Transcriptome analysis of treated and control samples from bladder carcinoma
RNA-seq (gene expression) · human · 18 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
- 18 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.
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 GSE326853_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 PRJNA1435562 and SRA study SRP682782. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 9 samples read as cases, 9 as controls.
How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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.
- GSM9641292 MGHU3_hIGFBP5_knockdown_replicate_1 MGHU3_hIGFBP5_knockdown
- GSM9641293 MGHU3_hIGFBP5_knockdown_replicate_2 MGHU3_hIGFBP5_knockdown
- GSM9641294 MGHU3_hIGFBP5_knockdown_replicate_3 MGHU3_hIGFBP5_knockdown
- GSM9641295 MGHU3_sgScr_control_replicate_1 MGHU3_sgScr_control
- GSM9641296 MGHU3_sgScr_control_replicate_2 MGHU3_sgScr_control
- GSM9641297 MGHU3_sgScr_control_replicate_3 MGHU3_sgScr_control
- GSM9641298 GEMM_sgIGFBP5_knockdown_replicate_1 GEMM_sgIGFBP5_knockdown
- GSM9641299 GEMM_sgIGFBP5_knockdown_replicate_2 GEMM_sgIGFBP5_knockdown
- GSM9641300 GEMM_sgIGFBP5_knockdown_replicate_3 GEMM_sgIGFBP5_knockdown
- GSM9641301 GEMM_sgScr_control_replicate_1 GEMM_sgScr_control
- GSM9641302 GEMM_sgScr_control_replicate_2 GEMM_sgScr_control
- GSM9641303 GEMM_sgScr_control_replicate_3 GEMM_sgScr_control
- GSM9641304 GEMM_chemotherapy_treated_replicate_1 GEMM_chemotherapy_treat…
- GSM9641305 GEMM_chemotherapy_treated_replicate_2 GEMM_chemotherapy_treat…
- GSM9641306 GEMM_chemotherapy_treated_replicate_3 GEMM_chemotherapy_treat…
- GSM9641307 GEMM_control_replicate_1 GEMM_control
- GSM9641308 GEMM_control_replicate_2 GEMM_control
- GSM9641309 GEMM_control_replicate_3 GEMM_control
- GSE193754 Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2 - untreated 6 samples same disease briefing · shares treated, bladder
- GSE181389 Transcriptome profiling of HOXA13 and HOXB13 expression knockdown in bladder cancer cell lines. 59 samples same disease briefing · shares bladder
- GSE182310 Transcriptome sequence of Human bladder cancer cell line 6 samples same disease briefing · shares bladder
- GSE212328 RNA-Seq analysis of bladder cancer cells after protodioscin treatment 4 samples same disease briefing · shares bladder
- GSE193755 Human bladder cancer cell line high throughput sequencing - genes regulated by hMSH2 12 samples same disease briefing · shares bladder
- 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
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.