Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2
RNA-seq (gene expression) · human · 12 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
- Bladder cancerThis series is part of our curated briefing on it.
- Samples
- 12 samples: 3 × EJ_CDDP_KO vs 3 × EJ_CDDP_Cas9 vs 3 × EJ_KO vs 3 × EJ_Cas9Groups 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 GSE193755_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 PRJNA797648. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM5820498 EJ_CDDP_KO_1 EJ_CDDP_KO
- GSM5820499 EJ_CDDP_KO_2 EJ_CDDP_KO
- GSM5820500 EJ_CDDP_KO_3 EJ_CDDP_KO
- GSM5820501 EJ_CDDP_Cas9_1 EJ_CDDP_Cas9
- GSM5820502 EJ_CDDP_Cas9_2 EJ_CDDP_Cas9
- GSM5820503 EJ_CDDP_Cas9_3 EJ_CDDP_Cas9
- GSM5820504 EJ_KO_1 EJ_KO
- GSM5820505 EJ_KO_2 EJ_KO
- GSM5820506 EJ_KO_3 EJ_KO
- GSM5820507 EJ_Cas9_1 EJ_Cas9
- GSM5820508 EJ_Cas9_2 EJ_Cas9
- GSM5820509 EJ_Cas9_3 EJ_Cas9
- GSE193753 Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2 - CDDP therapy 6 samples same disease briefing · shares hmsh2, bladder, line
- GSE193754 Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2 - untreated 6 samples same disease briefing · shares hmsh2, bladder, line
- GSE181389 Transcriptome profiling of HOXA13 and HOXB13 expression knockdown in bladder cancer cell lines. 59 samples same disease briefing · shares bladder, line
- GSE182310 Transcriptome sequence of Human bladder cancer cell line 6 samples same disease briefing · shares bladder, line
- GSE214886 Downregulation of CBX7 induced by EZH2 upregulates FGFR3 expression to reduce sensitivity to cisplatin in bladder cancer 12 samples same disease briefing · shares bladder
- GSE211924 UCHL5 promotes Tumorigenesis of Bladder Cancer by Activating AKT/mTOR signaling pathway and targeting c-myc, SLC25A19, and ICAM5. 9 samples same disease briefing · shares bladder
- GSE172359 Combination of urine exosomal mRNAs and lncRNAs as novel diagnostic biomarkers for bladder cancer 6 samples same disease briefing · shares bladder
- GSE222567 Benchmarking pathway analysis methods offer novel prognostic cancer biomarkers and therapeutics: application in bladder cancer 6 samples same disease briefing · shares bladder
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.