|
| Status |
Public on May 12, 2023 |
| Title |
Lipo-246, 10uM Nutlin, 12.5nM Carfilzomib 28hr, Combo replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
Lipo-246 liposarcoma cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Lipo-246
cell type: liposarcoma cells
treatment: 28 hr 10µM Nutlin3R + 12.5nM Carfilzomib
|
| Treatment protocol |
94T778 and Lipo-246 cells were treated with vehicle (DMSO 0.05%) or 10 uM Nutlin3R and/or 12.5 nM Carfilzomib for 28 hr
|
| Growth protocol |
94T778 and Lipo-246 cells were cultured in DMEM/F12 supplemented with 10% Equa Fetal and 1x anti-anti and were maintained at 37°C in a humidified atmosphere with 5% CO2.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Qiagen RNeasy
Strand-specific poly(A)+-enriched mRNA library (Illumina TruSEQ mRNA)
RNA library sequencing
|
| |
|
| Library strategy |
ssRNA-seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Signal processing, base-calling, and quality scoring was carried out automatically by the NovaSeq 6000 software (Illumina).
Demultiplexing and conversion to FASTQ format was carried out using bcl2fastq (Illumina).
Data quality was assessed using FASTQC (v0.11.5) (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) and FastQ Screen (v0.11.0, https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/).
For some samples, FASTQ files from multiple sequencing runs were merged to obtain ≥40x10^6 raw reads.
Trimming and filtering of low-quality reads was performed using bbduk from BBTools (v37.99) and fastq-mcf from ea-utils (v1.05, https://expressionanalysis.github.io/ea-utils/).
Alignment to the human reference genome (GRCh38) was carried out using HISAT2 (v2.1.0) in paired, spliced-alignment mode with a GRCh38 index with a Gencode v33 annotation GTF.
Alignments were sorted and filtered for mapping quality (MAPQ>10) using Samtools (v1.5).
Gene-level count data were quantified using HTSeq-count (v0.6.1) with the following options (--stranded=reverse –minaqual=10 –type=exon --mode=intersection-nonempty) using a Gencode v33 GTF annotation file.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text files containing per gene strand-specific fragment counts or normalized fragments-per-kilobase-per-million-mapped (RPKM).
|
| |
|
| Submission date |
Mar 02, 2023 |
| Last update date |
May 12, 2023 |
| Contact name |
Matthew D Galbraith |
| Organization name |
University of Colorado Anschutz Medical Campus
|
| Department |
Pharmacology & Linda Crnic Institute for Down Syndrome
|
| Street address |
RC1-N, Mail Stop 8303, Rm. P18-6114 12800 E. 19th Ave.
|
| City |
Aurora |
| State/province |
CO |
| ZIP/Postal code |
80045 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE214891 |
Proteasome Inhibition Sensitizes Liposarcoma to Nutlin-3-induced Apoptosis via the ATF4/CHOP Axis |
| GSE226530 |
PolyA RNA-seq from liposarcoma cells treated with Nutlin3R and/or Carfilzomib |
|
| Relations |
| BioSample |
SAMN33574549 |
| SRA |
SRX19554549 |
