|
| Status |
Public on Mar 26, 2014 |
| Title |
Whole genome sequencing of the IMR90 cell line; IMR90-05_Genome_PE |
| Sample type |
SRA |
| |
|
| Source name |
IMR90 Cell Line, biological replicate 2; IMR90-05_Genome_PE
|
| Organism |
Homo sapiens |
| Characteristics |
sra sample accession: SRS024804
disease: None
biomaterial_provider: ATCC
biomaterial_type: Cell Line
line: IMR90
lineage: NA
batch: 5
differentiation_stage: Fetal lung fibroblast
differentiation_method: NA
passage: NA
medium: Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)
Sex: Female
experiment_type: Whole Genome Sequencing
extraction_protocol: Qiagen DNeasy Mini kit, performed as per manufacturer's instructions
extraction_protocol_type_of_sonicator: Covaris S2
extraction_protocol_sonication_cycles: Standard fragment express, 6 cycles
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Library construction protocol: Genomic DNA was extracted from frozen cell pellets using the DNeasy Mini Kit (Qiagen, Valencia, CA). The DNA was used to create one fragmented DNA library as described in the Applied Biosystems SOLiDTM 4 System Library Preparation Guide (Applied Biosystems, Foster City, CA).
|
| |
|
| Library strategy |
WGS |
| Library source |
genomic |
| Library selection |
RANDOM |
| Instrument model |
AB SOLiD 4 System |
| |
|
| Description |
sample_term_id: EFO_0001196
assay_term_id: OBI_0000124
nucleic_acid_term_id: SO_0000352
Design description: Whole genome sequencing of the IMR90 cell line
Library name: IMR90-05_Genome_PE
EDACC Genboree Experiment Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FEXPERIMENT%2FEDACC.18898
EDACC Genboree Sample Page:
http://genboree.org/java-bin/project.jsp?projectName=XML%20Submissions%2FUCSD%2FSAMPLE%2FEDACC.1961
****************
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 |
Dec 23, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
UCSD AND SALK |
| Organization name |
University of California, San Diego
|
| Street address |
Health Sciences Drive
|
| City |
La Jolla |
| State/province |
CA |
| ZIP/Postal code |
92092 |
| Country |
USA |
| |
|
| Platform ID |
GPL13393 |
| Series (1) |
| GSE16256 |
UCSD Human Reference Epigenome Mapping Project |
|
| Relations |
| BioSample |
SAMN00009763 |
| SRA |
SRX398163 |
