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| Status |
Public on Jan 31, 2011 |
| Title |
aTconv-H3K4me1 |
| Sample type |
SRA |
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| Source name |
aTconv cells from PBMC, normal
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| Organism |
Homo sapiens |
| Characteristics |
gender: male
cell type: aTconv cells
chip antibody: H3K4me1
chip antibody vendor: Abcam
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
the expanded and sorted Treg and aTconv cells were used for ChIP analysis. For mapping enzyme target sites, 2×10e6 cells were crosslinked with formaldehyde and sonicated to obtain chromatin fragments of 200 to 300 bp. Sonicated chromatin was pre-cleared and incubated with 2mg of anti-H3K4me1(Abcam, United Kingdom), anti-H3K3me3 (Abcam) or anti-rabbit IgG (Upstate, USA) overnight at 4°C. The crosslinks were reversed, and The ChIP DNA fragments were blunt-ended, ligated to the Solexa adaptors, and sequenced with the Illumina 1G Genome Analyzer.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer |
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| Data processing |
Alignment: Sequence reads were obtained and mapped to the human (March, 2006) genome using the SOAP(Short Oligonucleotide Analysis Package). All reads mapping with two or fewer mismatches were retained.
Peaks: Peak detection was performed with the Model-based Analysis of ChIP-Seq (MACS) algorithm (http://liulab.dfci.harvard.edu/MACS/)
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| Submission date |
Jan 04, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Ni Bing |
| E-mail(s) |
nibingxi@yahoo.com
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| Phone |
+86-23-68772348
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| Fax |
+86-23-68772348
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| Organization name |
PLA, Third Military Medical University
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| Department |
Institute of Immunology
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| Street address |
PLA, Third Military Medical University
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| City |
Chongqing |
| ZIP/Postal code |
400038 |
| Country |
China |
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| Platform ID |
GPL9052 |
| Series (1) |
| GSE26427 |
Global Mapping of H3K4me1 and H3K4me3 in human CD4+CD25+FOXP3+ Treg cells |
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| Relations |
| SRA |
SRX037432 |
| BioSample |
SAMN00189623 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM648494_aTconv-H3K4me1.bed.32_MACS_wiggle.tar.gz |
11.1 Mb |
(ftp)(http) |
TAR |
| GSM648494_aTconv-H3K4me1.peak.txt.gz |
569.8 Kb |
(ftp)(http) |
TXT |
| GSM648494_aTconv-H3K4me1.sop.bed.gz |
17.2 Mb |
(ftp)(http) |
BED |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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