Time-resolved small-RNA sequencing identifies microRNAs critical for formation of embryonic stem cells from the inner cell mass of mouse embryos
RNA-seq (gene expression) · mouse · 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
- Mus musculus (mouse)
- Samples
- 18 samples: 9 conditions, mostly in duplicateGroups 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
- Time-resolved Small-RNA Sequencing Identifies MicroRNAs Critical for Formation of Embryonic Stem Cells from the Inner Cell Mass of Mouse EmbryosStem cell reviews and reports · 2023
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 GSE205361_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 PRJNA844614 and SRA study SRP378169. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 9 replicated groups read from 18 sample titles; they account for 18 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.
- GSM6210952 day 0 (ICM) Rep1 day 0 (ICM)
- GSM6210953 day 0 (ICM) Rep2 day 0 (ICM)
- GSM6210954 day 0.5 Rep1 day 0.5
- GSM6210955 day 0.5 Rep2 day 0.5
- GSM6210956 day 1 Rep1 day 1
- GSM6210957 day 1 Rep2 day 1
- GSM6210958 day 2 Rep1 day 2
- GSM6210959 day 2 Rep2 day 2
- GSM6210960 day 3 Rep1 day 3
- GSM6210961 day 3 Rep2 day 3
- GSM6210962 day 5 Rep1 day 5
- GSM6210963 day 5 Rep2 day 5
- GSM6210964 ESC passage #2 Rep1 ESC passage #2
- GSM6210965 ESC passage #2 Rep2 ESC passage #2
- GSM6210966 ESC passage #4 Rep1 ESC passage #4
- GSM6210967 ESC passage #4 Rep2 ESC passage #4
- GSM6210968 ESC passage #15 Rep1 ESC passage #15
- GSM6210969 ESC passage #15 Rep2 ESC passage #15
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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.