GSM2175577 Query DataSets for GSM2175577
Status Public on Jul 26, 2016
Title hg19_shMLL1_H3K4me2_150408_rep1
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: H3K4me2 (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) ash@northwestern.edu
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 SAMN05164203
SRA SRX1794292

Supplementary file Size Download File type/resource
GSM2175577_hg19_shMLL1_H3K4me2_150408_rep1.bw 2.1 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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