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Status |
Public on Jul 18, 2013 |
Title |
ChIP-Seq analysis of H3K9me3 in human CD25- CD45RA+ naive cells; DNA_Lib 2210 |
Sample type |
SRA |
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|
Source name |
CD25- CD45RA+ naive is one of CD4+ T cell subsets that purified by microbeads, LS column and FACS ; DNA_Lib 2210
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Organism |
Homo sapiens |
Characteristics |
sample alias: BioSam 718 sample common name: CD4+ CD25- CD45RA+ Naive Primary Cells donor_health_status: normal molecule: genomic DNA disease: 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 332 biomaterial_provider: Dana Farber donor_age: NA chip_protocol_bead_type: Protein A-Sepharose 4B chip_antibody: H3K9me3 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: ab8898 chip_antibody_provider: Abcam chip_antibody_lot: 877391 experiment_type: Histone H3K9me3 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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Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
Instrument model |
Illumina HiSeq 2000 |
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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 2210 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13141 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13318 **************** 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: GSM997228_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K9me3.Donor_332.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 2210.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by H3K9me3 ChIP-Seq on CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17296 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 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 35,528,554 FINDPEAKS_SCORE: 0.019 FINDPEAKS_PERCENTILE: 15 HOTSPOT_SCORE: 0.0565 HOTSPOT_PERCENTILE: 10 IROC_SCORE: 0.8463 IROC_PERCENTILE: 58 POISSON_SCORE: 0.1816 POISSON_PERCENTILE: 15 MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
ANALYSIS FILE NAME: GSM997228_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K9me3.Donor_332.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 2210.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina H3K9me3 ChIP-Seq read mappings from CD4+ CD25- CD45RA+ Naive Primary Cells, Donor Donor 332, 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.17479 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 9 BROWSER_TRACK_NAME: CCCNN H3K9me3 32 10 BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K9me3 Donor 332 Library DNA_Lib 2210 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 35,528,554 FINDPEAKS_SCORE: 0.019 FINDPEAKS_PERCENTILE: 15 HOTSPOT_SCORE: 0.0565 HOTSPOT_PERCENTILE: 10 IROC_SCORE: 0.8463 IROC_PERCENTILE: 58 POISSON_SCORE: 0.1816 POISSON_PERCENTILE: 15 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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Submission date |
Sep 04, 2012 |
Last update date |
Jan 29, 2015 |
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 |
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Relations |
BioSample |
SAMN01161887 |
Named Annotation |
GSM997228_BI.CD4+_CD25-_CD45RA+_Naive_Primary_Cells.H3K9me3.Donor_332.wig.gz |