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Sample GSM3004532 Query DataSets for GSM3004532
Status Public on Sep 11, 2018
Sample type SRA
Source name ALL-SIL cell line
Organism Homo sapiens
Characteristics cell line: ALL-SIL
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 ATAC-seq was performed as previously described (Buenrostro et al. 2015) with minor changes. In brief, 50,000 cells were lysed and fragmented using Tn5 transposase (Illumina). Next, the samples were purified using the MinElute kit (Qiagen). The transposased DNA fragments were amplified and purified using the PCR Cleanup kit (Qiagen).
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2000
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 Mar 13, 2019
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 GPL11154
Series (2)
GSE110630 ATAC-seq of ALL-SIL cells
GSE110637 T-ALL
BioSample SAMN08537122
SRA SRX3700577

Supplementary file Size Download File type/resource
GSM3004532_ATAC_ALL-SIL.bed.gz 197.3 Kb (ftp)(http) BED
GSM3004532_sample_1_peaks.xls.gz 534.7 Kb (ftp)(http) XLS
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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