|
| Status |
Public on Mar 22, 2013 |
| Title |
ChIP-Seq Input of CD4 Primary Cells; Histone.DS21541 |
| Sample type |
SRA |
| |
|
| Source name |
flow sorted CD4+ Cells,year 21; Histone.DS21541
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: CD4.RO_01721
sample common name: CD4 Primary Cells
molecule: genomic DNA
disease: None
biomaterial_provider: FHCRC HEIMFELD
biomaterial_type: Primary Cell
cell_type: CD4 Primary Cells
markers: CD4+
donor_id: RO 01679
donor_age: year 21
donor_health_status: NA
donor_sex: Male
donor_ethnicity: Caucasian
passage_if_expanded: NA
experiment_type: ChIP-Seq Input
extraction_protocol: http://www.roadmapepigenomics.org/protocols/type/experimental
extraction_protocol_type_of_sonicator: Diagenode Bioruptor
extraction_protocol_sonication_cycles: 20-40 cycles of 0.5 minute on and 0.5 minute off
chip_protocol: Input
chip_protocol_chromatin_amount: 50ng
|
| 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 HiSeq 2000 |
| |
|
| Description |
sample_term_id: CL_0000492
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Input
Library name: Histone.DS21541
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15773
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5345
****************
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: GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21541-Histone.DS21541.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD4 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Input ChIP-Seq on CD4 Primary Cells, Donor RO 01679, 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.16807
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: 40,969,799
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0028
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.025
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS21541-Histone.DS21541.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Primary Cells Input ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Input ChIP-Seq read mappings from CD4 Primary Cells, Donor RO 01679, 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.16903
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: CD4 Input 79 41
BROWSER_TRACK_DESCRIPTION: UW CD4 Primary Cells ChIP-Seq Input Donor RO 01679 Library Histone.DS21541 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 40,969,799
FINDPEAKS_SCORE: 0.0044
FINDPEAKS_PERCENTILE: 22
HOTSPOT_SCORE: 0.0028
HOTSPOT_PERCENTILE: 8
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.025
POISSON_PERCENTILE: 17
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
|
| |
|
| Submission date |
Mar 20, 2013 |
| 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 |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE18927 |
University of Washington Human Reference Epigenome Mapping Project |
|
| Relations |
| SRA |
SRX252742 |
| BioSample |
SAMN00204016 |
| Named Annotation |
GSM1102805_UW.CD4_Primary_Cells.Input.RO_01679.Histone.DS21541.wig.gz |
