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Status |
Public on Jul 18, 2013 |
Title |
ChIP-Seq analysis of WCE in human CD25+ CD127- Treg cells; DNA_Lib 2094 |
Sample type |
SRA |
|
|
Source name |
CD25+ CD127- Treg is one of CD4+ T cell subsets that purified by microbeads, LS column and FACS ; DNA_Lib 2094
|
Organism |
Homo sapiens |
Characteristics |
sample alias: BioSam 713 sample common name: CD4+ CD25+ CD127- Treg Primary Cells donor_health_status: normal molecule: genomic DNA disease: normal markers: CD4+ T cell passage_if_expanded: NA cell_type: CD25+ CD127- Treg donor_ethnicity: NA donor_sex: Unknown biomaterial_type: Primary Cell donor_id: Donor 332 biomaterial_provider: Dana Farber donor_age: NA extraction_protocol_sonication_cycles: 1 chip_protocol_chromatin_amount: standard extraction_protocol: cell/nuclei lysis experiment_type: ChIP-Seq Input chip_protocol: Input 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 |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
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|
Description |
sample_term_id: CL_0000792 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: DNA_Lib 2094 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13147 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13312 **************** 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: GSM997234_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.Input.Donor_332.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 2094.hg19.level.1.release.9 ANALYSIS TITLE: Mapping of CD4+ CD25+ CD127- Treg Primary Cells Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4+ CD25+ CD127- Treg 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.17216 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: 36,012,367 FINDPEAKS_SCORE: 0.0074 FINDPEAKS_PERCENTILE: 79 HOTSPOT_SCORE: 0.0053 HOTSPOT_PERCENTILE: 29 IROC_SCORE: 0.0 IROC_PERCENTILE: 26 POISSON_SCORE: 0.0228 POISSON_PERCENTILE: 10 MAXIMUM_REPLICATE_CORRELATION: 0.98
**********************************************************************
ANALYSIS FILE NAME: GSM997234_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.Input.Donor_332.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: DNA_Lib 2094.hg19.level.2.release.9 ANALYSIS TITLE: Raw Signal Density Graphs of CD4+ CD25+ CD127- Treg Primary Cells Input ChIP-Seq Data ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4+ CD25+ CD127- Treg 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.17399 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: CCCTregreg Input 32 94 BROWSER_TRACK_DESCRIPTION: BI CD4+ CD25+ CD127- Treg Primary Cells ChIP-Seq Input Donor 332 Library DNA_Lib 2094 EA Release 9
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 36,012,367 FINDPEAKS_SCORE: 0.0074 FINDPEAKS_PERCENTILE: 79 HOTSPOT_SCORE: 0.0053 HOTSPOT_PERCENTILE: 29 IROC_SCORE: 0.0 IROC_PERCENTILE: 26 POISSON_SCORE: 0.0228 POISSON_PERCENTILE: 10 MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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|
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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 |
|
Relations |
BioSample |
SAMN01161881 |
Named Annotation |
GSM997234_BI.CD4+_CD25+_CD127-_Treg_Primary_Cells.Input.Donor_332.wig.gz |