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| Status |
Public on Mar 25, 2013 |
| Title |
HSC_Brg1 |
| Sample type |
SRA |
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| Source name |
Blood
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Blood
developmental stage: Adult
genotype/variation: wild type
cell type: HSC
chip antibody details: Anti-Brg1 (Khavari, P. A., et al., 1993, Nature, 366:170-174)
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| Growth protocol |
N/A
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Treated as described in SRP000801. To examine the changes of chromatin modifications before and after differentiation, we fragmented the chromatin from CD133+ cells using micrococcal nuclease (MNase) digestion and performed ChIP-Seq analysis as described previously (Barski et al., 2007 A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837.
As described in Barski et al., 2007 (A. Barski, S. Cuddapah, K. Cui, T.Y. Roh, D.E. Schones, Z. Wang, G. Wei, I. Chepelev and K. Zhao, High-resolution profiling of histone methylations in the human genome, Cell 129 (2007), pp. 823-837).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer II |
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| Data processing |
Illumina Casava1.7 software used for basecalling.
Reads mapped to hg18 using bowtie 0.12.7, with -m 1 allowing one location per read
Mapped reads filtered to allow one read per position
Pol II and p300 binding sites calculated using MACS 1.4.1, -s hg, --p-value=1e-8
H2AZ analyzed with SICER using -w 200 -g 400 -t 0.68 -e 100 -f 150 -p 1e-5
H3K4 analyzed with SICER using -w 200 -g 200 -t 0.68 -e 100 -f 150 -p 1e-5
Brg1 analyzed with SICER using -w 200 -g 600 -t 0.68 -e 100 -f 150 -p 1e-5
H3K27 analyzed with SICER using predicted -w -I 150 -t 0.68 -e 100 -g 0 -f 150 -p 1e-5,
Outermost windows of H3K27 islands were trimmed to maximize the difference between island and non-island bins of 50bp
Genome_build: hg18
Supplementary_files_format_and_content: BED: chromosome, start, end, ReadID, number of mapping locations of read, strand
Supplementary_files_format_and_content: Island: chromosome, start, end, reads in island in control, reads in island in test, pvalue, normalized fold change, FDR
Supplementary_files_format_and_content: bsites (Peak): chromosome, start, end, peak ID, -10(log10(pvalue))
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| Submission date |
Jul 20, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian J Abraham |
| Organization name |
St. Jude Children's Research Hospital
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| Department |
Computational Biology
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| Street address |
262 Danny Thomas Blvd
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| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38112 |
| Country |
USA |
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| Platform ID |
GPL9115 |
| Series (2) |
| GSE39229 |
Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis |
| GSE39538 |
Mapping Epigenomic Type-Specific Differences Occurring During Hematopoiesis [ChIP-Seq] |
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| Relations |
| SRA |
SRX170346 |
| BioSample |
SAMN01091971 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM971333_CD34-J1_Brg1.bed.gz |
106.0 Mb |
(ftp)(http) |
BED |
| GSM971333_CD34-J1_Brg1.islands.txt.gz |
376.2 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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