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Sample GSM2174882 Query DataSets for GSM2174882
Status Public on Dec 26, 2016
Title BJATAClib8
Sample type SRA
 
Source name Neonatal foreskin
Organism Homo sapiens
Characteristics cell type: human foreskin fibroblast
cell line: BJ
passages: 19
Growth protocol Cells were grown in EMEM media (ATCC) supplemented with 10% Heat-inactivated Fetal Bovine Serum and 100 U/mL penicillin-streptomycin in T175 flasks. They were harvested at 80% confluence by incubation with Accutase and washed in cold PBS, with centrifugation for 5 min at 500 x g to collect cells prior to lysis.
Extracted molecule genomic DNA
Extraction protocol Simultaneously lysed and transposed with 0.01% w/v digitonin in ATAC-seq transposition reaction.
Libraries were constructed by transposition of permeabilized cells with Illumina Nextera Tn5 transposase that inserts short sequencing adapters. The transposed DNA was purified using a Qiagen MinElute PCR cleanup kit and overhangs were extended by 5 minute incubation at 72˚C, followed by PCR with barcoding primers to introduce the remaining adapter sequence. i7 barcodes were used for multiplexing (TAAGGCGA, CGTACTAG, AGGCAGAA, TCCTGAGC, GGACTCCT, TAGGCATG, CGAGGCTG, AAGAGGCA).
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 2500
 
Description cultured cells used to prepare ATAC-seq library for nucleosome calling and open chromatin mapping
Data processing Library strategy: ATAC-seq
Adapter sequences were trimmed using a custom Python script that aligns Read 1 and Read 2 to each other.
Paired-end alignment was performed on hg19 using bowtie2 with parameters "-X 2000 -p18".
Reads were filtered for all scaffolds except chromosomes 1-22 and X.
Reads were filtered for mapping quality with a threshold of 30 using samtools 0.1.19 and for reads falling within ENCODE DAC and Duke blacklists using bedtools 2.20.1.
Duplicates were removed with Picard tools (version 1.117) MarkDuplicates.
Technical replicates were pooled as BAM files using samtools 0.1.19.
Broad peaks were called using MACS2 (version 2.1.0.20140616) using parameters "--nomodel --nolambda --keep-dup all --broad --call-summits -slocal 10000"
Peaks were extended by 120 bp on both sides, filtered to remove peaks of less than 500 bp, then merged peaks within 120 bp using bedtools (version 2.20.1).
Nucleosomes were then called within these peaks using NucleoATAC using default parameters (Schep et al., Genome Research 2015).
ATAC-seq insertions were calculated over the genome and converted to a bigwig file using UCSC tool bedGraphToBigWig.
Genome_build: hg19
Supplementary_files_format_and_content: .bw file is a bigwig file containing ATAC-seq insertion density.
Supplementary_files_format_and_content: BJatac2pooled.peaks.bed file is a BED file containing MACS2 called broad peaks after extension, filtering and merging.
Supplementary_files_format_and_content: BJatacNucCalls_DefaultParams.nucpos.occscore.bed file is a BED file of nucleosome calls with the occupancy score in column 5
 
Submission date May 23, 2016
Last update date May 15, 2019
Contact name William J Greenleaf
Organization name Stanford University
Department Genetics
Lab Greenleaf
Street address 279 Campus Drive, Beckman Center B257
City Stanford
State/province CA
ZIP/Postal code 94305
Country USA
 
Platform ID GPL16791
Series (2)
GSE81736 Variable chromatin secondary structures in live cells revealed by radiation-induced spatially correlated DNA cleavage mapping [ATAC-Seq]
GSE81807 Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping
Relations
BioSample SAMN05163281
SRA SRX1792441

Supplementary data files not provided
SRA Run SelectorHelp
Processed data are available on Series record
Raw data are available in SRA

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