Effect of knockdown of CENPU on gene expression of Huh-7 and MHCC-97H hepatoma cells
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 × Huh-7 cells, si-NC, vs 3 × Huh-7 cells, si-CENPU, vs 3 × MHCC-97H cells, si-NC, vs 3 × MHCC-97H cells, si-CENPU,Groups 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 GSE203625_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 PRJNA841635 and SRA study SRP376687. 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.
- GSM6180854 Huh-7 cells, si-NC, rep1 Huh-7 cells, si-NC,
- GSM6180855 Huh-7 cells, si-NC, rep2 Huh-7 cells, si-NC,
- GSM6180856 Huh-7 cells, si-NC, rep3 Huh-7 cells, si-NC,
- GSM6180857 Huh-7 cells, si-CENPU, rep1 Huh-7 cells, si-CENPU,
- GSM6180858 Huh-7 cells, si-CENPU, rep2 Huh-7 cells, si-CENPU,
- GSM6180859 Huh-7 cells, si-CENPU, rep3 Huh-7 cells, si-CENPU,
- GSM6180860 MHCC-97H cells, si-NC, rep1 MHCC-97H cells, si-NC,
- GSM6180861 MHCC-97H cells, si-NC, rep2 MHCC-97H cells, si-NC,
- GSM6180862 MHCC-97H cells, si-NC, rep3 MHCC-97H cells, si-NC,
- GSM6180863 MHCC-97H cells, si-CENPU, rep1 MHCC-97H cells, si-CENP…
- GSM6180864 MHCC-97H cells, si-CENPU, rep2 MHCC-97H cells, si-CENP…
- GSM6180865 MHCC-97H cells, si-CENPU, rep3 MHCC-97H cells, si-CENP…
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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.