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| Status |
Public on Apr 28, 2024 |
| Title |
ASPC1PSB_PS02ULAASPC1PSBS134_CAGTGACTG_L003_R1_001 |
| Sample type |
SRA |
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| Source name |
PDA tumor
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| Organism |
Homo sapiens |
| Characteristics |
tissue: PDA tumor
cell line: ASPC1
cell type: Human PDA cell line
treatment: PLX8394
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| Growth protocol |
Panc1 and Aspc1 pancreatic cancer cells were cultured in white 96-well tissue culture-treated plates at optimized density, in 100 μl of Dulbecco's Modified Eagle Medium (DMEM) media supplemented with 10% fetal bovine
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| Extracted molecule |
total RNA |
| Extraction protocol |
After 24 h of incubation, the plates were treated with following drugs: RAF inhibitors – Sorafenib, Dabrafenib, RAF709, PLX8394, GDC-0879; MEK inhibitors – Trametinib, Cobimetinib, Binimetinib, Selumetinib, Rafametinib; and ERK inhibitors – SCH772984, Ulixertinib, AZD0364, Ravoxertinib. Each drug was dosed at the concentration at which the cells were 80% viable after 48 h of treatment. After 24 h of treatment, the medium was replaced with 100 ml of FBS supplemented with 10% DMSO and the plates were frozen at −80 °C prior to PLATE-Seq.
Detailed protocol for preparation of the automated PLATE-SEQ experiment was described by Bush et al. (Bush et al., 2017).
Samples were sequenced using PlateSeq approach
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
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| Description |
ASPC1PSB_PS02ULAASPC1PSBS134_CAGTGACTG_L003_R1_001
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| Data processing |
The PLATE-Seq FASTQ files were pseudoaligned to the GRCh38 human transcriptome (mRNA & ncRNA) and gene expression was quantified using kallisto (version 0.44.0), tximport package (Soneson et al., 2015), and biomaRt package (Durinck et al., 2009).
The gene expression was quantified as both raw counts (i.e. sequencing fragments per genomic locus) and transcripts per million (i.e. sequencing fragments per genomic locus normalized for transcript/gene length and sample sequencing depth).
Assembly: GRCh38
Supplementary files format and content: Table containing reads count of each gene (row) in each sample (column)
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| Submission date |
Dec 26, 2023 |
| Last update date |
Apr 28, 2024 |
| Contact name |
Lorenzo Tomassoni |
| E-mail(s) |
lt2736@cumc.columbia.edu
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| Organization name |
Columbia University
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| Street address |
1130 St Nicholas Avenue
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| City |
New York |
| ZIP/Postal code |
10032 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE252002 |
In vitro drug screening of RAF/MEK/ERK Inhibitors in two PDA Cell Lines |
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| Relations |
| BioSample |
SAMN39121282 |
| SRA |
SRX23023098 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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