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Sample GSM1918430 Query DataSets for GSM1918430
Status Public on Oct 27, 2015
Title Exp004-5_H3K27me3_Ad_BC01_DMSO
Sample type SRA
 
Source name K562
Organism Homo sapiens
Characteristics experiment: C646_GSK126/Exp004-5
histone modification: H3K27me3
mnase units: 25u
treatment: DMSO
Treatment protocol K562 cells were treated for 48 hours with C646 (25 µM), 48 hours with GSK126 (2 µM), or 96 hours with KDM5-C70 (5 µM). Pfeiffer, SKM-1 and Toledo were treated for 72 hours with GSK126 (1 µM).
Growth protocol K562 cells and mouse YAC-1 cells were cultured in RPMI with 10% FCS, penicillin-streptomycin and L-glutamine. Pfeiffer, SKM-1 and Toledo were cultured in RPMI with 20% FCS, penicillin-streptomycin, L-glutamine and β-mercaptoethanol (3.5 µl in 1000 ml).
Extracted molecule genomic DNA
Extraction protocol Cell lysis immediately followed by MNase digestion of native chromatin, T7-adapter ligation, pool-and-split multiplexing, immunoprecipitation and magnetic bead isolation of immunoprecipitated DNA.
Mint-ChIP: In vitro transcription, reverse transcription, PCR (see manuscript).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
 
Description Mint-ChIP
This sample is missing processed data because the data was not processed beyond alignment (bam). The number of reads was simply used to generate figures for the manuscript.
Data processing Provided fastq files are already demultiplexed according to adapter barcode and trimmed.
Alignment: BWA paired-end alignment to hg19
Filter1: Remove all unmapped reads and reads with X0 > 2 from bam files
Filter2: Remove all PCR duplicates using PicardTools MarkDuplicates with REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=LENIENT
Filter3: Of pairs with identical R1 starting position alignment, keep only the pair with the longest fragment size.
Make tdf files using igvtools count --includeDuplicates --pairs
Genome_build: hg19
Supplementary_files_format_and_content: For visualization in IGV, tdf files are provided.
 
Submission date Oct 26, 2015
Last update date May 15, 2019
Contact name Peter van Galen
E-mail(s) petervangalen@gmail.com, pvangalen@bwh.harvard.edu
Organization name Brigham and Women's Hospital / Broad Institute of MIT and Harvard
Department Hematology
Lab Van Galen Lab
Street address 4 Blackfan Circle
City Boston
State/province Massachusetts
ZIP/Postal code 02115
Country USA
 
Platform ID GPL18573
Series (1)
GSE74359 A multiplexed system for quantitative comparisons of chromatin landscapes
Relations
BioSample SAMN04215847
SRA SRX1383676

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data not provided for this record

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