RNA-seq analysis of CSNK2B and P300 knockdown in NCI-H69 small cell lung cancer cells
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
- Small cell lung cancerThis series is part of our curated briefing on it.
- Samples
- 9 samples: 3 × NCI-H69 cells, negative control siRNA, vs 3 × NCI-H69 cells, CSNK2B knockdown, vs 3 × NCI-H69 cells, P300 knockdown,Groups 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 GSE337503_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 PRJNA1489543 and SRA study SRP715040. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 6 samples read as cases, 3 as controls.
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.
- GSM9856724 NCI-H69 cells, negative control siRNA, biological replicate 1 NCI-H69 cells, negative…
- GSM9856725 NCI-H69 cells, negative control siRNA, biological replicate 2 NCI-H69 cells, negative…
- GSM9856726 NCI-H69 cells, negative control siRNA, biological replicate 3 NCI-H69 cells, negative…
- GSM9856727 NCI-H69 cells, CSNK2B knockdown, biological replicate 1 NCI-H69 cells, CSNK2B k…
- GSM9856728 NCI-H69 cells, CSNK2B knockdown, biological replicate 2 NCI-H69 cells, CSNK2B k…
- GSM9856729 NCI-H69 cells, CSNK2B knockdown, biological replicate 3 NCI-H69 cells, CSNK2B k…
- GSM9856730 NCI-H69 cells, P300 knockdown, biological replicate 1 NCI-H69 cells, P300 kno…
- GSM9856731 NCI-H69 cells, P300 knockdown, biological replicate 2 NCI-H69 cells, P300 kno…
- GSM9856732 NCI-H69 cells, P300 knockdown, biological replicate 3 NCI-H69 cells, P300 kno…
- GSE337244 ChIP-seq profiling of RBBP4 and P300 occupancy after CSNK2B knockdown in small cell lung cancer cells 8 samples same disease briefing · shares csnk2b, p300, knockdown, small, lung
- GSE337245 Transcriptome profiling of SCRMP knockout and control NCI-H69 small cell lung cancer cells 6 samples same disease briefing · shares nci-h69, small, lung
- GSE281525 RNA-sequence data of clinically never-metastatic primary small cell lung cancer cases and small cell lung cancer metastasis cases, FOXA2 knock-down and overexpression in cell lines 61 samples same disease briefing · shares rna-seq, small, lung
- GSE296155 Loss of the USP22 deubiquitylase confers resistance to chemotherapy in small cell lung cancer [RNA-seq] 20 samples same disease briefing · shares rna-seq, small, lung
- GSE300624 The function of FTO in small cell lung cancer [RNA-seq] 15 samples same disease briefing · shares rna-seq, small, lung
- GSE256347 SMARCA4 controls state plasticity in small cell lung cancer through regulation of neuroendocrine transcription factors and REST splicing [RNA-seq] 13 samples same disease briefing · shares rna-seq, small, lung
- GSE268219 Phase separation of RXRγ drives tumor chemoresistance and represents a therapeutic target for small cell lung cancer [RNA-Seq] 8 samples same disease briefing · shares rna-seq, small, lung
- GSE318538 Effect of KIFC1 knockdown on gene expression in H146 small-cell lung cancer cells 6 samples same disease briefing · shares knockdown, small, lung
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.