RNA-Seq analysis SIRT6 or KDM5C knockdown effect on pancreatic cancer cell line
RNA-seq (gene expression) · human · 9 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Homo sapiens (human)
- Topic
- Pancreatic cancerThis series is part of our curated briefing on it.
- Samples
- 9 samples: 3 × PANC-1_Control vs 3 × PANC-1_siSIRT6 vs 3 × PANC-1_siKDM5CGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
- Paper
- SIRT6 cooperates with KDM5C to transcriptionally silence MICAL2 and inhibit tumorigenesis in pancreatic cancerCell communication and signaling : CCS · 2026
Read the full summary ↓
Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.
Processed table
The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.
Supplementary files
The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE315634_RAW.tar (it can run to tens of gigabytes).
Raw sequencing reads
The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.
What the files usually look like: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1398363 and SRA study SRP659808. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.
- GSM9433589 PANC-1_Control_1 PANC-1_Control
- GSM9433590 PANC-1_Control_2 PANC-1_Control
- GSM9433591 PANC-1_Control_3 PANC-1_Control
- GSM9433592 PANC-1_siSIRT6_1 PANC-1_siSIRT6
- GSM9433593 PANC-1_siSIRT6_2 PANC-1_siSIRT6
- GSM9433594 PANC-1_siSIRT6_3 PANC-1_siSIRT6
- GSM9433595 PANC-1_siKDM5C_1 PANC-1_siKDM5C
- GSM9433596 PANC-1_siKDM5C_2 PANC-1_siKDM5C
- GSM9433597 PANC-1_siKDM5C_3 PANC-1_siKDM5C
- GSE147549 Transcriptomic profiling of human pancreatic cancer-derived cell lines MiaPACA-2 depleted of TRIP12 mRNA compared to control cells 8 samples same disease briefing · shares pancreatic, line
- GSE288221 RNA sequencing human melanoma, glioblastoma and pancreatic adenocarcinoma cell lines 32 samples same disease briefing · shares pancreatic, line
- GSE111672 Integrating microarray-based spatial transcriptomics and single-cell RNA-seq reveals tissue architecture in pancreatic ductal adenocarcinomas 23 samples same disease briefing · shares pancreatic, rna-seq
- GSE224502 RNA-Seq profiles of pancreatic adenocarcinoma PANC-1 and osteosarcoma U2OS cells with Pin1 knocking down 18 samples same disease briefing · shares pancreatic, rna-seq
- GSE113616 Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer 189 samples same disease briefing · shares pancreatic
- GSE333988 Transcriptomic analysis of GKB202-treated circulating tumor cells isolated from patients with lung cancer and pancreatic cancer 10 samples same disease briefing · shares pancreatic
- GSE148188 NOXA dependent induction of apoptosis in pancreatic cancer cells 49 samples same disease briefing · shares pancreatic
- GSE273492 Selective NSD2 Inhibition Reveals an Epigenetic Vulnerability of KRAS-Driven Cancers [RNA-Seq] 36 samples same disease briefing · shares rna-seq
Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.