RNA-Seq experiment of wild-type mouse livers with mLMRs knockdown and hLMRs rescue
RNA-seq (gene expression) · mouse · 48 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
- 48 samples: 12 conditions, mostly with about 4 replicates eachGroups 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
- Systemic identification of functionally conserved lncRNA metabolic regulators in human and mouse liversbioRxiv : the preprint server for biology · 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 GSE234310_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 PRJNA980736 and SRA study SRP441432. Searching any of these in the dataset finder brings you back here.
Supports a case/control comparison: 16 samples read as cases, 16 as controls.
How we read this: 12 replicated groups read from 48 sample titles; they account for 48 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.
- GSM7462089 LMR1_control_1 LMR1_control
- GSM7462090 LMR1_control_2 LMR1_control
- GSM7462091 LMR1_control_3 LMR1_control
- GSM7462092 LMR1_control_4 LMR1_control
- GSM7462093 mLMR1_knockdown_1 mLMR1_knockdown
- GSM7462094 mLMR1_knockdown_2 mLMR1_knockdown
- GSM7462095 mLMR1_knockdown_3 mLMR1_knockdown
- GSM7462096 mLMR1_knockdown_4 mLMR1_knockdown
- GSM7462097 hLMR1_rescue_1 hLMR1_rescue
- GSM7462098 hLMR1_rescue_2 hLMR1_rescue
- GSM7462099 hLMR1_rescue_3 hLMR1_rescue
- GSM7462100 hLMR1_rescue_4 hLMR1_rescue
- GSM7462113 LMR2_control_1 LMR2_control
- GSM7462114 LMR2_control_2 LMR2_control
- GSM7462115 LMR2_control_3 LMR2_control
- GSM7462116 LMR2_control_4 LMR2_control
- GSM7462117 mLMR2_knockdown_1 mLMR2_knockdown
- GSM7462118 mLMR2_knockdown_2 mLMR2_knockdown
- GSM7462119 mLMR2_knockdown_3 mLMR2_knockdown
- GSM7462120 mLMR2_knockdown_4 mLMR2_knockdown
- GSM7462121 hLMR2_rescue_1 hLMR2_rescue
- GSM7462122 hLMR2_rescue_2 hLMR2_rescue
- GSM7462123 hLMR2_rescue_3 hLMR2_rescue
- GSM7462124 hLMR2_rescue_4 hLMR2_rescue
- GSM7462125 LMR3_control_1 LMR3_control
- GSM7462126 LMR3_control_2 LMR3_control
- GSM7462127 LMR3_control_3 LMR3_control
- GSM7462128 LMR3_control_4 LMR3_control
- GSM7462129 mLMR3_knockdown_1 mLMR3_knockdown
- GSM7462130 mLMR3_knockdown_2 mLMR3_knockdown
- GSM7462131 mLMR3_knockdown_3 mLMR3_knockdown
- GSM7462132 mLMR3_knockdown_4 mLMR3_knockdown
- GSM7462133 hLMR3_rescue_1 hLMR3_rescue
- GSM7462134 hLMR3_rescue_2 hLMR3_rescue
- GSM7462135 hLMR3_rescue_3 hLMR3_rescue
- GSM7462136 hLMR3_rescue_4 hLMR3_rescue
- GSM7462137 LMR-NC_control_1 LMR-NC_control
- GSM7462138 LMR-NC_control_2 LMR-NC_control
- GSM7462139 LMR-NC_control_3 LMR-NC_control
- GSM7462140 LMR-NC_control_4 LMR-NC_control
+ 8 more — browse all 48 samples with per-sample file links →
- GSE262879 Single-cell RNA-sequencing of murine pancreatic tumors derived from the orthotopic transplantation of Smad4 wild-type (WT) or Smad4 knockout (KO) pancreatic ductal adenocarcinoma (PDAC) KPC organoids in nu/nu mice. 18 samples shares wild-type, rna-seq
- GSE264105 Plate-based scRNA-seq of plasma-positive microglia and plasma-negative microglia in young mice 1111 samples shares rna-seq
- GSE326100 scRNA-seq of mouse cochlea organoid cells 768 samples shares rna-seq
- GSE311449 Single cell RNA-seq of mouse brain vascular cells with Smart-seq2 method 391 samples shares rna-seq
- GSE319614 Bulk RNA-seq transcriptome profiling of hippocampus across 17 autism spectrum disorder mouse models 269 samples shares rna-seq
- GSE326452 Bulk RNA-seq of mouse brain following closed head injury: role of IL-1R1 signaling 200 samples shares rna-seq
- GSE98969 Single cell RNA-seq identifies a unique microglia type associated with Alzheimer’s disease [RNA] 97 samples shares rna-seq
- GSE342349 CT26 multi-tissue RNA-seq under immunotherapy combinations 72 samples shares 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.