Expression changes in mouse proximal tubules during primary culture
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 18 samples: 18 samples, each with a distinct title — no replicated groupsGroups 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
- Sustained alterations in proximal tubule gene expression in primary culture associate with HNF4A lossScientific 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 GSE273058_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 PRJNA1139850 and SRA study SRP522065. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
How we read this: Read from 18 sample titles: 18 distinct titles with little repetition. 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.
- GSM8420470 Day_00_rep_A
- GSM8420471 Day_01_rep_A
- GSM8420472 Day_02_rep_A
- GSM8420473 Day_04_rep_A
- GSM8420474 Day_07_rep_A
- GSM8420475 Day_14_rep_A
- GSM8420476 Day_00_rep_B
- GSM8420477 Day_01_rep_B
- GSM8420478 Day_02_rep_B
- GSM8420479 Day_04_rep_B
- GSM8420480 Day_07_rep_B
- GSM8420481 Day_14_rep_B
- GSM8420482 Day_00_rep_C
- GSM8420483 Day_01_rep_C
- GSM8420484 Day_02_rep_C
- GSM8420485 Day_04_rep_C
- GSM8420486 Day_07_rep_C
- GSM8420487 Day_14_rep_C
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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.