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| Status |
Public on Dec 30, 2014 |
| Title |
24 month H3K4me1 |
| Sample type |
SRA |
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| Source name |
Hematopoietic stem cells (HSC)
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| Organism |
Mus musculus |
| Characteristics |
cell type: Murine bone marrow derived primary HSCs
cell surface marker: SP-KSL-CD150+
strain: C57BL/6
chip antibody: Abcam ab8895
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Genomic DNA were extracted from the cells and fragmented to 200-500 bp via biorupter. Followed by immunoprecipitation with specific antibody, ChIPed DNA were successfully made library using ThruPLEX preparation kit without extra amplification (Rubicon, Ann Arbor, MI)
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
technical replicate of biological replicate 1
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| Data processing |
Reads were mapped with Bowtie2. Uniquely mapped reads were used for peak calling by Macs2 with multiple testing correction q value cutoff 0.01.
ChIP-seq reads were aligned to the mm9 genome assembly using Bowtie2 version 2.0.6 with 1 mismatch in seed allowed, command=bowtie2 -p12 -k 2 -N 1. Peak calling was performed on uniquely aligned reads (lacking bowtie2 flag XS:i) with Macs2 version 2.0.10.20131216, command=macs2 callpeak -f BAMPE -g mm -m 2 50 --verbose 3 --bdg --SPMR -t treatment.bam -c control.bam , where treatment is immunoprecipitate and control is input DNA.
Genome_build: mm9
Supplementary_files_format_and_content: The narrowPeak are BED6+4 format file which contains the peak locations together with peak summit, pvalue and qvalue. Definition of some specific columns are: 5th: integer score for display, 7th: fold-change, 8th: -log10pvalue, 9th: -log10qvalue, 10th: relative summit position to peak start. The bigWig files were created from the Macs2 bedgraph files, representing signal density of fragment pileup as signal per million reads More information may be found in the Macs2 documentation.
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| Submission date |
Nov 13, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
deqiang sun |
| E-mail(s) |
dsun@tamu.edu
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| Phone |
(713) 677-7439
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| Organization name |
Texas A&M University
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| Street address |
2121 W Holcombe Blvd
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (2) |
| GSE63276 |
Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function (ChIP-Seq) |
| GSE63277 |
Long Non-coding RNAs Control Hematopoietic Stem Cell (HSC) Function |
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| Relations |
| BioSample |
SAMN03178084 |
| SRA |
SRX759474 |
| Named Annotation |
GSM1545000_m24_H3K4me1_treat_pileup.bw |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1545000_m24_H3K4me1.narrowPeak.txt.gz |
2.8 Mb |
(ftp)(http) |
TXT |
| GSM1545000_m24_H3K4me1_treat_pileup.bw |
306.2 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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