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Status |
Public on Jan 15, 2014 |
Title |
Bisulfite-Seq analysis of WGBS_Lib 64 derived from human adult CD56 cells; WGBS_Lib 64 |
Sample type |
SRA |
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Source name |
Adult Primary CD56+ cells; WGBS_Lib 64
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Organism |
Homo sapiens |
Characteristics |
sample alias: BioSam 1237 sample common name: CD56 Primary Cells donor_health_status: presumed normal disease: presumed normal markers: CD56+ passage_if_expanded: NA cell_type: adult CD56 donor_ethnicity: Unknown donor_sex: Male biomaterial_type: Primary Cell donor_id: UW RO 02035 biomaterial_provider: UW donor_age: 37.0 Years 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: 250-400 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: 130-280 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_0000623 assay_term_id: OBI_0001863 nucleic_acid_term_id: SO_0000352 Design description: WGBS REMC Sequencing on Illumina Library name: WGBS_Lib 64 EDACC Genboree Experiment Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17365 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17375 **************** 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 |
Various levels of processed data files will be made available as this project proceeds.
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Submission date |
Jul 16, 2013 |
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 |
SRA |
SRX323154 |
BioSample |
SAMN02252538 |
Supplementary data files not provided |
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Raw data are available in SRA |
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