RNA-seq analysis to examine the effect of Jmjd1a knockdown in 3T3-L1 pre-adipocyte cells
RNA-seq (gene expression) · mouse · 15 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
- 15 samples: 5 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
- Iron-Dependent JMJD1A-Mediated Demethylation of H3K9me2 Regulates Gene Expression During Adipogenesis in a Spatial Genome Organization-Dependent MannerGenes to cells : devoted to molecular & cellular mechanisms · 2025
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 GSE269147_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 PRJNA1120408 and SRA study SRP511965. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 5 replicated groups read from 15 sample titles; they account for 15 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.
- GSM8307004 shEmpty, Day 2, Rep 1 shEmpty, Day 2,
- GSM8307005 shEmpty, Day 2, Rep 2 shEmpty, Day 2,
- GSM8307006 shEmpty, Day 2, Rep 3 shEmpty, Day 2,
- GSM8307007 shJmjd1a, Day 2, Rep 1 shJmjd1a, Day 2,
- GSM8307008 shJmjd1a, Day 2, Rep 2 shJmjd1a, Day 2,
- GSM8307009 shJmjd1a, Day 2, Rep 3 shJmjd1a, Day 2,
- GSM8307010 shJmjd1a plus LacZ, Day 2, Rep 1 shJmjd1a plus LacZ, Day…
- GSM8307011 shJmjd1a plus LacZ, Day 2, Rep 2 shJmjd1a plus LacZ, Day…
- GSM8307012 shJmjd1a plus LacZ, Day 2, Rep 3 shJmjd1a plus LacZ, Day…
- GSM8307013 shJmjd1a plus Mut, Day 2, Rep 1 shJmjd1a plus Mut, Day …
- GSM8307014 shJmjd1a plus Mut, Day 2, Rep 2 shJmjd1a plus Mut, Day …
- GSM8307015 shJmjd1a plus Mut, Day 2, Rep 3 shJmjd1a plus Mut, Day …
- GSM8307016 shJmjd1a plus WT, Day 2, Rep 1 shJmjd1a plus WT, Day 2,
- GSM8307017 shJmjd1a plus WT, Day 2, Rep 2 shJmjd1a plus WT, Day 2,
- GSM8307018 shJmjd1a plus WT, Day 2, Rep 3 shJmjd1a plus WT, Day 2,
- GSE284471 H3K9me2 CUT&Tag analysis to examine the effect of Jmjd1a knockdown in 3T3-L1 pre-adipocyte cells 9 samples shares jmjd1a, 3t3-l1, pre-adipocyte, knockdown, examine
- GSE268800 RNA-seq analysis to examine the effect of the Ube2e1 and Ube2e1 knockdown on gene expression profile in 3T3-L1 pre-adipocyte cells 18 samples shares 3t3-l1, pre-adipocyte, knockdown, rna-seq, examine
- GSE266317 RNA-seq and ChIP-seq analysis of H3K27ac, H3K27me3, H3K9me2, and JMJD1A in 3T3-L1 cells and ChIP-seq analysis of NFIC in imSVF cells. 14 samples shares jmjd1a, 3t3-l1, rna-seq
- GSE253544 Effect of knockdown of Zbtb9 on gene expression during adipogenic differentiation of 3T3-L1 preadipocytes 32 samples shares 3t3-l1, knockdown
- GSE236733 RNA-sequence analysis of JMJD1A target genes in subcutanous white adipose tissue. 12 samples shares jmjd1a, rna-seq
- GSE53249 Transcriptomics analysis of gene expression in normal and FTO, METTL3 deficient Mouse embryo fibroblast 3T3-L1 pre-adipocytes 6 samples shares 3t3-l1, pre-adipocyte
- GSE53244 m6a peak analysis in normal, FTO deficient and five stages of adipogenesis (D-2/0/2/5/10) in Mouse embryo fibroblast 3T3-L1 pre-adipocytes 18 samples shares 3t3-l1, pre-adipocyte
- GSE266318 Microarray, RNA-seq, and ChIP-seq data of 3T3-L1 cells 22 samples shares 3t3-l1, 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.