|
| Status |
Public on Sep 30, 2024 |
| Title |
PolyA_RNAseq_Patient_4_BM_pretreatment |
| Sample type |
SRA |
| |
|
| Source name |
Bone marrow
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Bone marrow
cell line: AML Patient 4
cell type: Haematopoietic
genotype: SF3B1-K700E
treatment: Pre-treatment
|
| Treatment protocol |
K562 cells wild-type for SF3B1/SRSF2 or with knock-in of a single allele mutation in SF3B1-K700E, SF3B1-K666N, or SRSF2-P95H or NKM1 cells (which harbor a naturaly occurring U2AF1-Q157P mutation) were treated for 24 hours with DMSO vehicle or E7820 (1uM) treatment .
|
| Growth protocol |
K562 cells wild-type for SF3B1/SRSF2 or with knock-in of a single allele mutation in SF3B1-K700E, SF3B1-K666N, or SRSF2-P95H or NKM1 cells (which harbor a naturaly occurring U2AF1-Q157P mutation) were cultured under standard in vitro culture conditions reccomended by vendors.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was extracted using the Qiagen RNeasy extraction kit, according to the manufacturer’s instructions.
A minimum of 500 ng of high-quality RNA (as determined by Agilent Bioanalyzer) per replicate was used as input for library preparation. Poly(A)-selected, strand-specific (dUTP method) Illumina libraries were prepared by the Integrated Genomics Operation (IGO) at Memorial Sloan Kettering Cancer Center (MSKCC) with a modified TruSeq protocol.
Libraries were sequenced on the Illumina HiSeq 2000 to obtain ∼100M 2x101 bp paired-end reads per sample.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
E7820_PolyA_RNAseq_raw_counts.csv
|
| Data processing |
Prior to mapping, raw FASTQ files were trimmed using Trim_galore (v0.6.4) to remove residual Illumina adapter and/or low quality (Q<15) sequences. Trimmed sequencing reads were then aligned to the human Hg19 reference genome (GENCODE, GRCh37.p13) using STAR (v2.7.5).
Samtools (v1.9) was used to convert SAM files to BAM files, as well as sorting, and indexing.
Sorted BAM files were used for read counting across genomic features (exons) with featureCounts (part of the subread package; v1.5.0) (Liao et al., 2014) using the following parameters: -p -T 20 -O -F GTF -t exon.
The resultant counts file was used as input for differential gene expression analysis, which was performed using the edgeR (v3.32.1), DESeq2 (v1.30.1) (Love et al., 2014), and limma voom (v3.46.0) (Law et al., 2014) R packages.
Differential alternative splicing events were detected using Multivariate Analysis of Transcript Splicing (rMATS, v4.1.1) using the GENCODE (v19) GTF annotation for GRCh37.
Assembly: Hg19
Supplementary files format and content: CSV file of raw (non-normalized) gene expression counts produced by featureCounts.
|
| |
|
| Submission date |
Mar 14, 2023 |
| Last update date |
Sep 30, 2024 |
| Contact name |
Simon J Hogg |
| Organization name |
AbbVie
|
| Department |
Oncology Discovery Research
|
| Street address |
1000 Gateway Boulevard
|
| City |
South San Francisco |
| State/province |
California |
| ZIP/Postal code |
94080 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE227343 |
E7820, an Anti-Cancer Sulfonamide, Degrades RBM39 in Patients with Splicing Factor Mutant Myeloid Malignancies: A Phase II Clinical Trial |
|
| Relations |
| BioSample |
SAMN33759785 |
| SRA |
SRX19676362 |
