|
| Status |
Public on Dec 31, 2013 |
| Title |
CG-SH gDNA |
| Sample type |
SRA |
| |
|
| Source name |
acute myeloid leukemia
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: CG-SH
|
| Treatment protocol |
Cells were grown in exponential phase before 1x10^7 cells were collected and placed into either DNAzol or Trizol in order to extract gDNA or RNA respectively
|
| Growth protocol |
Cells were cultured in IMDM medium with 10% FBS, penicillin (100 U/ml) and streptomycin (100 µg/ml) supplemented with cytokines (human stem cell factor (H-SCF) (100 ng/ml), interleukin 3 (IL-3) (20 ng/ml), granulocyte colony-stimulating factor (G-CSF) (20 ng/ml)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
gDNA was extracted from DNAzol (Invitrogen) according to manufacturers protocol. gDNA was used to created paired-end libraries using Illumina Truseq V3 kit according to manufacturers protocol.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Eland2 was used (through Casava 1.7) for mapping to the human reference genome
Variants were called usign Samtools with a quality filter of 20 and a minimum number of reads equal or greater than 3
Genome Build: hg19
supplementary files format and content: Sequence variants in BCF format
|
| |
|
| Submission date |
Aug 17, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Brian Wilhelm |
| E-mail(s) |
brian.wilhelm@umontreal.ca
|
| Organization name |
University of Montreal
|
| Street address |
2950 Chemin Polytechnique
|
| City |
Montreal |
| ZIP/Postal code |
H1J 3R4 |
| Country |
Canada |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE40199 |
Whole Genome sequencing of a normal karyotype AML cell line |
|
| Relations |
| SRA |
SRX179256 |
| BioSample |
SAMN01120801 |
