|
| 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
**********************************************************************
|
| |
|
| 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 |
