|
| Status |
Public on Nov 27, 2024 |
| Title |
Murine AML, control shRNA, D2, uninduced sorted, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
KL974
|
| Organism |
Mus musculus |
| Characteristics |
cell line: KL974
cell type: Murine AML
time: D2
genotype: Trp53R172H;shMll3;shNf1
treatment: doxycycline
|
| Treatment protocol |
Prior to doxycycline induction, cells were transduced with lentiviral vectors expressing the indicated BFP-linked, doxycycline-inducible shRNAs
|
| Growth protocol |
Murine AML cells were maintained in culture in RPMI + 10% FBS + 1% penicillin-streptomycin + murine IL3/IL6/SCF and stimulated with doxycycline for the indicated durations. BFP negative (min; uninduced) and BFP positive (plus;induced) cells were isolated by FACS. Approximately 5x105-1x106 cells were harvested for RNA extraction for each condition.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen)
PolyA mRNA was selected using beads coated with polyT oligonucleotides. Purified polyA mRNA was subsequently fragmented, and first and second strand cDNA synthesis performed using standard Illumina mRNA TruSeq library preparation protocols. Double stranded cDNA was subsequently processed for TruSeq dual-index Illumina library generation.
For sequencing, pooled multiplexed libraries were run on a HiSeq 2500 machine on RAPID mode. Approximately 10 million 76bp single-end reads were retrieved per replicate condition. Resulting RNA-Seq data was analyzed by removing adaptor sequences using Trimmomatic (29), aligning sequencing data to GRCh37.75(hg19) with STAR (30), and genome wide transcript counting using HTSeq (31) to generate a RPKM matrix of transcript counts.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
Library name: KL17_D05_shRen713_D2BFPmin
|
| Data processing |
Illumina read quality was checked for each sample using FastQC v0.11.5.
Raw fastq files were analyzed by removing adaptor sequences using Trimmomatic (0.36), aligned to the mouse genome using STAR (2.6.1a), and quantified transcript counts using featureCounts (1.6.3).
Assembly: Reads were aligned to the mouse transcriptome (mm10, GRCm38.91)
Supplementary files format and content: Tab-delimited text file includes raw count table for each sample
|
| |
|
| Submission date |
Nov 27, 2024 |
| Last update date |
Nov 27, 2024 |
| Contact name |
Yu-Jui Ho |
| E-mail(s) |
[email protected]
|
| Organization name |
Memorial Sloan Kettering Cancer Center
|
| Department |
Cancer Biology & Genetics Program
|
| Street address |
417 E 68th St
|
| City |
New York |
| State/province |
New York |
| ZIP/Postal code |
10065 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE282977 |
Alpha-ketoglutarate dehydrogenase is a therapeutic vulnerability in acute myeloid leukemia [KL974_shOGDH] |
|
| Relations |
| BioSample |
SAMN45078812 |
| SRA |
SRX26896362 |
