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Sample GSM753438 Query DataSets for GSM753438
Status Public on Jul 06, 2011
Title Reference Epigenome: ChIP-Seq Analysis of H3K4me2 in BMP4 Trophoblast Cells; renlab.H3K4me2.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.H3K4me2.BMP4T.01.01
Organism Homo sapiens
Characteristics sample alias: BMP4-05
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: 28
medium: mTeSR1
Sex: Male
batch: BMP4-5
experiment_type: Histone H3K4me2
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: H3K4me2
chip_antibody_provider: Abcam
chip_antibody_catalog: ab32356
chip_antibody_lot: 727055
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 H3K4me2 in BMP4 Trophoblast Cells. Sequencing was done on the Illumina HiSeq 2000 platform.
Library name: SK497
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.7869
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.7840
****************
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: GSM753438_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me2.SK497.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.BMP4T.01.01.hg19.level.1.release.5
ANALYSIS TITLE: Mapping of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by Histone H3K4me2 ChIP-Seq on H1 BMP4 Derived Trophoblast Cultured Cells, Library SK497, 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.10504
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: 53,104,623
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.18
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

ANALYSIS FILE NAME: GSM753438_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me2.SK497.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: renlab.H3K4me2.BMP4T.01.01.hg19.level.2.release.5
ANALYSIS TITLE: Raw Signal Density Graphs of H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me2 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina Histone H3K4me2 ChIP-Seq read mappings from the H1 BMP4 Derived Trophoblast Cultured Cells, Library SK497, 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.10577
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: HBDT H3K4me2 97
BROWSER_TRACK_DESCRIPTION: UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me2 Library SK497 EA Release 5


QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 53,104,623
NUMBER_OF_H3K4me2_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 4
FINDPEAKS_SCORE: 0.18
FINDPEAKS_PERCENTILE: 75
HOTSPOT_SCORE: 0.2
HOTSPOT_PERCENTILE: 50
IROC_SCORE: 1.0
IROC_PERCENTILE: 100
POISSON_SCORE: 0.25
POISSON_PERCENTILE: 50
MAXIMUM_REPLICATE_CORRELATION: 0.98

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

 
Submission date Jul 01, 2011
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 SRX081159
BioSample SAMN00631722
Named Annotation GSM753438_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me2.SK497.wig.gz

Supplementary file Size Download File type/resource
GSM753438_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me2.SK497.bed.gz 779.0 Mb (ftp)(http) BED
GSM753438_UCSD.H1_BMP4_Derived_Trophoblast_Cultured_Cells.H3K4me2.SK497.wig.gz 59.8 Mb (ftp)(http) WIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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