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SRX323152: Bisulfite-Seq analysis of WGBS_Lib 62 derived from human adult CD14 cells
4 ILLUMINA (Illumina HiSeq 2000) runs: 464.1M spots, 92.8G bases, 54.3Gb downloads

Design: WGBS REMC Sequencing on Illumina
Submitted by: Gene Expression Omnibus (GEO)
Study: BI Human Reference Epigenome Mapping Project
 • SRP000996 • All experiments • All runs
show Abstracthide Abstract
The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps for stem cells and primary ex vivo tissues selected to represent the normal counterparts of tissues and organ systems frequently involved in human disease. Characterization of the reference epigenome in humans by use of ChIP-Seq in a diverse panel of ES cells, tissue stem cells, reprogrammed stem cells, primary cells and tissues.
Sample: Adult Primary CD14+ cells
SAMN02252540 • SRS458103 • All experiments • All runs
Organism: Homo sapiens
Library:
Name: WGBS_Lib 62
Instrument: Illumina HiSeq 2000
Strategy: Bisulfite-Seq
Source: GENOMIC
Selection: RANDOM
Layout: SINGLE
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.
Spot descriptor:
1  forward

Experiment attributes: (show all 20 attributes...) (hide...)
BISULFITE_CONVERSION_PROTOCOL: 2x5hrs Epitect Kit
DNA_PREPARATION_INITIAL_DNA_QNTY: 5 ug
EXTRACTION_PROTOCOL_SONICATION_CYCLES: Covaris shearing, duty cycle 5%, intensity 5, cycl (show full text...)(hide...)
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, 226-2 (show full text...)(hide...)
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)
GEO accession: GSM1186661
Pipeline: show...hide...
NameStepPrev StepProgramVersion
BASE_CALLS1NILGAPipelineRTA1.15.19.5
QUALITY_SCORES21GAPipelineRTA1.15.19.5
Links:
External link:
Runs: 4 runs, 464.1M spots, 92.8G bases, 54.3Gb
Run# of Spots# of BasesSizePublished
SRR1104848117,549,74423.5G14Gb2014-01-08
SRR1104855112,708,76422.5G13.1Gb2014-01-08
SRR1104856118,178,29923.6G13.7Gb2014-01-08
SRR1104857115,640,49323.1G13.4Gb2014-01-08

ID:
451789

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