|
| 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 |
