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Sample GSM4255760 Query DataSets for GSM4255760
Status Public on Jan 08, 2020
Title 1199 NEU
Sample type SRA
 
Source name peripheral blood
Organism Mus musculus
Characteristics strain: C57BL6
developmental stage: adult
cell type: neutrophil
Extracted molecule genomic DNA
Extraction protocol Approximately 50,000 cells were collected by centrifugation at 600 xg for 10 min at 4 °C. Cells were washed once with cold 1x PBS and centrifuged as above. Cells were lysed by gently pipetting to resuspend cell pellet in cold lysis buffer (10 mM Tris–HCl pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and centrifuged as above. 
Cells were suspended in the following mix: 25 μl 2X Tagment DNA buffer (Illumina cat# FC-121-1030), 3 μl Tn5 Transposase (Illumina cat#FC-121-1030), 22 μl nuclease-free H2O and incubated for 30 min at 37 °C. Reactions were terminated by adding 5 μl of 1% SDS solution and purified using SPRIselect beads. Following purification, library fragments were amplified using NEBnext PCR master mix and 1.25 μM of custom Nextera PCR primers 1 and 2 using the following PCR conditions: 72 °C for 5 min; 98 °C for 30 s; and thermocycling at 98 °C for 10 s, 63 °C for 30 s, and 72 °C for 1 min.  Libraries were amplified for a total of 17–19 cycles and then purified using AMPure XP beads (Beckman Coulter cat #A63881).
 
Library strategy ATAC-seq
Library source genomic
Library selection other
Instrument model Illumina NextSeq 500
 
Data processing Illumina's bcl2fastq2 to generate fastq files
Custom script to trim reads to 30nts
Map reads with Bowtie 0.12.8 with parameters -y -v 2 -p 7 --best --strata -k 1 --sam-nohead --sam
Samtools v1.6 to filter chrM and unmapped reads
Fseq v1.85 to generate wiggles. Use parameters -v -of wig -f 0
Homer v36 to call peaks. Use parameter -style dnase.
Custom script to format peaks in bed format and bedtools to remove blacklist regions
UCSC's wigToBigWig to convert wiggle track
Genome_build: mm10
Supplementary_files_format_and_content: bigWig, signal from Fseq
Supplementary_files_format_and_content: bed, peaks from Homer
 
Submission date Jan 07, 2020
Last update date Jan 08, 2020
Contact name Ross Hardison
E-mail(s) rch8@psu.edu
Organization name Pennsylvania State University
Street address 303 Wartik Lab
City University Park
State/province PA
ZIP/Postal code 16802
Country USA
 
Platform ID GPL19057
Series (2)
GSE143270 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis [ATAC-seq]
GSE143271 An integrative view of the regulatory and transcriptional landscapes in mouse hematopoiesis
Relations
BioSample SAMN13751653
SRA SRX7518366

Supplementary file Size Download File type/resource
GSM4255760_1199.bed.gz 1.1 Mb (ftp)(http) BED
GSM4255760_1199.mm10.bw 3.3 Gb (ftp)(http) BW
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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