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Sample GSM1227088 Query DataSets for GSM1227088
Status Public on Jan 15, 2014
Title Whole Genome Sequencing analysis of derived from human H9 ES cells; WGS_Lib 5
Sample type SRA
Source name Human Embryonic Stem Cell 9 ; WGS_Lib 5
Organism Homo sapiens
Characteristics sample alias: BioSam 1819
sample common name: H9 Cell Line
lineage: embrionic stem cell
medium: HUES general media - KO DMEM, 20% KSR, bFGF (10ng/mL)
disease: presumed normal
passage: 59
line: H9 ES cells
differentiation_method: adherence
batch: BioSAli 2828
biomaterial_type: Cell Line
differentiation_stage: undifferentiated
Sex: Unknown
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_0000838
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: WGS REMC Sequencing on Illumina
Library name: WGS_Lib 5
EDACC Genboree Experiment Page:
EDACC Genboree Sample Page:
For data usage terms and conditions, please refer to:
Data processing Various levels of processed data files will be made available as this project proceeds.
Submission date Sep 09, 2013
Last update date May 15, 2019
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
SRA SRX347299
BioSample SAMN02351515

Supplementary data files not provided
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Raw data are available in SRA

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