|
| Status |
Public on Mar 31, 2011 |
| Title |
ChIP-Seq analysis of H3K4me1 in BM-MSC cells; Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow was aspirated from the iliac crest, isolated by density gradient and adhesion to plastic, and expanded in monolayer culture, containing 10% FBS; Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: 78
sample common name: Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
donor_health_status: healthy
molecule: genomic DNA
disease: none
markers: NA
culture_conditions: Medium: DMEM/FBS; Differentiation Method: adherence
passage_if_expanded: NA
cell_type: BM-MSC
donor_ethnicity: NA
donor_sex: Unknown
biomaterial_type: Primary Cell Culture
donor_id: 60
biomaterial_provider: Rikshospitalet University Hospital
donor_age: 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: 151304
experiment_type: Histone H3K4me1
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 |
ChIP |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
sample_term_id: EFO_0000586
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5721
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5950
****************
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: GSM669980_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.60.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 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.6450
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 3
QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2346
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3071
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9741
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4041
POISSON_PERCENTILE: 32
**********************************************************************
ANALYSIS FILE NAME: GSM669980_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.60.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 60 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.6660
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 3
BROWSER_TRACK_NAME: BMDMSC H3K4me1 60
BROWSER_TRACK_DESCRIPTION: BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 60 Library Lib:MC:20100713:08--ChIP:MC:20100706:08:BM-MSC:H3K4Me1 EA Release 3
QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.2346
FINDPEAKS_PERCENTILE: 32
HOTSPOT_SCORE: 0.3071
HOTSPOT_PERCENTILE: 32
IROC_SCORE: 0.9741
IROC_PERCENTILE: 50
POISSON_SCORE: 0.4041
POISSON_PERCENTILE: 32
**********************************************************************
|
| |
|
| Submission date |
Feb 07, 2011 |
| Last update date |
Jan 29, 2015 |
| 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 |
GPL10999 |
| Series (1) |
| GSE19465 |
BI Human Reference Epigenome Mapping Project: ChIP-Seq in human subject |
|
| Relations |
| BioSample |
SAMN00205686 |
| Named Annotation |
GSM669980_BI.Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.60.wig.gz |
