RNA-Seq experiment of primary hepatic stellate cells (HSCs) and LX-2 cell line treated with TGFb
RNA-seq (gene expression) · human · 12 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
- 12 samples: 3 × PHSC_Solvent vs 3 × PHSC_TGFβ vs 3 × LX2_Solvent vs 3 × LX2_TGFβGroups 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
- An Integrative Transcriptome Subtraction Strategy to Identify Human lncRNAs That Specifically Play a Role in Activation of Human Hepatic Stellate CellsNon-coding RNA · 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 GSE253493_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 PRJNA1065892 and SRA study SRP484285. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 12 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.
- GSM8021665 PHSC_Solvent_1 PHSC_Solvent
- GSM8021666 PHSC_Solvent_2 PHSC_Solvent
- GSM8021667 PHSC_Solvent_3 PHSC_Solvent
- GSM8021668 PHSC_TGFβ_1 PHSC_TGFβ
- GSM8021669 PHSC_TGFβ_2 PHSC_TGFβ
- GSM8021670 PHSC_TGFβ_3 PHSC_TGFβ
- GSM8021671 LX2_Solvent_1 LX2_Solvent
- GSM8021672 LX2_Solvent_2 LX2_Solvent
- GSM8021673 LX2_Solvent_3 LX2_Solvent
- GSM8021674 LX2_TGFβ_1 LX2_TGFβ
- GSM8021675 LX2_TGFβ_2 LX2_TGFβ
- GSM8021676 LX2_TGFβ_3 LX2_TGFβ
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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.