RNA-seq of osteogenesis following siRNA depletion of SERPINA3
RNA-seq (gene expression) · human · 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
- Homo sapiens (human)
- 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.
- Paper
- SERPINA3 is a marker of cartilage differentiation and is essential for the expression of extracellular matrix genes during early chondrogenesisMatrix biology : journal of the International Society for Matrix Biology · 2024
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 GSE247528_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 PRJNA1039295 and SRA study SRP471353. Searching any of these in the dataset finder brings you back here.
Any grouping that defines a comparison lives in the sample characteristics, which GEO records separately from the titles.
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.
- GSM7892318 Day0_Control_1 [osteogeneic differentiation]
- GSM7892319 Day0_Control_2 [osteogeneic differentiation]
- GSM7892320 Day0_Control_3 [osteogeneic differentiation]
- GSM7892321 Day0_KD_1 [osteogeneic differentiation]
- GSM7892322 Day0_KD_2 [osteogeneic differentiation]
- GSM7892323 Day0_KD_3 [osteogeneic differentiation]
- GSM7892324 Day3_Control_1 [osteogeneic differentiation]
- GSM7892325 Day3_Control_2 [osteogeneic differentiation]
- GSM7892326 Day3_Control_3 [osteogeneic differentiation]
- GSM7892327 Day3_KD_1 [osteogeneic differentiation]
- GSM7892328 Day3_KD_2 [osteogeneic differentiation]
- GSM7892329 Day3_KD_3 [osteogeneic differentiation]
- GSM7892330 Day7_Control_1 [osteogeneic differentiation]
- GSM7892331 Day7_Control_2 [osteogeneic differentiation]
- GSM7892332 Day7_Control_3 [osteogeneic differentiation]
- GSM7892333 Day7_KD_1 [osteogeneic differentiation]
- GSM7892334 Day7_KD_2 [osteogeneic differentiation]
- GSM7892335 Day7_KD_3 [osteogeneic differentiation]
- GSE288346 Multi-Omics Analysis of the Immunological State at Baseline and Following SARS-CoV-2 mRNA Vaccination in Lung Transplant Recipients [RNA-seq] 106 samples shares following, rna-seq
- GSE298803 ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC [CRISPRi RNA-seq] 70 samples shares depletion, rna-seq
- GSE298925 ZBTB11 Depletion Targets Metabolic Vulnerabilities in K-Ras Inhibitor Resistant PDAC [Degrader RNA-seq] 48 samples shares depletion, rna-seq
- GSE334189 RNA-seq analysis of global gene expression changes in human FSHD immortalized myotubes following treatment with the BAZ1A inhibitor C06 18 samples shares following, rna-seq
- GSE301166 PURPL bidirectionally controls senescence: depletion rejuvenates fibroblasts while overexpression accelerates aging [RNA-Seq2] 18 samples shares depletion, rna-seq
- GSE278405 Phenotypic plasticity and increased tissue infiltration of TREM1+ mono-macrophages following radiotherapy in rectal cancer. [RNA-Seq] 16 samples shares following, rna-seq
- GSE271915 Reconstitution of the Multiple Myeloma Microenvironment Following Lymphodepletion with BCMA CAR-T Therapy 14 samples shares following, depletion
- GSE342354 Time-series RNA-seq of U2OS cells following CCCP-induced mitochondrial damage and recovery upon drug washout 12 samples shares following, 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.