|
Status |
Public on Mar 31, 2011 |
Title |
ChIP-Seq analysis of WCE in fetal brain cells; Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE |
Sample type |
SRA |
|
|
Source name |
Primary fetal brain tissue; Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE
|
Organism |
Homo sapiens |
Characteristics |
sample alias: UW DS # 14803 sample common name: Fetal Brain collection_method: surgery donor_health_status: NA molecule: genomic DNA disease: none tissue_type: Fetal brain passage_if_expanded: NA donor_ethnicity: NA donor_sex: Female biomaterial_type: Primary Tissue tissue_depot: brain donor_id: UW H23284 biomaterial_provider: UW donor_age: 96 days extraction_protocol_sonication_cycles: 1 chip_protocol_chromatin_amount: standard extraction_protocol: SDS lysis experiment_type: ChIP-Seq Input chip_protocol: Input extraction_protocol_type_of_sonicator: Bioruptor
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Single read - Illumina
|
|
|
Library strategy |
ChIP-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina Genome Analyzer IIx |
|
|
Description |
sample_term_id: UBERON_0000955 assay_term_id: OBI_0000716 nucleic_acid_term_id: SO_0000352 Design description: Human Chromatin IP REMC Sequencing on Illumina Library name: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5685 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5942 **************** 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: GSM669944_BI.Fetal_Brain.Input.UW_H23284.bed ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE.hg19.level.1.release.3 ANALYSIS TITLE: Mapping of Fetal Brain ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Fetal Brain, Donor UW H23284 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.6492 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 3
QUALITY SCORES: NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61 FINDPEAKS_SCORE: 0.0028 FINDPEAKS_PERCENTILE: 3 HOTSPOT_SCORE: 0.0 HOTSPOT_PERCENTILE: 3 IROC_SCORE: 0.8899 IROC_PERCENTILE: 45 POISSON_SCORE: 0.0865 POISSON_PERCENTILE: 80
**********************************************************************
ANALYSIS FILE NAME: GSM669944_BI.Fetal_Brain.Input.UW_H23284.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE.hg19.level.2.release.3 ANALYSIS TITLE: Raw Signal Density Graphs of Fetal Brain ChIP-Seq Input Data ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Fetal Brain, Donor UW H23284 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.6702 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 3 BROWSER_TRACK_NAME: FB Input 84 BROWSER_TRACK_DESCRIPTION: BI Fetal Brain ChIP-Seq Input Donor UW H23284 Library Lib:XZ:20100731:09--ChIP:XZ:20100726:09:fetal brain:WCE EA Release 3
QUALITY SCORES: NUMBER_OF_Input_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 61 FINDPEAKS_SCORE: 0.0028 FINDPEAKS_PERCENTILE: 3 HOTSPOT_SCORE: 0.0 HOTSPOT_PERCENTILE: 3 IROC_SCORE: 0.8899 IROC_PERCENTILE: 45 POISSON_SCORE: 0.0865 POISSON_PERCENTILE: 80
**********************************************************************
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|
|
Submission date |
Feb 07, 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 |
GPL10999 |
Series (1) |
GSE19465 |
BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject |
|
Relations |
SRA |
SRX040991 |
BioSample |
SAMN00205678 |
Named Annotation |
GSM669944_BI.Fetal_Brain.Input.UW_H23284.wig.gz |