TF overexpression assay in PDA cell lines (Bulk RNA-Seq)
RNA-seq (gene expression) · human · 69 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)
- Samples
- 69 samples: 23 conditions, mostly in triplicateGroups 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.
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 GSE161368_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 PRJNA677968 and SRA study SRP292376. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 69 samples.
How we read this: 23 replicated groups read from 69 sample titles; they account for 69 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.
- GSM4905468 HPAFII_TARGET_CELL_LINE_1 HPAFII_TARGET_CELL_LINE
- GSM4905469 HPAFII_TARGET_CELL_LINE_2 HPAFII_TARGET_CELL_LINE
- GSM4905470 HPAFII_TARGET_CELL_LINE_3 HPAFII_TARGET_CELL_LINE
- GSM4905471 KP4_EGFP_1 KP4_EGFP
- GSM4905472 KP4_EGFP_2 KP4_EGFP
- GSM4905473 KP4_EGFP_3 KP4_EGFP
- GSM4905474 KP4_EGFP_M2RTTA_1 KP4_EGFP_M2RTTA
- GSM4905475 KP4_EGFP_M2RTTA_2 KP4_EGFP_M2RTTA
- GSM4905476 KP4_EGFP_M2RTTA_3 KP4_EGFP_M2RTTA
- GSM4905477 KP4_ELF3_1 KP4_ELF3
- GSM4905478 KP4_ELF3_2 KP4_ELF3
- GSM4905479 KP4_ELF3_3 KP4_ELF3
- GSM4905480 KP4_ELF3_M2RTTA_1 KP4_ELF3_M2RTTA
- GSM4905481 KP4_ELF3_M2RTTA_2 KP4_ELF3_M2RTTA
- GSM4905482 KP4_ELF3_M2RTTA_3 KP4_ELF3_M2RTTA
- GSM4905483 KP4_ESRRA_1 KP4_ESRRA
- GSM4905484 KP4_ESRRA_2 KP4_ESRRA
- GSM4905485 KP4_ESRRA_3 KP4_ESRRA
- GSM4905486 KP4_ESRRA_M2RTTA_1 KP4_ESRRA_M2RTTA
- GSM4905487 KP4_ESRRA_M2RTTA_2 KP4_ESRRA_M2RTTA
- GSM4905488 KP4_ESRRA_M2RTTA_3 KP4_ESRRA_M2RTTA
- GSM4905489 KP4_ETV4_1 KP4_ETV4
- GSM4905490 KP4_ETV4_2 KP4_ETV4
- GSM4905491 KP4_ETV4_3 KP4_ETV4
- GSM4905492 KP4_ETV4_M2RTTA_1 KP4_ETV4_M2RTTA
- GSM4905493 KP4_ETV4_M2RTTA_2 KP4_ETV4_M2RTTA
- GSM4905494 KP4_ETV4_M2RTTA_3 KP4_ETV4_M2RTTA
- GSM4905495 KP4_FOXA2_1 KP4_FOXA2
- GSM4905496 KP4_FOXA2_2 KP4_FOXA2
- GSM4905497 KP4_FOXA2_3 KP4_FOXA2
- GSM4905498 KP4_FOXA2_M2RTTA_1 KP4_FOXA2_M2RTTA
- GSM4905499 KP4_FOXA2_M2RTTA_2 KP4_FOXA2_M2RTTA
- GSM4905500 KP4_FOXA2_M2RTTA_3 KP4_FOXA2_M2RTTA
- GSM4905501 KP4_FOXA3_1 KP4_FOXA3
- GSM4905502 KP4_FOXA3_2 KP4_FOXA3
- GSM4905503 KP4_FOXA3_3 KP4_FOXA3
- GSM4905504 KP4_FOXA3_M2RTTA_1 KP4_FOXA3_M2RTTA
- GSM4905505 KP4_FOXA3_M2RTTA_2 KP4_FOXA3_M2RTTA
- GSM4905506 KP4_FOXA3_M2RTTA_3 KP4_FOXA3_M2RTTA
- GSM4905507 KP4_HNF1A_1 KP4_HNF1A
+ 29 more — browse all 69 samples with per-sample file links →
- GSE205154 Bulk RNA-Seq gene expression data for 289 primary and metastatic pancreatic ductal adenocarcinoma (PDAC) tumor samples from FFPE blocks. 289 samples shares pda, rna-seq, bulk
- GSE278688 Integrated Single-Cell and Spatial Transcriptomics Uncover Distinct Cellular Subtypes Involved in Neural Invasion in PDAC [scRNA-Seq] 29 samples shares pda, rna-seq
- GSE327707 Sorted bulk RNA-seq profiling of human peripheral blood mononuclear cell populations across diverse in vitro immune stimuli 150 samples shares rna-seq, bulk
- GSE317207 Transcriptomic profiling of human hepatocellular carcinoma biopsy samples using bulk RNA-seq 33 samples shares rna-seq, bulk
- GSE297742 Bulk RNA-seq of primary tumor biopsy samples from prostate adenocarcinoma patients 234 samples shares rna-seq, bulk
- GSE294272 Tumor-resident T cells and dendritic cells form an in situ archetype for immunotherapy response in melanoma [bulk RNA-seq] 29 samples shares rna-seq, bulk
- GSE319969 Spatial and Bulk Transcriptomic Profiling Defines the Molecular Evolution of Cutaneous Squamous Cell Carcinoma and Reveals Stage-Specific Biomarkers of Clinical Relevance [RNA-Seq] 24 samples shares rna-seq, bulk
- GSE272346 Late-stage tertiary lymphoid structures in hepatocellular carcinoma treated with neoadjuvant immune checkpoint blockade [bulk RNA-seq] 14 samples shares rna-seq, bulk
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.