|
| Status |
Public on Mar 31, 2011 |
| Title |
ChIP-Seq analysis of H3K4me1; chondr. dif cls; Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1 |
| Sample type |
SRA |
| |
|
| Source name |
chondrocytes derived via in vitro culture from mesenchymal stem cells; Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1
|
| Organism |
Homo sapiens |
| Characteristics |
sample alias: 81
sample common name: Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
donor_health_status: healthy
molecule: genomic DNA
disease: none
markers: NA
culture_conditions: Medium: NA; Differentiation Method: alginate hydrogel scaffold (SR Herlofsen et al, Tissue Eng Part A. 2011)
passage_if_expanded: NA
cell_type: chondrogenic dif cells
donor_ethnicity: NA
donor_sex: Unknown
biomaterial_type: Primary Cell Culture
donor_id: 59
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: CL_0000138
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.5741
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.5935
****************
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: GSM670000_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.59.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1.hg19.level.1.release.3
ANALYSIS TITLE: Mapping of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me1 ChIP-Seq on Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 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.6516
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: 0.6159
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6161
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9983
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7046
POISSON_PERCENTILE: 96
**********************************************************************
ANALYSIS FILE NAME: GSM670000_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.59.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1.hg19.level.2.release.3
ANALYSIS TITLE: Raw Signal Density Graphs of Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me1 ChIP-Seq read mappings from Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells, Donor 59 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.6726
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: CfBMDMSC H3K4me1 59
BROWSER_TRACK_DESCRIPTION: BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K4me1 Donor 59 Library Lib:MC:20100729:01--ChIP:MC:20100726:01:chondrogenic dif cells:H3K4Me1 EA Release 3
QUALITY SCORES:
NUMBER_OF_H3K4me1_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 50
FINDPEAKS_SCORE: 0.6159
FINDPEAKS_PERCENTILE: 96
HOTSPOT_SCORE: 0.6161
HOTSPOT_PERCENTILE: 96
IROC_SCORE: 0.9983
IROC_PERCENTILE: 93
POISSON_SCORE: 0.7046
POISSON_PERCENTILE: 96
**********************************************************************
|
| |
|
| Submission date |
Feb 07, 2011 |
| Last update date |
Jan 29, 2015 |
| Contact name |
BROAD INSTITUTE |
| E-mail(s) |
[email protected]
|
| 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 |
SAMN00205672 |
| Named Annotation |
GSM670000_BI.Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells.H3K4me1.59.wig.gz |
