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| Status |
Public on Dec 05, 2011 |
| Title |
ChIP-Seq analysis of H3K4me1 in human Mobilized CD34 cells; DNA_Lib 256 |
| Sample type |
SRA |
| |
|
| Source name |
flow sorted CD34+ cells from cord blood; DNA_Lib 256
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: RO 01536
sample common name: CD34 Primary Cells
molecule: genomic DNA
disease: None
biomaterial_provider: FHCRC HEIMFELD
biomaterial_type: Primary Cell
cell_type: CD34 Primary Cells
markers: CD34+
donor_id: RO 01536
donor_age: 27 years
donor_health_status: NA
donor_sex: Female
donor_ethnicity: Hispanic
passage_if_expanded: NA
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_antibody: H3K4me1
chip_protocol_chromatin_amount: 10 million cells
extraction_protocol: SDS lysis
chip_protocol_antibody_amount: 2-15 ug
chip_protocol_bead_amount: 70 ul bed volume
chip_protocol: Bernstein_BROAD_ENCODE_protocol
extraction_protocol_sonication_cycles: 1
chip_antibody_catalog: ab8895
chip_antibody_provider: Abcam
chip_antibody_lot: 151302
experiment_type: Histone H3K4me1
extraction_protocol_type_of_sonicator: Bioruptor
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
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| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sample_term_id: CL_0000837
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 256
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.7527
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUniversity%20of%20Washington%2FSAMPLE%2FEDACC.2397
****************
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: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256.hg19.level.1.release.4
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536 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.8234
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 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,168,042
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.629
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6316
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9994
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6949
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
ANALYSIS FILE NAME: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256.hg19.level.2.release.4
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536 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.8261
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 4
BROWSER_TRACK_NAME: MCD34 H3K4me1 36 56
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01536 Library DNA_Lib 256 EA Release 4
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,168,042
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 12
FINDPEAKS_SCORE: 0.629
FINDPEAKS_PERCENTILE: 92
HOTSPOT_SCORE: 0.6316
HOTSPOT_PERCENTILE: 92
IROC_SCORE: 0.9994
IROC_PERCENTILE: 83
POISSON_SCORE: 0.6949
POISSON_PERCENTILE: 92
MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
ANALYSIS FILE NAME: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536_release5.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Mobilized CD34 Primary Cells, Donor RO 01536, 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.10750
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 5
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,307,060
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6258
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6276
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6924
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
ANALYSIS FILE NAME: GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536_release5.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256-DNA_Lib 256.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Mobilized CD34 Primary Cells, Donor RO 01536, 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.11014
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 5
BROWSER_TRACK_NAME: MCD34 H3K4me1 36 56
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells Histone H3K4me1 Donor RO 01536 Library DNA_Lib 256 EA Release 5
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,307,060
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 54
FINDPEAKS_SCORE: 0.6258
FINDPEAKS_PERCENTILE: 100
HOTSPOT_SCORE: 0.6276
HOTSPOT_PERCENTILE: 100
IROC_SCORE: 0.9994
IROC_PERCENTILE: 98
POISSON_SCORE: 0.6924
POISSON_PERCENTILE: 98
MAXIMUM_REPLICATE_CORRELATION: 0.97
**********************************************************************
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| Submission date |
Aug 03, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
BROAD INSTITUTE |
| E-mail(s) |
rharris1@bcm.tmc.edu
|
| Organization name |
Broad Institute
|
| Street address |
-
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE17312 |
BI Human Reference Epigenome Mapping Project |
|
| Relations |
| Reanalyzed by |
GSE99453 |
| SRA |
SRX088649 |
| BioSample |
SAMN00113440 |
| Named Annotation |
GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536_release5.wig.gz |
| Named Annotation |
GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536.bed.gz |
140.7 Mb |
(ftp)(http) |
BED |
| GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536.wig.gz |
20.8 Mb |
(ftp)(http) |
WIG |
| GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536_release5.bed.gz |
143.8 Mb |
(ftp)(http) |
BED |
| GSM772734_BI.Mobilized_CD34_Primary_Cells.H3K4me1.RO_01536_release5.wig.gz |
21.1 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
| Raw data are available in SRA |
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