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Status |
Public on Dec 28, 2011 |
Title |
ChIP-Seq analysis of H3K27ac in human CD25- CD45RO+ mem cells; DNA_Lib 723 |
Sample type |
SRA |
|
|
Source name |
CD25- CD45RO+ mem is one of CD4+ T cell subsets that purified by microbeads, LS column and FACS ; DNA_Lib 723
|
Organism |
Homo sapiens |
Characteristics |
sample alias: BioSam 132 sample common name: CD4+ CD25- CD45RO+ Memory Primary Cells donor_health_status: presumed normal molecule: genomic DNA disease: presumed normal markers: CD4+ T cell passage_if_expanded: NA cell_type: CD25- CD45RO+ mem 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: H3K27ac 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: ab4729 chip_antibody_provider: Abcam chip_antibody_lot: 509313 experiment_type: Histone H3K27ac extraction_protocol_type_of_sonicator: Branson
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Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
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|
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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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|
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 723 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.8549 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.9449 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
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Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM772859_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27ac.Donor_62.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 723-DNA_Lib 723-DNA_Lib 723-DNA_Lib 723.hg19.level.1.release.5 ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K27ac ChIP-Seq on CD4+ CD25- CD45RO+ Memory 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.10665 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: 8,623,532 NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34 FINDPEAKS_SCORE: 0.3905 FINDPEAKS_PERCENTILE: 85 HOTSPOT_SCORE: 0.434 HOTSPOT_PERCENTILE: 85 IROC_SCORE: 0.9989 IROC_PERCENTILE: 85 POISSON_SCORE: 0.4534 POISSON_PERCENTILE: 82 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM772859_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27ac.Donor_62.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 723-DNA_Lib 723-DNA_Lib 723-DNA_Lib 723.hg19.level.2.release.5 ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27ac ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Histone H3K27ac ChIP-Seq read mappings from CD4+ CD25- CD45RO+ Memory 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.10929 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: CCCM H3K27ac 62 23 BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RO+ Memory Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 723 EA Release 5
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 8,623,532 NUMBER_OF_H3K27ac_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 34 FINDPEAKS_SCORE: 0.3905 FINDPEAKS_PERCENTILE: 85 HOTSPOT_SCORE: 0.434 HOTSPOT_PERCENTILE: 85 IROC_SCORE: 0.9989 IROC_PERCENTILE: 85 POISSON_SCORE: 0.4534 POISSON_PERCENTILE: 82 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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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 |
SRX088774 |
BioSample |
SAMN00691462 |
Named Annotation |
GSM772859_BI.CD4+_CD25-_CD45RO+_Memory_Primary_Cells.H3K27ac.Donor_62.wig.gz |