|
| Status |
Public on Jul 04, 2016 |
| Title |
Kasumi_1_MEIS2_KD_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
leukemic cell line derived from peripheral blood (contains t(8;21) chromosome translocation)
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Kasumi-1
tissue: peripheral blood derived
transduction: MEIS2_KD
|
| Treatment protocol |
Cells were transduced with scrambled and sh-RNA targetting MEIS2 VCM. Cells were puromycin selected before RNA extraction
|
| Growth protocol |
Kasumi-1 cells were cultured in 20% RPMI medium
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy micro kit (Qiagen) and according to the manufacturer's manual
We used Illumina TruSeq™ RNA Sample preparation Kit version 2 and strictly followed the manufacturer's protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
MEIS2 shRNA transduced Kasumi-1
Sample_123B
|
| Data processing |
Illumina Casava1.8.4 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, then mapped to hg19 using tophat with default parameters
Fragments Per Kilobase of transcript per Million mapped reads (FPKM) calculation, normalization, and differential expression analysis were calculated using Cufflinks and cuffdiff
Genome_build: hg19
Supplementary_files_format_and_content: One tab-delimited text file with FPKM values of genes across all samples
|
| |
|
| Submission date |
May 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Medhanie Assmelash Mulaw |
| E-mail(s) |
medhanie.mulaw@uni-ulm.de
|
| Organization name |
University of Ulm
|
| Street address |
Albert-Einstein-Allee 11
|
| City |
Ulm |
| ZIP/Postal code |
89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE81328 |
MEIS2 is a novel oncogenic partner in AML1-ETO positive AML [RNA-Seq human] |
| GSE81330 |
MEIS2 is a novel oncogenic partner in AML1-ETO positive AML |
|
| Relations |
| BioSample |
SAMN04979191 |
| SRA |
SRX1756613 |
