|
| Status |
Public on Feb 12, 2024 |
| Title |
RNA-seq of bone marrow cells from UBTF-TD PDX model treated with SNDX, R19 |
| Sample type |
SRA |
| |
|
| Source name |
human blasts from UBTF-TD PDX Model
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: human blasts from UBTF-TD PDX Model
treatment: UBTF-TD PDX model treated with SNDX
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was harvested using Quikc-RNA Miniprep Kit (Zymo Research R1055)). RNA was then quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).
Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
RNASeq_SNDX-Veh_log2CPM.txt
SJAML015373_R19- HMP_18_PDX_FMZVC_S13_bm_SNDX
|
| Data processing |
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.
|
| |
|
| Submission date |
Apr 13, 2023 |
| Last update date |
Feb 12, 2024 |
| Contact name |
Guangchun Song |
| Phone |
901-595-5722
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Pathology
|
| Lab |
Klco
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE229663 |
UBTF tandem duplication acute myeloid leukemias are sensitive to menin inhibition [RNA-seq] |
| GSE229666 |
UBTF tandem duplication acute myeloid leukemias are sensitive to menin inhibition |
|
| Relations |
| SRA |
SRX19960031 |
| BioSample |
SAMN34172497 |
