Comprehensive transcriptome analysis of osteoclasts with the SIK3 deletion and pterosin B treatment.
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: 6 × SC vs 3 × WT vs 3 × KO vs 3 × SCRPGroups 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
- Impact of the SIK3 pathway inhibition on osteoclast differentiation via oxidative phosphorylationJournal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 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 GSE234221_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 PRJNA980570 and SRA study SRP441303. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 15 samples.
How we read this: 4 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.
- GSM7457537 WT_1 WT
- GSM7457538 WT_2 WT
- GSM7457539 WT_3 WT
- GSM7457540 KO_1 KO
- GSM7457541 KO_2 KO
- GSM7457542 KO_3 KO
- GSM7457543 SC_1 SC
- GSM7457544 SC_2 SC
- GSM7457545 SC_3 SC
- GSM7457546 SCR_1 SC
- GSM7457547 SCR_2 SC
- GSM7457548 SCR_3 SC
- GSM7457549 SCRP_1 SCRP
- GSM7457550 SCRP_2 SCRP
- GSM7457551 SCRP_3 SCRP
- GSE310090 The orally available SIK2/SIK3 inhibitor SK-124 increases bone mass in hypogonadal male mice 12 samples shares sik3
- GSE249630 Modeling T cell temporal response to cancer immunotherapy rationalize development of combinatorial treatments protocols 1372 samples shares treatment
- GSE276682 Single-cell transcriptome analysis revealed cellular reprogramming following Tetramethylpyrazine treatment in LPS-induced acute lung injury 12 samples shares treatment
- GSE332646 Bulk RNA-seq of juvenile mouse liver following NDMA or saline treatment in WT and Mgmt-/- genotypes across multiple timepoints 214 samples shares treatment
- GSE305242 Effects of Sphk1 deletion in smooth muscle cells on murine arterial transcriptome in hypertension 26 samples shares deletion
- GSE269328 Glucagon receptor agonism and treatment withdrawal effect on liver transcriptomes of diet-induced obese mice 24 samples shares treatment
- GSE301479 RNA-seq analysis of pulmonary arterial smooth muscle cells (PASMCs) and bronchial smooth muscle cells (BSMCs) after pulmonary arterial hypertension (PAH) treatment 12 samples shares treatment
- GSE235623 MERTK inhibition for the treatment of tissue fibrosis [RNA-seq] 86 samples shares treatment
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.