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Sample GSM1186666 Query DataSets for GSM1186666
Status Public on Jan 15, 2014
Title Bisulfite-Seq analysis of WGBS_Lib 69 derived from human fSpinal Cord cells; WGBS_Lib 69
Sample type SRA
 
Source name Primary fetal spinal cord tissue; WGBS_Lib 69
Organism Homo sapiens
Characteristics sample alias: BioSam 1240
sample common name: Fetal Spinal Cord
collection_method: Post-Mortem
donor_health_status: presumed normal
disease: presumed normal
tissue_type: Fetal Spinal Cord
donor_ethnicity: Unknown
donor_sex: Female
biomaterial_type: Primary Tissue
tissue_depot: Spinal Cord
donor_id: UW H24943
biomaterial_provider: University of Washington
donor_age: 115.0 Days
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)
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.
 
Library strategy Bisulfite-Seq
Library source genomic
Library selection RANDOM
Instrument model Illumina HiSeq 2000
 
Description sample_term_id: UBERON_0002240
assay_term_id: OBI_0001863
nucleic_acid_term_id: SO_0000352
Design description: WGBS REMC Sequencing on Illumina
Library name: WGBS_Lib 69
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.17368
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.17378
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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.
 
Submission date Jul 16, 2013
Last update date May 15, 2019
Contact name BROAD INSTITUTE
E-mail(s) rharris1@bcm.tmc.edu
Organization name Broad Institute
Street address -
City Cambridge
State/province MA
ZIP/Postal code 02142
Country USA
 
Platform ID GPL11154
Series (1)
GSE17312 BI Human Reference Epigenome Mapping Project
Relations
SRA SRX323157
BioSample SAMN02252541

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA

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