|
| Status |
Public on May 17, 2010 |
| Title |
MeDIP-Seq analysis of peripheral mononuclear cell from TC003 (HS1772) |
| Sample type |
SRA |
| |
|
| Source name |
HS1772-1
|
| Organism |
Homo sapiens |
| Characteristics |
submitted sample id: JOC40-DNA
donor_id: TC003
Sex: female
body site: Blood
histological type: Peripheral blood mononuclear cell
is tumor: No
biomaterial_type: primary cell
cell_type: Peripheral blood mononuclear cell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
library construction protocol: Refer to document 'MeDIP-seq library construction protocol v2' from the Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
|
| |
|
| Library strategy |
MeDIP-Seq |
| Library source |
genomic |
| Library selection |
5-methylcytidine antibody |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
design description: MeDIP-Seq analysis of peripheral mononuclear cell from TC003 (HS1772) using Illumina Genome Analyzer IIx
library name: HS1772
EXPERIMENT_TYPE: DNA Methylation
EXTRACTION_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
EXTRACTION_PROTOCOL_TYPE_OF_SONICATOR: Diagenode Bioruptor
EXTRACTION_PROTOCOL_SONICATION_CYCLES: 25 min
MeDIP_PROTOCOL: Refer to document 'MeDIP-seq library construction protocol v2' by Costello Lab at the Roadmap Epigenomics Project site, Experimental Protocols page (URL: http://www.roadmapepigenomics.org/protocols/type/experimental/)
MeDIP_PROTOCOL_DNA_AMOUNT: 2 ug
MeDIP_PROTOCOL_BEAD_TYPE: Protein A/G Beads
MeDIP_PROTOCOL_BEAD_AMOUNT: 100 ul
MeDIP_PROTOCOL_ANTIBODY_AMOUNT: N/A ug
MeDIP_ANTIBODY: Methylcytidine
MeDIP_ANTIBODY_PROVIDER: Eurogentec
MeDIP_ANTIBODY_CATALOG: BI-MECY-0100
MeDIP_ANTIBODY_LOT: 80604
****************
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: GSM543025_UCSF-UBC.CD4-Naive-Primary-Cells.MeDIP-Seq.wig
ANALYSIS ALIAS: UCSF-UBC.CD4-Naive-Primary-Cells.MeDIP-Seq
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings for DNA methylation assessment 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.2825
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 0bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
**********************************************************************
ANALYSIS FILE NAME: GSM543025_UCSF-UBC.CD4_Naive_Primary_Cells.MeDIP-Seq.TC003.bed
ANALYSIS ALIAS: HS1772-1_612TYAAXX-HS1772-1_42TCVAAXX.hg19.level.1
ANALYSIS TITLE: Mapping of CD4 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by MeDIP-Seq on CD4 Naive Primary Cells, Donor TC003 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.4260
DATA_ANALYSIS_LEVEL: 1
EXPERIMENT_TYPE: MeDIP-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: None
ALIGNMENT_POSTPROCESSING: None
RELEASE_NUMBER: Human Epigenome Atlas 2
QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.1717
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2893
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9355
IROC_PERCENTILE: 41
POISSON_SCORE: 0.6536
POISSON_PERCENTILE: 20
**********************************************************************
ANALYSIS FILE NAME: GSM543025_UCSF-UBC.CD4_Naive_Primary_Cells.MeDIP-Seq.TC003.wig
ANALYSIS ALIAS: HS1772-1_612TYAAXX-HS1772-1_42TCVAAXX.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of CD4 Naive Primary Cells MeDIP-Seq Data
ANALYSIS DESCRIPTION: Illumina MeDIP-Seq read mappings from CD4 Naive Primary Cells, Donor TC003 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.4236
DATA_ANALYSIS_LEVEL: 2
EXPERIMENT_TYPE: MeDIP-Seq
GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19
SOFTWARE: In house programs and scripts
SOFTWARE_VERSION: NA
READ_EXTENSION: 200bp
GENOMIC_WINDOW: 20bp
TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None
RELEASE_NUMBER: Human Epigenome Atlas 2
BROWSER_TRACK_NAME: CD4N MeDIP 03
BROWSER_TRACK_DESCRIPTION: UCSF-UBC-UCD CD4 Naive Primary Cells MeDIP-Seq Donor TC003 EA Release 2
QUALITY SCORES:
NUMBER_OF_MEDIP-SEQ_EXPERIMENTS_SCORED: 24
FINDPEAKS_SCORE: 0.1717
FINDPEAKS_PERCENTILE: 29
HOTSPOT_SCORE: 0.2893
HOTSPOT_PERCENTILE: 29
IROC_SCORE: 0.9355
IROC_PERCENTILE: 41
POISSON_SCORE: 0.6536
POISSON_PERCENTILE: 20
**********************************************************************
|
| |
|
| 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 |
| Reanalyzed by |
GSE69894 |
| Named Annotation |
GSM543025_UCSF-UBC.CD4_Naive_Primary_Cells.MeDIP-Seq.TC003.wig.gz |
| Named Annotation |
GSM543025_UCSF-UBC.CD4-Naive-Primary-Cells.MeDIP-Seq.wig.gz |
| SRA |
SRX1157908 |
| BioSample |
SAMN03416850 |
