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Sample GSM772954 Query DataSets for GSM772954
Status Public on Dec 28, 2011
Title ChIP-Seq analysis of H3K4me3 in human CD45RO CD4 cells; DNA_Lib 536
Sample type SRA
 
Source name Memory CD4+ T cells; DNA_Lib 536
Organism Homo sapiens
Characteristics sample alias: BioSam 181
sample common name: CD4 Memory Primary Cells
donor_health_status: presumed normal
molecule: genomic DNA
disease: presumed normal
markers: CD4+
passage_if_expanded: NA
cell_type: CD45RO CD4
donor_ethnicity: NA
donor_sex: Unknown
biomaterial_type: Primary Cell
donor_id: Donor 100 7 pooled leukopaks Jan 7 2011
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_0000897
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 536
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8644
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9467
****************
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: GSM772954_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 536-DNA_Lib 536-DNA_Lib 536.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me3 ChIP-Seq on CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10653
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: 28,213,970
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0623
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9791
IROC_PERCENTILE: 19
POISSON_SCORE: 0.1401
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

ANALYSIS FILE NAME: GSM772954_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 536-DNA_Lib 536-DNA_Lib 536.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Memory Primary Cells Histone H3K4me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me3 ChIP-Seq read mappings from CD4 Memory Primary Cells, Donor Donor 100 7 pooled leukopaks Jan 7 2011, 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.10917
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: CD4M H3K4me3 00 36
BROWSER_TRACK_DESCRIPTION: BI CD4 Memory Primary Cells Histone H3K4me3 Donor 100 7 pooled leukopaks Jan 7 2011 Library DNA_Lib 536 EA Release 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 28,213,970
NUMBER_OF_H3K4me3_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.0623
FINDPEAKS_PERCENTILE: 6
HOTSPOT_SCORE: 0.0994
HOTSPOT_PERCENTILE: 4
IROC_SCORE: 0.9791
IROC_PERCENTILE: 19
POISSON_SCORE: 0.1401
POISSON_PERCENTILE: 4
MAXIMUM_REPLICATE_CORRELATION: 0.87

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

 
Submission date Aug 03, 2011
Last update date May 30, 2017
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
Reanalyzed by GSE99453
BioSample SAMN00691480
Named Annotation GSM772954_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig.gz

Supplementary file Size Download File type/resource
GSM772954_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.bed.gz 437.6 Mb (ftp)(http) BED
GSM772954_BI.CD4_Memory_Primary_Cells.H3K4me3.Donor_100_7_pooled_leukopaks_Jan_7_2011.wig.gz 48.0 Mb (ftp)(http) WIG
Processed data provided as supplementary file
Raw data not provided for this record

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