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Status |
Public on Sep 13, 2012 |
Title |
Bisulfite-Seq analysis of WGBS_Lib 6 derived from human HUES64 derived CD184+ cells; WGBS_Lib 6 |
Sample type |
SRA |
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Source name |
CD184+ endoderm differentiated in vitro from stem cells; WGBS_Lib 6
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Organism |
Homo sapiens |
Characteristics |
cell_type: CD184+ endoderm cultured cells sample alias: BioSam 311 sample common name: hESC Derived CD184+ Endoderm Cultured Cells lineage: endoderm medium: RPMI 100ng/mL Activin A 50ng/mL Wnt3a molecule: genomic DNA disease: presumed normal passage: 27 line: HUES64 derived CD184+ differentiation_method: in vitro culture batch: BioSAli 396 biomaterial_type: Cell Line differentiation_stage: differentiated Sex: Male biomaterial_provider: Harvard bisulfite_conversion_protocol: 2x5hrs Epitect Kit dna_preparation_initial_dna_qnty: 5 ug extraction_protocol_sonication_cycles: Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes dna_preparation_adaptor_ligation_protocol: T4 Ligase (2,000U/ul) 16C o/n dna_preparation_adaptor_sequence: Illumina paired end adapter library_generation_pcr_r_primer_sequence: PE1.0 dna_preparation_post-ligation_fragment_size_selection: 220-380 bisulfite_conversion_percent: 99.5% extraction_protocol: Standard Protocol (Smith et al., Methods 48, 226-232) library_generation_pcr_primer_conc: 25uM dna_preparation_fragment_size_range: 160-340 experiment_type: DNA Methylation library_generation_pcr_thermocycling_program: Smith et al., Methods 48, 226-232 library_generation_pcr_product_isolation_protocol: SPRI Beads library_generation_pcr_f_primer_sequence: PE2.0 library_generation_pcr_template_conc: NA library_generation_pcr_polymerase_type: Pfu Turbo Cx hot start library_generation_pcr_number_cycles: 5-8 extraction_protocol_type_of_sonicator: Covaris S2 (TM)
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Extracted molecule |
genomic DNA |
Extraction protocol |
Library construction protocol: Genomic DNA (1.5~5µg) was fragmented to 100-500 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with methylated paired-end adapters. Adapter-attached DNA fragments of 300-400 bp, which contain 150-250 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were subjected to two cycles of sodium bisulfite conversion using the EpiTect Bisulfite kit (Qiagen). Adapter-attached, bisulfite-converted DNA molecules were enriched by PCR using PfuTurboCx Hotstart DNA polymerase (Stratagene). The PCR amplified DNA fragments were subjected to a second gel size selection to remove PCR primers and adapter dimers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit. Library sequencing was performed using 101 BP PE Illumina technology.
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Library strategy |
Bisulfite-Seq |
Library source |
genomic |
Library selection |
RANDOM |
Instrument model |
Illumina HiSeq 2000 |
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Description |
sample_term_id: CL_0000223 assay_term_id: OBI_0001863 nucleic_acid_term_id: SO_0000352 Design description: WGBS REMC Sequencing on Illumina Library name: WGBS_Lib 6 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.11650 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.11680 **************** 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: GSM916051_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_6.wig ANALYSIS CENTER: EDACC ANALYSIS ALIAS: WGBS_Lib 6.hg19.level.2.release.8 ANALYSIS TITLE: Methylation Proportion Graphs of hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Data ANALYSIS DESCRIPTION: Illumina Bisulfite-Seq read mappings from hESC Derived CD184+ Endoderm Cultured Cells, Donor WGBS_Lib 6 were processed into graphs of methylation proportions. Methylation proportions were calculated as (methylated calls / (methylated calls + unmethylated calls)) for all CpGs covered by at least 4 reads. Reads from the + and - strands were combined for methylation proportion calculations. ANALYSIS TYPE: ABUNDANCE_MEASUREMENT EDACC Genboree Analysis Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FEDACC%2FANALYSIS%2FEDACC.13768 DATA_ANALYSIS_LEVEL: 2 EXPERIMENT_TYPE: Bisulfite-Seq GENOME_ASSEMBLY: NCBI Build GRCh37/UCSC Build hg19 SOFTWARE: In house programs and scripts SOFTWARE_VERSION: NA READ_EXTENSION: 0bp 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: 2bp containing CpGs TREATMENT_OF_REGIONS_PRONE_TO_MULTIPLE_ALIGNMENTS: None RELEASE_NUMBER: Human Epigenome Atlas 8 BROWSER_TRACK_NAME: hDCE BS 6 BROWSER_TRACK_DESCRIPTION: BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8
QUALITY SCORES: NUMBER_OF_MAPPED_READS: 2,019,659,432 NUMBER_OF_Bisulfite-Seq_EXPERIMENTS_SCORED_IN_THIS_RELEASE: 6 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS: 99.18 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE: 33 MAXIMUM_REPLICATE_CORRELATION: NA
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Submission date |
Apr 16, 2012 |
Last update date |
May 15, 2019 |
Contact name |
BROAD INSTITUTE |
E-mail(s) |
rharris1@bcm.tmc.edu
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Organization name |
Broad Institute
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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 |
GSE46644 |
Reanalyzed by |
GSE90454 |
BioSample |
SAMN00857854 |
SRA |
SRX142783 |
Named Annotation |
GSM916051_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_6.wig.gz |
Supplementary file |
Size |
Download |
File type/resource |
GSM916051_BI.hESC_Derived_CD184+_Endoderm_Cultured_Cells.Bisulfite-Seq.WGBS_Lib_6.wig.gz |
225.7 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
Processed data provided as supplementary file |
Raw data not provided for this record |
Raw data are available in SRA |
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