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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Apr 10, 2023 |
| Title |
H3K4me1 iMK [1905] |
| Sample type |
SRA |
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| Source name |
bone marrow
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| Organism |
Mus musculus |
| Characteristics |
tissue: bone marrow
cell type: bone marrow derived progenitor cells, specifically Immature megakaryocytes, abbreviated iMK
target: H3K4me1
facs cell isolation sort markers: CD4-, CD8-, IL7Ra-, CD11b-, Ly6g-, CD45R-, Ter119-, Sca1-, CD41+, CD61+, cKit-
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were prepared from sonicated nuclei and protein-DNA complexes were isolated with antibody.
ChIP-seq samples were prepared by end repair, 3’ adenylation, and adaptor ligation using Illumina’s TruSeq ChIP-seq Sample Preparation Kit.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Basecalls using bcl2fastq-1.8.4, and parameters --no-eamss --mismatches 1
Mapping to reference genome mm10 canon with Bowtie 1.0.0 using parameters --chunkmbs 1024 -y -n 2 --best -k 1 --maxbts 800 -l 28 -e 80 --sam-nohead --sam
Wiggle generated with MACS using parameters --nomodel --shiftsize=120--format BAM --gsize 2615371906 --tsize 36 --bw 120 --mfold 12 --wig --space 1
peaks were called with Sicer V1.1 using parameters mm10 1 200 150 0.74 600 0.01
Filter blacklist regions from peaks, and convert to broadpeak format (see UCSC Genome Browser for format specs)
Assembly: mm10
Supplementary files format and content: bigWig signal from MACS
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| Submission date |
Apr 06, 2023 |
| Last update date |
Apr 11, 2023 |
| 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 |
GPL19057 |
| Series (2) |
| GSE229097 |
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes [mouse histones] |
| GSE229101 |
Cross-species regulatory landscapes and elements revealed by novel joint systematic integration of human and mouse blood cell epigenomes |
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| Relations |
| BioSample |
SAMN34091139 |
| SRA |
SRX19892445 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7152439_1905.mm10.bw |
3.6 Gb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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