Transcriptomic profiling of Gpc4 and Gpc2 loss-of-function in the embryonic cerebral cortex
RNA-seq (gene expression) · mouse · 9 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
- 9 samples: 3 × sh-NT vs 3 × sh-Gpc4 vs 3 × sh-Gpc2Groups 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 GSE327841_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 PRJNA1452884 and SRA study SRP691407. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 9 samples.
How we read this: 3 replicated groups read from 9 sample titles; they account for 9 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.
- GSM9667020 sh-NT_rep1 sh-NT
- GSM9667021 sh-NT_rep2 sh-NT
- GSM9667022 sh-NT_rep3 sh-NT
- GSM9667023 sh-Gpc4_rep1 sh-Gpc4
- GSM9667024 sh-Gpc4_rep2 sh-Gpc4
- GSM9667025 sh-Gpc4_rep3 sh-Gpc4
- GSM9667026 sh-Gpc2_rep1 sh-Gpc2
- GSM9667027 sh-Gpc2_rep2 sh-Gpc2
- GSM9667028 sh-Gpc2_rep3 sh-Gpc2
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- GSE327304 Transcriptomic characterization of Wild type mouse Embryonic Stem Cells (mESCs), β-actin Knock out mESC and upon rescue with a nuclear localization signal β-actin 45 samples shares embryonic
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- GSE252199 Quantification of subcellular mRNA kinetics in mouse embryonic stem cells 100 samples shares embryonic
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.