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Sample GSM772852 Query DataSets for GSM772852
Status Public on Dec 28, 2011
Title ChIP-Seq analysis of H3K4me3 in human CD25- CD45RA+ naive cells; DNA_Lib 726
Sample type SRA
 
Source name CD25- CD45RA+ naive is one of CD4+ T cell subsets that purified by microbeads, LS column and FACS ; DNA_Lib 726
Organism Homo sapiens
Characteristics sample alias: BioSam 133
sample common name: CD4+ CD25- CD45RA+ Naive Primary Cells
donor_health_status: presumed normal
molecule: genomic DNA
disease: presumed normal
markers: CD4+ T cell
passage_if_expanded: NA
cell_type: CD25- CD45RA+ naive
donor_ethnicity: NA
donor_sex: Unknown
biomaterial_type: Primary Cell
donor_id: Donor 62
biomaterial_provider: Dana Farber
donor_age: NA
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_antibody: H3K4me3
chip_protocol_chromatin_amount: 0.5 to 3 million cells
extraction_protocol: cell/nuclei lysis
chip_protocol_antibody_amount: ~1 ug
chip_protocol_bead_amount: 10 ul bed volume
chip_protocol: Bernstein_BROAD_ENCODE_protocol
extraction_protocol_sonication_cycles: 1
chip_antibody_catalog: 07-473
chip_antibody_provider: Millipore
chip_antibody_lot: DAM1644057
experiment_type: Histone H3K4me3
extraction_protocol_type_of_sonicator: Branson
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: Single read - Illumina
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 726
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8542
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9443
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
Data processing **********************************************************************

ANALYSIS FILE NAME: GSM772852_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_62.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 726-DNA_Lib 726-DNA_Lib 726-DNA_Lib 726.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, were mapped to the human genome using Pash.
ANALYSIS TYPE: REFERENCE_ALIGNMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.10809
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: Pash
SOFTWARE_VERSION: 3.0
MAXIMUM_ALIGNMENT_LENGTH: Read length
MISMATCHES_ALLOWED: 10% of read length
ALIGNMENTS_ALLOWED: 1
TREATMENT_OF_MULTIPLE_ALIGNMENTS: If a read maps to more than 1 position it is removed from consideration.
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
ALIGNMENT_POSTPROCESSING: None
READ_EXTENSION: 200bp
RELEASE_NUMBER: Human Epigenome Atlas 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,311,515
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2919
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2973
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

ANALYSIS FILE NAME: GSM772852_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_62.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 726-DNA_Lib 726-DNA_Lib 726-DNA_Lib 726.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 62, were processed into density graphs of raw signal representing the aligned read density.
ANALYSIS TYPE: ABUNDANCE_MEASUREMENT
EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.11073
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
TREATMENT_OF_IDENTICAL_ALIGNMENTS_OF_MULTIPLE_READS: If multiple reads map to the same start position on the + strand or stop position on the - strand, only a single read is retained.
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 5
BROWSER_TRACK_NAME: CCCN H3K4me3 62 26
BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 726 EA Release 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 12,311,515
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.23
FINDPEAKS_PERCENTILE: 52
HOTSPOT_SCORE: 0.2919
HOTSPOT_PERCENTILE: 44
IROC_SCORE: 0.9997
IROC_PERCENTILE: 76
POISSON_SCORE: 0.2973
POISSON_PERCENTILE: 37
MAXIMUM_REPLICATE_CORRELATION: NA

**********************************************************************

 
Submission date Aug 03, 2011
Last update date May 15, 2019
Contact name BROAD INSTITUTE
E-mail(s) rharris1@bcm.tmc.edu
Organization name Broad Institute
Street address -
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (1)
GSE17312 BI Human Reference Epigenome Mapping Project
Relations
SRA SRX088767
BioSample SAMN00691456
Named Annotation GSM772852_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_62.wig.gz

Supplementary file Size Download File type/resource
GSM772852_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_62.bed.gz 191.6 Mb (ftp)(http) BED
GSM772852_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K4me3.Donor_62.wig.gz 31.0 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data not provided for this record
Raw data are available in SRA

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