NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM971340 Query DataSets for GSM971340
Status Public on Mar 25, 2013
Title Bcell_H3K4me1
Sample type SRA
 
Source name Blood
Organism Homo sapiens
Characteristics tissue: Blood
developmental stage: Adult
genotype/variation: wild type
cell type: Bcell
chip antibody details: Abcam, ab8895
Growth protocol N/A
Extracted molecule genomic DNA
Extraction protocol Purified from whole blood using human Naive B cell isolation kit II kits (Miltenvi #130-091-150)
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).
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer II
 
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))
 
Submission date Jul 20, 2012
Last update date May 15, 2019
Contact name Brian J Abraham
Organization name St. Jude Children's Research Hospital
Department Computational Biology
Street address 262 Danny Thomas Blvd
City Memphis
State/province TN
ZIP/Postal code 38112
Country USA
 
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]
Relations
SRA SRX170353
BioSample SAMN01091978

Supplementary file Size Download File type/resource
GSM971340_Naive_B_cells-H3K4me1.bed.gz 107.0 Mb (ftp)(http) BED
GSM971340_Naive_B_cells-H3K4me1.islands.txt.gz 1.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap