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Sample GSM621414 Query DataSets for GSM621414
Status Public on Nov 12, 2010
Title ChIP-Seq analysis of WCE in human Mobilized CD34 cells; Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE
Sample type SRA
 
Source name CD34 cells mobilized into peripheral blood; Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE
Organism Homo sapiens
Characteristics donor_health_status: NA
molecule: genomic DNA
disease: none
markers: CD34+
passage_if_expanded: NA
cell_type: Mobilized CD34
donor_ethnicity: Cauc
donor_sex: Female
biomaterial_type: Primary Cell
donor_id: RO 01549
biomaterial_provider: UW
donor_age: NA
extraction_protocol_sonication_cycles: 1
chip_protocol_chromatin_amount: standard
extraction_protocol: SDS lysis
experiment_type: ChIP-Seq Input
chip_protocol: Input
extraction_protocol_type_of_sonicator: Bioruptor
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 Genome Analyzer II
 
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: Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.3754
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.3881
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
BED and WIG files were replaced on April 29, 2014
Data processing **********************************************************************

ANALYSIS FILE NAME: GSM621414_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01549.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE.hg19.level.1
ANALYSIS TITLE: Mapping of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina reads produced by ChIP-Seq Input on Mobilized CD34 Primary Cells, Donor RO 01549 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.4760
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_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2414
POISSON_PERCENTILE: 60

**********************************************************************

ANALYSIS FILE NAME: GSM621414_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01549.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:RI:20100524:08--ChIP:MA:20100517:08:Mobilized CD34:WCE.hg19.level.2
ANALYSIS TITLE: Raw Signal Density Graphs of Mobilized CD34 Primary Cells ChIP-Seq Input Data
ANALYSIS DESCRIPTION: Illumina ChIP-Seq Input read mappings from Mobilized CD34 Primary Cells, Donor RO 01549 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.5034
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: MCD34 Input 49
BROWSER_TRACK_DESCRIPTION: BI Mobilized CD34 Primary Cells ChIP-Seq Input Donor RO 01549 EA Release 2


QUALITY SCORES:
NUMBER_OF_Input_EXPERIMENTS_SCORED: 67
FINDPEAKS_SCORE: 0.0065
FINDPEAKS_PERCENTILE: 25
HOTSPOT_SCORE: 0.0042
HOTSPOT_PERCENTILE: 9
IROC_SCORE: 0.0
IROC_PERCENTILE: 18
POISSON_SCORE: 0.2414
POISSON_PERCENTILE: 60

**********************************************************************

 
Submission date Nov 10, 2010
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
 
Platform ID GPL9115
Series (1)
GSE19465 BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject
Relations
SRA SRX031408
BioSample SAMN00113441
Named Annotation GSM621414_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01549.wig.gz

Supplementary file Size Download File type/resource
GSM621414_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01549.bed.gz 476.8 Mb (ftp)(http) BED
GSM621414_BI.Mobilized_CD34_Primary_Cells.Input.UW_RO_01549.wig.gz 51.5 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Processed data provided as supplementary file
Raw data are available in SRA

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