Kabuki syndrome type I fibroblast multi-omics dataset: bulk RNA-seq profiles from primary skin fibroblasts
RNA-seq (gene expression) · human · 19 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
- 19 samples: 16 distinct titles, 3 of them repeatedGroups 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 GSE330762_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 PRJNA1465389 and SRA study SRP699809. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 19 sample titles: 16 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.
- GSM9732278 GDB339 control female batch 84
- GSM9732279 GDB418 control female batch 84
- GSM9732280 GDB809 control female batch 84
- GSM9732281 GDB813 control male batch 84
- GSM9732282 GDB374 Kabuki syndrome male batch 84
- GSM9732283 GDB380 Kabuki syndrome male batch 84
- GSM9732284 GDB425 Kabuki syndrome female batch 84
- GSM9732285 GDB447 Kabuki syndrome male batch 84
- GSM9732286 GDB587 Kabuki syndrome female batch 84
- GSM9732287 GDB598 Kabuki syndrome male batch 84
- GSM9732288 GDB491 Kabuki syndrome male batch 185
- GSM9732289 GDB380 Kabuki syndrome male batch 185
- GSM9732290 GDB447 Kabuki syndrome male batch 185
- GSM9732291 GDB424 control female batch 185
- GSM9732292 GDB682 control female batch 185
- GSM9732293 GDB728 control female batch 185
- GSM9732294 GDB339 control female batch 185
- GSM9732295 GDB1331a control female batch 185
- GSM9732296 GDB1331b control male batch 185
- GSE275647 Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC RNA-seq] 216 samples shares fibroblasts, fibroblast, rna-seq
- GSE327840 RNA-seq profiling of LPS tolerance in monocytes, THP-1, fibroblasts, smooth muscle cells, and endothelial cells 58 samples shares fibroblasts, fibroblast, rna-seq
- GSE246215 Cross-tissue human fibroblast atlas reveals myofibroblast subtypes with distinct roles in immune modulation [scRNA-seq] 38 samples shares fibroblast, rna-seq, type
- GSE294300 Single-cell gene expression profiles of cells from primary colorectal cancer and adjacent normal tissue [scRNA-Seq] 36 samples shares profiles, rna-seq, primary
- GSE275145 Creeping fat-derived mechanosensitive fibroblasts drive intestinal fibrosis in Crohn’s disease strictures [Human scRNA-seq] 29 samples shares fibroblasts, fibroblast, rna-seq
- GSE229047 RNA sequencing data of primary cancer-associated fibroblasts (CAF) isolated from fresh ex vivo germ cell tumor (GCT) patient tissue 19 samples shares fibroblasts, fibroblast, primary
- GSE330683 Mitophagy Competent Cancer Associated Fibroblasts fuel Chemoresistance by Rewiring Pyrimidine Metabolism in Pancreatic Cancer [RNA-Seq] 18 samples shares fibroblasts, fibroblast, rna-seq
- GSE275648 Role of Cancer-Associated Fibroblasts in Prognostic Stratification of Advanced-Stage Gastric Cancer through Interacting with Endothelial and Malignant Epithelial Cells [AGC scRNA-seq] 11 samples shares fibroblasts, fibroblast, rna-seq
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.