|
| Status |
Public on Dec 31, 2013 |
| Title |
CG-SH RNA |
| 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 |
total RNA |
| Extraction protocol |
Total RNA was extracted from Trizol (invitrogen) according the manufacturers guidelines. rRNA was removed through ribominus kit (Invitrogen) according to manufacturers protocol. Remaining RNA was converted into strand specific paired-end cDNA libraries using Illumina RNA-seq kit according to manufacturers protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| 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
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome Build: hg19
supplementary files format and content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| 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 |
SRX179257 |
| BioSample |
SAMN01120802 |
