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| Status |
Public on Feb 22, 2012 |
| Title |
Chromatin accessibility assay of Fibroblasts, Fetal Skin, Abdomen; DS19561 |
| Sample type |
SRA |
| |
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| Source name |
Fibroblasts, Fetal Skin, Abdomen, day 97 donor; DS19561
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: fSkin_fibro_abdomen.H-24259d97
sample common name: Fibroblasts, Fetal Skin, Abdomen
molecule: genomic DNA
disease: None
biomaterial_provider: University of Washington, Congenital Defects Lab. Ian Glass
biomaterial_type: Primary Cell Culture
cell_type: Fibroblasts, Fetal Skin, Abdomen
markers: NA
culture_conditions: None
donor_id: H-24259
donor_age: day 97
donor_health_status: NA
donor_sex: Male
donor_ethnicity: NA
passage_if_expanded: short term
experiment_type: Chromatin Accessibility
extraction_protocol: Qiagen minElut
dnase_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental/
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
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| Library strategy |
DNase-Hypersensitivity |
| Library source |
genomic |
| Library selection |
DNAse |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_term_id: CL_0002620
assay_term_id: OBI_0001853
nucleic_acid_term_id: SO_0000352
Design description: Chromatin accessibility determination via DNase-seq
Library name: DS19561
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.11371
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.11370
****************
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: GSM878636_UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19561.hg19.level.1.release.7
ANALYSIS TITLE: Mapping of Fibroblasts Fetal Skin Abdomen Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina reads produced by DNAse-Seq on Fibroblasts Fetal Skin Abdomen, Donor H-24259, Library DS19561 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.12745
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: Chromatin Accessibility
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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 7
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,280,788
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4991
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.5749
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9968
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5667
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
ANALYSIS FILE NAME: GSM878636_UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DS19561.hg19.level.2.release.7
ANALYSIS TITLE: Raw Signal Density Graphs of Fibroblasts Fetal Skin Abdomen Chromatin Accessibility Data
ANALYSIS DESCRIPTION: Illumina DNAse-Seq read mappings from Fibroblasts Fetal Skin Abdomen, Donor H-24259, Library DS19561 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.12803
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: Chromatin Accessibility
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 150bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 7
BROWSER_TRACK_NAME: FFSA DNase 59 61
BROWSER_TRACK_DESCRIPTION: UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19561 EA Release 7
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 45,280,788
NUMBER_OF_CHROMATIN_ACCESSIBILITY_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 58
FINDPEAKS_SCORE: 0.4991
FINDPEAKS_PERCENTILE: 74
HOTSPOT_SCORE: 0.5749
HOTSPOT_PERCENTILE: 79
IROC_SCORE: 0.9968
IROC_PERCENTILE: 76
POISSON_SCORE: 0.5667
POISSON_PERCENTILE: 74
MAXIMUM_REPLICATE_CORRELATION: 1.0
**********************************************************************
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| Submission date |
Feb 21, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Northwest REMC |
| E-mail(s) |
rharris1@bcm.tmc.edu
|
| Organization name |
University of Washington
|
| Street address |
-
|
| City |
Seattle |
| State/province |
WA |
| ZIP/Postal code |
98195 |
| Country |
USA |
| |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX121262 |
| BioSample |
SAMN00791499 |
| Named Annotation |
GSM878636_UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM878636_UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.bed.gz |
605.7 Mb |
(ftp)(http) |
BED |
| GSM878636_UW.Fibroblasts_Fetal_Skin_Abdomen.ChromatinAccessibility.H-24259.DS19561.wig.gz |
195.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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