|
| Status |
Public on Jan 12, 2016 |
| Title |
45 DMSO |
| Sample type |
SRA |
| |
|
| Source name |
AML 45 (292)
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary AML patient sample
genotype: inv(16)
growth conditions: OP9 co-culture in IMDM with 20% FBS, IL3, IL6 and SCF
|
| Treatment protocol |
5 uM EPZ004777 or DMSO control for 7 days.
|
| Growth protocol |
OP9 co-culture in IMDM with 20% FBS, IL3, IL6 and SCF
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using Qiagen RNAeasy kit
Illumina Stranded mRNA kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
sorted on day 7 after Cre induction, directly processed to RNA.
|
| Data processing |
Basecalling was performed by Illumina’s RTA (Real-Time Analysis) software version 1.18.61 with QTable version 6. CASAVA version 1.8.2 was used to demultiplex samples. Illumina Chastity quality filtering was performed.
Alignment was performed using GSNAP (version 2012-07-20): gsnap -d hg19_total -v snp135_strict --use-splicing=hg19_total.ucscRefGeneSpliceSites --gunzip --max-mismatches=0.06 -i2 -n1 -Q --nofails -B5 -t12 -A sam *.fastq.gz > *.sam. Sam format was converted to Bam format using Samtools. Bam-files were sorted using Samtools.
Differential gene expression was detemined using Cuffdiff. Genes with low levels (<0.5 in both samples, or 0 in one and <5 in the other sample) were excluded. Genes with 'Fail' and 'Notest' Cuffdiff status were excluded.
Genome_build: hg19
Supplementary_files_format_and_content: FPKM (Cuffdiff)
|
| |
|
| Submission date |
Jan 11, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Tobias Neff |
| E-mail(s) |
[email protected]
|
| Phone |
303-724-7445
|
| Organization name |
University of Colorado Denver AMC
|
| Department |
Pediatric Oncology
|
| Lab |
Neff
|
| Street address |
12800 E. 19th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE76747 |
The Histone Methyltransferases MLL1 and DOT1L Cooperate with Meningioma-1 to Induce AML [Human RNA-seq] |
| GSE76750 |
The Histone Methyltransferases MLL1 and DOT1L Cooperate with Meningioma-1 to Induce AML |
|
| Relations |
| BioSample |
SAMN04396100 |
| SRA |
SRX1527586 |
