|
| Status |
Public on May 17, 2010 |
| Title |
H3K36me3 ChIP-Seq analysis of peripheral cd4 naive from TC001 (HS1989) |
| Sample type |
SRA |
| |
|
| Source name |
HS1989-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: PF064-DNA
donor_id: TC001
Sex: male
body site: Blood
histological type: CD4 naive cell
is tumor: No
biomaterial_type: primary cell
cell_type: CD4 naive cell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
library construction protocol: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
design description: H3K36me3 ChIP-Seq analysis of peripheral cd4 naive from TC001 (HS1989) using Illumina Genome Analyzer IIx
library name: HS1989
EXPERIMENT_TYPE: Histone H3K36me3
EXTRACTION_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 20 min
CHIP_PROTOCOL: Refer to document 'REMC ChIP and Library Construction Protocol' from the Farnham Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
CHIP_PROTOCOL_CHROMATIN_AMOUNT: 1 ug
SIZE_FRACTION: 315-623 bp
CHIP_PROTOCOL_BEAD_TYPE: Protein G Mag Beads
CHIP_PROTOCOL_BEAD_AMOUNT: 15 ul
CHIP_PROTOCOL_ANTIBODY_AMOUNT: 2 ug
CHIP_ANTIBODY: H3K36me3
CHIP_ANTIBODY_PROVIDER: Abcam
CHIP_ANTIBODY_CATALOG: ab9050
CHIP_ANTIBODY_LOT: 395432
****************
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: GSM543035_UCSF-UBC.CD4-Naive-Primary-Cells.H3K36me3.wig
ANALYSIS ALIAS: UCSF-UBC.CD4-Naive-Primary-Cells.H3K36me3
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells H3K36me3 Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq read mappings for H3K36me3 in CD4 Naive Primary Cells 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.2824
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: ChIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
**********************************************************************
ANALYSIS FILE NAME: GSM543035_UCSF-UBC.CD4_Naive_Primary_Cells.H3K36me3.TC001.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1989-1_430RMAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K36me3 ChIP-Seq on CD4 Naive Primary Cells, Donor TC001 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.4321
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 2
QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2879
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3205
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9575
IROC_PERCENTILE: 44
POISSON_SCORE: 0.465
POISSON_PERCENTILE: 37
**********************************************************************
ANALYSIS FILE NAME: GSM543035_UCSF-UBC.CD4_Naive_Primary_Cells.H3K36me3.TC001.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: HS1989-1_430RMAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells Histone H3K36me3 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K36me3 ChIP-Seq read mappings from CD4 Naive Primary Cells, Donor TC001 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.4370
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 2
BROWSER_TRACK_NAME: CD4N H3K36me3 01
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD4 Naive Primary Cells Histone H3K36me3 Donor TC001 EA Release 2
QUALITY SCORES:
NUMBER_OF_H3K36me3_EXPERIMENTS_SCORED: 54
FINDPEAKS_SCORE: 0.2879
FINDPEAKS_PERCENTILE: 65
HOTSPOT_SCORE: 0.3205
HOTSPOT_PERCENTILE: 70
IROC_SCORE: 0.9575
IROC_PERCENTILE: 44
POISSON_SCORE: 0.465
POISSON_PERCENTILE: 37
**********************************************************************
|
| |
|
| Submission date |
May 12, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSF-UBC CENTER |
| Organization name |
UCSF-UBC
|
| Street address |
UCSF-UBC
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143 |
| Country |
USA |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE16368 |
UCSF-UBC Human Reference Epigenome Mapping Project |
|
| Relations |
| Named Annotation |
GSM543035_UCSF-UBC.CD4_Naive_Primary_Cells.H3K36me3.TC001.wig.gz |
| Named Annotation |
GSM543035_UCSF-UBC.CD4-Naive-Primary-Cells.H3K36me3.wig.gz |
| SRA |
SRX1157838 |
| BioSample |
SAMN03416748 |
