|
|
GEO help: Mouse over screen elements for information. |
|
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 Selector |
Processed data are available on Series record |
Raw data are available in SRA |
|
|
|
|
|