|
| Status |
Public on Jun 20, 2013 |
| Title |
shControl for shHEB |
| Sample type |
SRA |
| |
|
| Source name |
Kasumi-1 cells
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Hematopoietic
tumor stage: Acute myeloid leukemia
gene knockdown: none
|
| Treatment protocol |
Kasumi-1 cells were infected with the shRNA-expressing lentiviruses in the presence of 8 μg/ml polybrene (Sigma-Aldrich) for 24 hours and then selected with 1 μg/ml puromycin (Sigma-Aldrich). The cells were harvested for RNA purification at 4 days post-infection.
|
| Growth protocol |
Kasumi-1 cells were grown with RPMI 1640 medium (Invitrogen) plus 10% fetal bovine serum (FBS; Gemini Bio-Products) and penicillin-streptomycin (Invitrogen) at 37°C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with TRIzol Reagent according to the manufacturer’s protocol (Invitrogen). One μg of total RNA was treated with DNase I (Qiagen), purified and tested for integrity on the Agilent 2100 Bioanalyzer (Agilent Technologies).
Libraries were generated using the TruSeq RNA Sample Preparation Kit (Illumina). Briefly, mRNA was selected by using magnetic polydT beads and then fragmented. First-strand synthesis was performed using Superscipt II (Invitrogen). After second-strand synthesis a paired-end library was prepared following the Illumina protocol including end-repair, A-tailing, adaptor ligation, and library enrichment. Final products were verified using the Agilent 2100 Bioanalyzer. Each library was loaded onto an Illimina pair-end flowcell at a concentation of 7.5 pM (one library per lane), and sequenced for 50 cycles at each end with Illumina HiSeq2000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
shControl for shHEB
|
| Data processing |
Raw sequence reads were aligned with TopHat to the reference genome (hg19).
The aligned reads were processed with an in-house program to remove PCR duplicates.
The RPKM value for each gene were calculated following published methods (http://woldlab.caltech.edu/~alim/RNAseq/).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
|
| |
|
| Submission date |
Jan 28, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Yanwen Jiang |
| E-mail(s) |
yaj2001@med.cornell.edu
|
| Organization name |
Weill Cornell Medical College
|
| Street address |
413 E. 69th St. BB1462
|
| City |
New York |
| State/province |
NY |
| ZIP/Postal code |
10021 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE43834 |
A Stable Transcription Factor Complex Nucleated by Dimeric AML1-ETO Controls Leukaemogenesis |
|
| Relations |
| SRA |
SRX220347 |
| BioSample |
SAMN01906653 |
