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Sample GSM1227087

Query DataSets for GSM1227087

Status

Public on Jan 15, 2014

Title

Whole Genome Sequencing analysis of derived from human HUES64 cells; WGS_Lib 4

Sample type

SRA

Source name

Harvard University ES Cell 64 AKA HUES 64; WGS_Lib 4

Organism

Homo sapiens

Characteristics

sample alias: BioSam 1820
sample common name: HUES64 Cell Line
lineage: embrionic stem cell
medium: HUES general media - KO DMEM, 20% KSR, bFGF (10ng/mL)
disease: presumed normal
passage: 27
line: HUES64
differentiation_method: adherence
batch: BioSAli 2829
biomaterial_type: Cell Line
differentiation_stage: undifferentiated
Sex: Male
biomaterial_provider: Harvard
extraction_protocol_sonication_cycles: Covaris shearing conditions: four cycles of two consecutive treatments (T1-Duty cycle 5%, Intensity 5, cycle per burst 200, duration 30 sec; T2-Duty cycle 1%, Intensity 5, cycle per burst 200, duration 5 sec).
experiment_type: Whole Genome Sequencing
extraction_protocol: Standard Protocol (Smith et al., Methods 48, 226-232)
extraction_protocol_type_of_sonicator: Covaris S2 (TM)

Extracted molecule

genomic DNA

Extraction protocol

Library construction protocol: Genomic DNA (0.5~1.5µg) was fragmented to 100-1,000 bp using a Covaris S2. Purified DNA fragments were end-repaired. After A-tailing, the DNA fragments were ligated with paired-end adapters. Adapter-attached DNA fragments of 470-570 bp, which contain 350-450 bp genomic DNA inserts, were gel-purified. The purified DNA fragments were utilized as templates for PCR enrichment (5-6 cycles) by using Phusion HF polymerase (NEB). The PCR amplified DNA fragments were purified using 1.5X of Agencourt AMPure XP beads (Beckman Coulter) to remove PCR primers. The enriched library was quantified using a Qubit fluorometer and Quant-iT dsDNA HS Assay Kit (Invitrogen). Library sequencing was performed using 101 BP PE Illumina

Library strategy

WGS

Library source

genomic

Library selection

RANDOM

Instrument model

Illumina HiSeq 2000

Description

sample_term_id: NTR_0000853
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: WGS REMC Sequencing on Illumina
Library name: WGS_Lib 4
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.18844
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.18849
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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.