Effect of deletion of SPTLC1 on gene expression and differentiation of mouse Th17 cells in vitro
RNA-seq (gene expression) · mouse · 24 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
- 24 samples: 8 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.
- Paper
- Sphingolipid biosynthesis is essential for metabolic rewiring during T(H)17 cell differentiationScience advances · 2024
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 GSE254602_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 PRJNA1071114 and SRA study SRP486880. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 24 samples.
How we read this: 8 replicated groups read from 24 sample titles; they account for 24 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.
- GSM8046908 WT Th17 biol rep 1 WT Th17 biol
- GSM8046909 WT Th17 biol rep 2 WT Th17 biol
- GSM8046910 WT Th17 biol rep 3 WT Th17 biol
- GSM8046911 KO Th17 biol rep 1 KO Th17 biol
- GSM8046912 KO Th17 biol rep 2 KO Th17 biol
- GSM8046913 KO Th17 biol rep 3 KO Th17 biol
- GSM8046914 WT Th17 with 3-KDS biol rep 1 WT Th17 with 3-KDS biol
- GSM8046915 WT Th17 with 3-KDS biol rep 2 WT Th17 with 3-KDS biol
- GSM8046916 WT Th17 with 3-KDS biol rep 3 WT Th17 with 3-KDS biol
- GSM8046917 KO Th17 with 3-KDS biol rep 1 KO Th17 with 3-KDS biol
- GSM8046918 KO Th17 with 3-KDS biol rep 2 KO Th17 with 3-KDS biol
- GSM8046919 KO Th17 with 3-KDS biol rep 3 KO Th17 with 3-KDS biol
- GSM8046920 WT Th17 with NAC biol rep 1 WT Th17 with NAC biol
- GSM8046921 WT Th17 with NAC biol rep 2 WT Th17 with NAC biol
- GSM8046922 WT Th17 with NAC biol rep 3 WT Th17 with NAC biol
- GSM8046923 KO Th17 with NAC biol rep 1 KO Th17 with NAC biol
- GSM8046924 KO Th17 with NAC biol rep 2 KO Th17 with NAC biol
- GSM8046925 KO Th17 with NAC biol rep 3 KO Th17 with NAC biol
- GSM8046926 WT naïve CD4+ T cells biol rep 1 WT naïve CD4+ T cells b…
- GSM8046927 WT naïve CD4+ T cells biol rep 2 WT naïve CD4+ T cells b…
- GSM8046928 WT naïve CD4+ T cells biol rep 3 WT naïve CD4+ T cells b…
- GSM8046929 KO naïve CD4+ T cells biol rep 1 KO naïve CD4+ T cells b…
- GSM8046930 KO naïve CD4+ T cells biol rep 2 KO naïve CD4+ T cells b…
- GSM8046931 KO naïve CD4+ T cells biol rep 3 KO naïve CD4+ T cells b…
- GSE75111 Single-cell transcriptional profiling of Th17 cells, differentiated in vitro for 48h [TGFB1_IL6-48h-IL-17A/GFP+] 151 samples shares th17, vitro
- GSE303699 Autoimmune Disease Risk Gene ANKRD55 Promotes Th17 Effector Function Through Metabolic Modulation [RNA-Seq] 60 samples shares th17
- GSE290258 Satb1 directs the differentiation of TH17 cells through suppression of IL-2 expression [scMultiom ATAC/RNA-seq] 12 samples shares th17
- GSE296401 Interleukin-23 promotes a pro-inflammatory Th17 cell state by stabilizing RORγt and suppressing glucocorticoid receptor activity II 38 samples shares th17
- GSE296482 A cell-intrinsic glucocorticoid biosynthesis and sensing circuit maintains homeostatic Th17 cell state [RNA-seq] 31 samples shares th17
- GSE317634 Negative regulation of TH17-mediated inflammation by the nuclear receptor REV-ERBβ 26 samples shares th17
- GSE306371 Unconventional role of HMGCS1 in driving pathogenic-Th17 cell immunity and autoimmune diseases 16 samples shares th17
- GSE288624 Wild-Type vs ORAI 1/2/3 TKO_Pathogenic Th17 cells_ 6h vs 24h 12 samples shares th17
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.