|
| Status |
Public on Mar 22, 2013 |
| Title |
Histone H3K4me1 ChIP-Seq of CD14 Primary Cells; Histone.DS22403 |
| Sample type |
SRA |
| |
|
| Source name |
flow sorted CD14+ Cells,year 21; Histone.DS22403
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: CD14.RO_01721
sample common name: CD14 Primary Cells
molecule: genomic DNA
disease: None
biomaterial_provider: FHCRC HEIMFELD
biomaterial_type: Primary Cell
cell_type: CD14 Primary Cells
markers: CD14+
donor_id: RO 01679
donor_age: year 21
donor_health_status: NA
donor_sex: Male
donor_ethnicity: Caucasian
passage_if_expanded: NA
experiment_type: Histone H3K4me1
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: http://www.roadmapepigenomics.org/protocolstype/experimental
chip_protocol_chromatin_amount: 60ug
chip_protocol_bead_type: Millipore A/G agarose beads
chip_protocol_bead_amount: 30ul A/G bead slurry
chip_protocol_antibody_amount: 3ul
chip_antibody: Histone H3K4me1
chip_antibody_provider: Active Motif
chip_antibody_catalog: 39297
chip_antibody_lot: 21008001
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample_term_id: CL_0001054
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Histone H3K4me1 ChIP-Seq
Library name: Histone.DS22403
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FEXPERIMENT%2FEDACC.15722
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.5355
****************
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: GSM1102793_UW.CD14_Primary_Cells.H3K4me1.RO_01721.Histone.DS22403.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22403-Histone.DS22403-Histone.DS22403.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of CD14 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on CD14 Primary Cells, Donor RO 01721, 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.16824
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: 30,987,045
FINDPEAKS_SCORE: 0.7488
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7147
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.778
POISSON_PERCENTILE: 100
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM1102793_UW.CD14_Primary_Cells.H3K4me1.RO_01721.Histone.DS22403.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Histone.DS22403-Histone.DS22403-Histone.DS22403.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of CD14 Primary Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from CD14 Primary Cells, Donor RO 01721, 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.16920
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: CD14 H3K4me1 21 03
BROWSER_TRACK_DESCRIPTION: UW CD14 Primary Cells Histone H3K4me1 Donor RO 01721 Library Histone.DS22403 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 30,987,045
FINDPEAKS_SCORE: 0.7488
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.7147
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9999
IROC_PERCENTILE: 100
POISSON_SCORE: 0.778
POISSON_PERCENTILE: 100
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 |
| Reanalyzed by |
GSE99453 |
| SRA |
SRX252730 |
| BioSample |
SAMN00204012 |
| Named Annotation |
GSM1102793_UW.CD14_Primary_Cells.H3K4me1.RO_01721.Histone.DS22403.wig.gz |
