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Sample GSM3004534 Query DataSets for GSM3004534
Status Public on Sep 11, 2018
Title input DNA
Sample type SRA
Source name ALL-SIL cell line
Organism Homo sapiens
Characteristics cell line: ALL-SIL
Treatment protocol The ChIP-protocol has been adapted from previous studies (Lee et al. 2006). In brief, 1*107 cells were cross-linked with 1,1 % formaldehyde (Sigma-Aldrich, F1635) at room temperature for 10 min and the cross-linking reaction was quenched with glycine (125 mM final concentration, Sigma-Aldrich, G-8790). Nuclei were isolated and chromatin was purified by chemical lysis. Next, the purified chromatin was fragmented to 200-300 bp fragments by sonication (Covaris, M220, Focused-ultrasonicator). Chromatin immunoprecipitation was performed by incubation of the chromatin fraction overnight with 20 μl of protein-A coated beads (Thermo-Scientific, catalog number 53139) and 2 μg of H3K4me1 specific (Abcam, ab8895) or H3K4me3 specific (Abcam, ab8580) antibody. The next day, beads were washed to remove non-specific binding events and enriched chromatin fragments were eluted from the beads, followed by reverse cross-linking by incubation at 65°C overnight.
Growth protocol Cells were grown in RPMI supplemented with 20% fetal bovine serum, 1% glutamin and 1% penicilin/streptomycin
Extracted molecule genomic DNA
Extraction protocol DNA was purified by phenol/chloroform extraction, assisted by phase lock gel tubes (5Prime).
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina NextSeq 500
Data processing fastq files were aligned with STARv2.4.2a to GRCh38 with --alignIntronMax 1 --alignMatesGapMax 1000 to avoid splice awareness.
Peak calling was performed with MACS2 using broad setting
Genome_build: GRCh38
Supplementary_files_format_and_content: xls file with MACS2 output
Submission date Feb 14, 2018
Last update date Sep 11, 2018
Contact name Karen Verboom
Organization name Ghent University
Department Pediatrics and Genetics
Lab Center for Medical Genetics Ghent
Street address De Pintelaan 185
City Ghent
ZIP/Postal code 9000
Country Belgium
Platform ID GPL18573
Series (2)
GSE110631 H3K4me1 ChIP-seq in ALL-SIL
GSE110637 T-ALL
BioSample SAMN08537126
SRA SRX3700579

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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