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| Status |
Public on Jun 24, 2013 |
| Title |
ChIP-Seq analysis of H3K4me1 in human CD56+ ectoderm cells; DNA_Lib 1809 |
| Sample type |
SRA |
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| Source name |
CD56+ ectodermal germ layer cells derived in vitro from embrionic stem cells by culture in the presence of inhibitors of the BMP, TGFbeta, and WNT signaling pathways.; DNA_Lib 1809
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| Organism |
Homo sapiens |
| Characteristics |
sample alias: BioSam 707
sample common name: hESC Derived CD56+ Ectoderm Cultured Cells
lineage: ectoderm
medium: Days 0-5: DMEM F12, 15% KSR, Dorsomorphin (2um), A83-01 (2um), PNU 74654 (2um)
molecule: genomic DNA
disease: presumed normal
passage: 21
line: CD56+ ectoderm
differentiation_method: adherence
batch: BioSAli 877
biomaterial_type: Cell Line
differentiation_stage: NA
Sex: Male
biomaterial_provider: Harvard
chip_protocol_bead_type: Protein A-Sepharose 4B
chip_antibody: H3K4me1
chip_protocol_chromatin_amount: 0.5 to 3 million cells
extraction_protocol: cell/nuclei lysis
chip_protocol_antibody_amount: ~1 ug
chip_protocol_bead_amount: 10 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: 659352
experiment_type: Histone H3K4me1
extraction_protocol_type_of_sonicator: Branson
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Single read - Illumina
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
sample_term_id: CL_0000221
assay_term_id: OBI_0000716
nucleic_acid_term_id: SO_0000352
Design description: Human Chromatin IP REMC Sequencing on Illumina
Library name: DNA_Lib 1809
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.13167
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.13314
****************
For data usage terms and conditions, please refer to:
http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies
****************
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| Data processing |
**********************************************************************
ANALYSIS FILE NAME: GSM997254_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me1.DNA_Lib_1809.bed
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1809.hg19.level.1.release.9
ANALYSIS TITLE: Mapping of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina reads produced by H3K4me1 ChIP-Seq on the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1809, 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.17210
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 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,896,320
FINDPEAKS_SCORE: 0.3706
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4573
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9809
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5743
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
ANALYSIS FILE NAME: GSM997254_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me1.DNA_Lib_1809.wig
ANALYSIS CENTER: EDACC
ANALYSIS ALIAS: DNA_Lib 1809.hg19.level.2.release.9
ANALYSIS TITLE: Raw Signal Density Graphs of hESC Derived CD56+ Ectoderm Cultured Cells H3K4me1 ChIP-Seq Data
ANALYSIS DESCRIPTION: Illumina H3K4me1 ChIP-Seq read mappings from the hESC Derived CD56+ Ectoderm Cultured Cells, Library DNA_Lib 1809, 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.17393
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 9
BROWSER_TRACK_NAME: hDCEcto H3K4me1 09
BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD56+ Ectoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1809 EA Release 9
QUALITY SCORES:
NUMBER_OF_MAPPED_READS: 13,896,320
FINDPEAKS_SCORE: 0.3706
FINDPEAKS_PERCENTILE: 72
HOTSPOT_SCORE: 0.4573
HOTSPOT_PERCENTILE: 78
IROC_SCORE: 0.9809
IROC_PERCENTILE: 59
POISSON_SCORE: 0.5743
POISSON_PERCENTILE: 83
MAXIMUM_REPLICATE_CORRELATION: NA
**********************************************************************
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| Submission date |
Sep 04, 2012 |
| Last update date |
May 30, 2017 |
| Contact name |
BROAD INSTITUTE |
| E-mail(s) |
[email protected]
|
| Organization name |
Broad Institute
|
| Street address |
-
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| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
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| Platform ID |
GPL11154 |
| Series (1) |
| GSE17312 |
BI Human Reference Epigenome Mapping Project |
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| Relations |
| Reanalyzed by |
GSE99453 |
| BioSample |
SAMN01161883 |
| Named Annotation |
GSM997254_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me1.DNA_Lib_1809.wig.gz |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM997254_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me1.DNA_Lib_1809.bed.gz |
216.2 Mb |
(ftp)(http) |
BED |
| GSM997254_BI.hESC_Derived_CD56+_Ectoderm_Cultured_Cells.H3K4me1.DNA_Lib_1809.wig.gz |
30.3 Mb |
(ftp)(http) |
WIG |
| Raw data not provided for this record |
| Processed data not provided for this record |
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