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GEO help: Mouse over screen elements for information. |
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Status |
Public on Jan 08, 2020 |
Title |
852 MEP |
Sample type |
SRA |
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Source name |
bone marrow
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Organism |
Mus musculus |
Characteristics |
strain: C57BL6 developmental stage: adult cell type: megakaryocyte erythroid progenitor
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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).
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina HiSeq 2000 |
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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
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Submission date |
Jan 07, 2020 |
Last update date |
Jan 08, 2020 |
Contact name |
Ross Hardison |
E-mail(s) |
rch8@psu.edu
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Organization name |
Pennsylvania State University
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Street address |
303 Wartik Lab
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City |
University Park |
State/province |
PA |
ZIP/Postal code |
16802 |
Country |
USA |
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Platform ID |
GPL13112 |
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 |
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Relations |
BioSample |
SAMN13751664 |
SRA |
SRX7518355 |
Supplementary file |
Size |
Download |
File type/resource |
GSM4255749_852.bed.gz |
1.6 Mb |
(ftp)(http) |
BED |
GSM4255749_852.mm10.bw |
3.1 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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