Genetic dependencies associated with transcription factor activities in human cancer cell lines
RNA-seq (gene expression) · human · 23 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
- 23 samples: 6 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.
- Paper
- Genetic dependencies associated with transcription factor activities in human cancer cell linesCell reports · 2024
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 GSE263748_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 PRJNA1099147 and SRA study SRP501169. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 6 replicated groups read from 23 sample titles; they account for 15 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.
- GSM8057898 SNU761, Unlabelled, VT107-experiment
- GSM8057899 SNU761, DMSO 4h, rep1 SNU761, DMSO 4h,
- GSM8057900 SNU761, DMSO 4h, rep2 SNU761, DMSO 4h,
- GSM8057901 SNU761, VT107 0.1uM 4h, rep1 SNU761, VT107 0.1uM 4h,
- GSM8057902 SNU761, VT107 0.1uM 4h, rep2 SNU761, VT107 0.1uM 4h,
- GSM8057903 SNU761, VT107 2.15uM 4h, rep1 SNU761, VT107 2.15uM 4h,
- GSM8057904 SNU761, VT107 2.15uM 4h, rep2 SNU761, VT107 2.15uM 4h,
- GSM8057905 SNU761, Unlabelled, Intetumumab-experiment
- GSM8057906 SNU761, IgG-Ctrl 4h, rep1 SNU761, IgG-Ctrl 4h,
- GSM8057907 SNU761, IgG-Ctrl 4h, rep2 SNU761, IgG-Ctrl 4h,
- GSM8057908 SNU761, IgG-Ctrl 4h, rep3 SNU761, IgG-Ctrl 4h,
- GSM8057909 SNU761, Intetumumab-1.5ug/ml 4h, rep1 SNU761, Intetumumab-1.5…
- GSM8057910 SNU761, Intetumumab-1.5ug/ml 4h, rep2 SNU761, Intetumumab-1.5…
- GSM8057911 SNU761, Intetumumab-1.5ug/ml 4h, rep3 SNU761, Intetumumab-1.5…
- GSM8057912 SNU761, Intetumumab-5ug/ml 4h, rep1 SNU761, Intetumumab-5ug…
- GSM8057913 SNU761, Intetumumab-5ug/ml 4h, rep2 SNU761, Intetumumab-5ug…
- GSM8057914 SNU761, Intetumumab-5ug/ml 4h, rep3 SNU761, Intetumumab-5ug…
- GSM8197841 Transcriptome reads, day 5 [SNU_D5_GEX]
- GSM8197842 Transcriptome reads, day 10 [SNU_D10_GEX]
- GSM8197843 Guide reads, day 5 [SNU_D5_sgRNA]
- GSM8197844 Guide reads, day 10 [SNU_D10_sgRNA]
- GSM8197845 Hash labels, day 5 [SNU_D5_ST]
- GSM8197846 Hash labels, day 10 [SNU_D10_ST]
- GSE302930 Epigenetic Atlas of Bladder Cancer Reveals Master Transcription Factors and Risk-Associated Regulatory Elements in Luminal and Basal-Squamous Molecular Subtypes 92 samples shares transcription, genetic, factor
- GSE273995 Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models 36 samples shares genetic, lines
- GSE274006 Cell-intrinsic platinum response and associated genetic and gene expression signatures in ovarian cancer cell lines and isogenic models [isogenic models] 33 samples shares genetic, lines
- GSE296831 Epigenetic Context Defines the Transcriptional Activity of Canonical and Noncanonical NF-kappaB Signaling in Pancreatic Cancer [ChIP-Seq] 48 samples shares transcription, genetic
- GSE295823 Integrative multi-omics identifies AP-1 transcription factor as a targetable mediator of acquired osimertinib resistance in non-small cell lung cancer 20 samples shares transcription, factor
- GSE299348 Single-cell epigenetic, transcriptional, protein, and TCR states of HIV-1-infected cells in gut 117 samples shares transcription, genetic
- GSE301298 Functional redundancy between UTY and UTX in regulating the localization of transcription factors involved in pluripotency 88 samples shares transcription, factor
- GSE306993 Transcriptional and epigenetic targets of MEF2C in human microglia contribute to cellular functions related to autism risk and age-related disease. 76 samples shares transcription, genetic
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.