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Sample GSM906387 Query DataSets for GSM906387
Status Public on Mar 30, 2012
Title Reference Epigenome: ChIP-Seq Analysis of H2A.Z in BMP4 Trophoblast Cells; renlab.H2A.Z.BMP4T.01.01
Sample type SRA
 
Source name Human embryonic stem cells received from the James Thomson laboratory. Cells are from the H1 line and are differentiated into trophoblast by treatment with BMP4.; renlab.H2A.Z.BMP4T.01.01
Organism Homo sapiens
Characteristics sample alias: BMP4-09
sample common name: H1 BMP4 Derived Trophoblast Cultured Cells
molecule: genomic DNA
disease: None
biomaterial_provider: James Thomson Laboratory
biomaterial_type: Cell Line
line: H1
lineage: Embryonic Stem Cell
differentiation_stage: Embryonic stem cell differentiated into trophoblast by treatment with BMP4
differentiation_method: H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days
passage: 31
medium: mTeSR1
Sex: Male
batch: BMP4-9
experiment_type: Histone H2A.Z
extraction_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
extraction_protocol_type_of_sonicator: Biorupter
extraction_protocol_sonication_cycles: 80
chip_protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf
chip_protocol_chromatin_amount: 500 micrograms
chip_protocol_bead_type: magnetic anti-rabbit
chip_protocol_bead_amount: 33,500,000
chip_protocol_antibody_amount: 5 micrograms
chip_antibody: H2A.Z
chip_antibody_provider: Abcam
chip_antibody_catalog: ab4174-100
chip_antibody_lot: 460460
Extracted molecule genomic DNA
Extraction protocol Library construction protocol: See http://bioinformatics-renlab.ucsd.edu/RenLabLibraryProtocolV1.pdf
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: UBERON_0000088
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: ChIP-Seq Analysis of H2A.Z in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: AY68
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.11920
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.11191
****************
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: GSM906387_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY68.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.BMP4T.01.01.hg19.level.1.release.8
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H2A.Z ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library AY68, 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.13515
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 8


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,332,005
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2243
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3979
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9339
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4865
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

ANALYSIS FILE NAME: GSM906387_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY68.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H2A.Z.BMP4T.01.01.hg19.level.2.release.8
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells H2A.Z ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H2A.Z ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library AY68, 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.13635
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 8
BROWSER_TRACK_NAME: HBDT H2A.Z 68
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY68 EA Release 8


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 9,332,005
NUMBER_OF_H2A.Z_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 3
FINDPEAKS_SCORE: 0.2243
FINDPEAKS_PERCENTILE: 67
HOTSPOT_SCORE: 0.3979
HOTSPOT_PERCENTILE: 67
IROC_SCORE: 0.9339
IROC_PERCENTILE: 67
POISSON_SCORE: 0.4865
POISSON_PERCENTILE: 67
MAXIMUM_REPLICATE_CORRELATION: 0.95

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

 
Submission date Mar 29, 2012
Last update date May 15, 2019
Contact name UCSD AND SALK
Organization name University of California, San Diego
Street address Health Sciences Drive
City La Jolla
State/province CA
ZIP/Postal code 92092
Country USA
 
Platform ID GPL11154
Series (1)
GSE16256 UCSD Human Reference Epigenome Mapping Project
Relations
SRA SRX134725
BioSample SAMN00778288
Named Annotation GSM906387_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY68.wig.gz

Supplementary file Size Download File type/resource
GSM906387_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY68.bed.gz 142.7 Mb (ftp)(http) BED
GSM906387_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H2A.Z.AY68.wig.gz 25.4 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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