|
|
GEO help: Mouse over screen elements for information. |
|
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: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FEXPERIMENT%2FEDACC.18845 EDACC Genboree Sample Page: http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FBroad%2FSAMPLE%2FEDACC.18852 **************** For data usage terms and conditions, please refer to: http://www.drugabuse.gov/funding/funding-opportunities/nih-common-fund/epigenomics-data-access-policies ****************
|
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 |
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 |
SRX347299 |
BioSample |
SAMN02351515 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
|
|
|
|
|