RNA-seq analysis of thick ascending limb (TAL) epithelium isolated from uromodulin (UMOD) deletion mutation and wild type (WT) kidney organoids with or without mesencephalic astrocyte-derived neurotrophic factor (MANF) overexpression
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)
- Samples
- 12 samples: 3 × WT vs 3 × WT_MANF vs 3 × DEL vs 3 × DEL_MANFGroups 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.
Read the full summary ↓
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 GSE329325_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 PRJNA1458668 and SRA study SRP695612. 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.
- GSM9701775 WT1 WT
- GSM9701776 WT2 WT
- GSM9701777 WT3 WT
- GSM9701778 WT_MANF_1 WT_MANF
- GSM9701779 WT_MANF_2 WT_MANF
- GSM9701780 WT_MANF_3 WT_MANF
- GSM9701781 DEL1 DEL
- GSM9701782 DEL2 DEL
- GSM9701783 DEL3 DEL
- GSM9701784 DEL_MANF_1 DEL_MANF
- GSM9701785 DEL_MANF_2 DEL_MANF
- GSM9701786 DEL_MANF_3 DEL_MANF
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- GSE263733 Single-cell transcriptome analysis reveals subtype-specific clonal evolution and microenvironmental changes in liver metastasis of pancreatic adenocarcinoma and their clinical implications 218 samples shares tal
- GSE289582 Baseline tumor features and peripheral blood immune dynamics that underlie efficacy in MSS metastatic colorectal cancer treated with regorafenib, ipilimumab, and nivolumab [Blood] 115 samples shares tal
- GSE330465 Gene expression profiling of neoadjuvant ABFOLFOX treatment in patients with unresectable colorectal cancer with liver metastases 104 samples shares tal
- GSE267010 A consensus molecular subtypes classification strategy for clinical colorectal cancer tissues 104 samples shares tal
- GSE254249 Remodeling of T and endothelial cells during total neoadjuvant therapy in rectal cancer 92 samples shares tal
- GSE256207 Accessible chromatin profiles (ATAC) at single-cell level of human post-mortem brain tissue from the orbitofrontal cortex 92 samples shares tal
- GSE254877 Molecular Subtypes of Human Skeletal Muscle in Cancer Cachexia 84 samples shares tal
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.