|
| Status |
Public on Mar 01, 2023 |
| Title |
DFAM22359_NPM1c_vehicle_7d_rep1 |
| Sample type |
SRA |
| |
|
| Source name |
bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: bone marrow
cell line: Patient-derived xenograft (PDX)
cell type: leukemia cells
genotype: NPM1c
treatment: vehicle for 7 days
|
| Treatment protocol |
upon confirmation of engraftment mice were treated for 1 week (7d) with SNDX-5613 (0.1% supplemented rodent special diet) or vehicle as control.
|
| Growth protocol |
human leukemia cells were trnsplanted into non-conditioned NXG mice and leukemia burden mas monitored in the peripheral blood
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
1Mio MV4;11 cells were lysed in 350 µl of RLT buffer and RNA was isolated using the RNeasy Mini Kit (Qiagen) according to manufacturers instructions for cell ine experiments. PDX-derived human leukemia cells from the bone marrow were depleted for mouse cells using magnetic cell sorting (mouse cell depletion kit, Milteny)
Poly-A tail selection and library preparation were performed using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA).
Sequencing was done using the Illumina Next Gen Sequencing NextSeq platform (Illumina, San Diego, CA) with 37bp, paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
polyA enriched mRNAseq
|
| Data processing |
Raw Illumina sequencer output was converted to FASTQ format using bcl2fastq (v2.20.0.422).
Reads (paired-end 37-mers) were aligned to the human (Gencode GRCh38/hg38) using STAR (v2.7.5a, sorted and duplicates marked/removed with picard pipeline tools (v2.9.4).
Final “deduped” .BAM files were indexed using SAMtools (v1.95).
RNA-seq data visualizations were produced using IGVtools (TDF signal pileups; v2.3.75).
Raw per-gene counts calculated with HTSeq (htseq-count, v0.6.1pl). Differential RNA-seq expression was calculated using the BioConductor DESeq2 package (v1.24,0), using raw unnormalized per-gene counts from deduplicated BAMs.
Assembly: GRCh38/hg38
Supplementary files format and content: IGVtools tiled data file (TDF)
Supplementary files format and content: rlog_normalized gene counts_DESeq2 (csv)
Supplementary files format and content: z-scores_from rlog counts_DESEq2 (txt)
Supplementary files format and content: differentially expressed genes_DESeq2 (csv)
|
| |
|
| Submission date |
Oct 27, 2022 |
| Last update date |
Mar 01, 2023 |
| Contact name |
Florian Perner |
| E-mail(s) |
f.perner@googlemail.com
|
| Phone |
+49 1515 9980628
|
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Pediatric oncology
|
| Lab |
Armstrong
|
| Street address |
360 Longwood Ave, LC8210
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE216730 |
The menin inhibitor SNDX-5613 for KMT2A rearranged or NPM1 mutant leukemia |
|
| Relations |
| BioSample |
SAMN31492784 |
| SRA |
SRX18050310 |
