Identifying Macrophage-specific L13a Knockout Transcriptomic Signatures
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.
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 GSE190710_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 PRJNA788140 and SRA study SRP350356. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 9 samples read as cases, 3 as controls.
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.
- GSM5729425 Control replicate 1 (no treatment)
- GSM5729426 Control replicate 2 (no treatment)
- GSM5729427 Control replicate 3 (no treatment)
- GSM5729428 Control replicate 4 (treated by IFN)
- GSM5729429 Control replicate 5 (treated by IFN)
- GSM5729430 Control replicate 6 (treated by IFN)
- GSM5729431 Control replicate 7 (treated by IL4)
- GSM5729432 Control replicate 8 (treated by IL4)
- GSM5729433 Control replicate 9 (treated by IL4)
- GSM5729434 L13a knockout replicate 1 (no treatment)
- GSM5729435 L13a knockout replicate 2 (no treatment)
- GSM5729436 L13a knockout replicate 3 (no treatment)
- GSM5729437 L13a knockout replicate 4 (treated by IFN)
- GSM5729438 L13a knockout replicate 5 (treated by IFN)
- GSM5729439 L13a knockout replicate 6 (treated by IFN)
- GSM5729440 L13a knockout replicate 7 (treated by IL4)
- GSM5729441 L13a knockout replicate 8 (treated by IL4)
- GSM5729442 L13a knockout replicate 9 (treated by IL4)
- GSE280875 Transcriptomics profiling of gonadal white adipose tissue (gWAT) of wild-type (WT) and macrophage-specific Bnip3 knockout (MKO) mice fed a normal chow diet (NCD) or high-fat diet (HFD) 12 samples shares macrophage-specific, knockout
- GSE334689 m6Am-seq profiling of macrophage-specific Pcif1 knockout mice during experimental colitis 8 samples shares macrophage-specific, knockout
- GSE255212 Transcriptomic Signatures of WNT-Driven Pathways and Granulosa Cell-Oocyte Interaction during Primordial Follicle Activation 762 samples shares signatures
- GSE291420 Deciphering the Transcriptomic Signatures of Aging Across Organs in Mice 270 samples shares signatures
- GSE272929 Transcriptomic and Epigenomic Signatures Distinguish High- and Low-Risk Endotypes for Liver Tumor Development [RNA-Seq liver] 75 samples shares signatures
- GSE239946 Signatures of IL1b, IL6 and TNFa in immune cell-types 209 samples shares signatures
- GSE288772 Genomic and Behavioral Signatures of Selection for Ethanol Preference from the Heterogeneous Stock Collaborative Cross Mice – The Central Nucleus of the Amygdala 200 samples shares signatures
- GSE276773 Magnesium supplementation modifies synovial and splenic transcriptomic signatures and biologic pathways in arthritis mice 26 samples shares signatures
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.