NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
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
E-mail(s) karen.verboom@ugent.be
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
Relations
BioSample SAMN08537126
SRA SRX3700579

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

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap