Leveraging dynamic cell responses to design new protocols for pluripotency maintenance
RNA-seq (gene expression) · mouse · 21 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
- 21 samples: 7 conditions, mostly in triplicateGroups 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.
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 GSE298835_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 PRJNA1271470 and SRA study SRP589563. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 21 samples.
How we read this: 7 replicated groups read from 21 sample titles; they account for 21 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.
- GSM9024857 mESCs, 2i+LIF PO, rep1 mESCs, 2i+LIF PO,
- GSM9024858 mESCs, 2i+LIF PO, rep2 mESCs, 2i+LIF PO,
- GSM9024859 mESCs, 2i+LIF PO, rep3 mESCs, 2i+LIF PO,
- GSM9024860 mESCs, 2i+LIF LP, rep1 mESCs, 2i+LIF LP,
- GSM9024861 mESCs, 2i+LIF LP, rep2 mESCs, 2i+LIF LP,
- GSM9024862 mESCs, 2i+LIF LP, rep3 mESCs, 2i+LIF LP,
- GSM9024863 mESCs, CH+LIF LP, rep1 mESCs, CH+LIF LP,
- GSM9024864 mESCs, CH+LIF LP, rep2 mESCs, CH+LIF LP,
- GSM9024865 mESCs, CH+LIF LP, rep3 mESCs, CH+LIF LP,
- GSM9024866 mESCs, LIF LP, rep1 mESCs, LIF LP,
- GSM9024867 mESCs, LIF LP, rep2 mESCs, LIF LP,
- GSM9024868 mESCs, LIF LP, rep3 mESCs, LIF LP,
- GSM9024869 mESCs, 2i+LIF HP, rep1 mESCs, 2i+LIF HP,
- GSM9024870 mESCs, 2i+LIF HP, rep2 mESCs, 2i+LIF HP,
- GSM9024871 mESCs, 2i+LIF HP, rep3 mESCs, 2i+LIF HP,
- GSM9024872 mESCs, CH+LIF HP, rep1 mESCs, CH+LIF HP,
- GSM9024873 mESCs, CH+LIF HP, rep2 mESCs, CH+LIF HP,
- GSM9024874 mESCs, CH+LIF HP, rep3 mESCs, CH+LIF HP,
- GSM9024875 mESCs, LIF HP, rep1 mESCs, LIF HP,
- GSM9024876 mESCs, LIF HP, rep2 mESCs, LIF HP,
- GSM9024877 mESCs, LIF HP, rep3 mESCs, LIF HP,
- GSE249389 Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause [RNA-seq] 32 samples shares pluripotency, maintenance
- GSE225240 Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit 13 samples shares pluripotency, maintenance
- GSE225237 Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit (RNA-Seq) 12 samples shares pluripotency, maintenance
- GSE249392 Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause 83 samples shares pluripotency, maintenance
- GSE269920 Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause [ChIP-Seq] 30 samples shares pluripotency, maintenance
- GSE249630 Modeling T cell temporal response to cancer immunotherapy rationalize development of combinatorial treatments protocols 1372 samples shares protocols
- GSE199855 shRNA-mediated silencing of candidate pluripotency regulators in mouse epibladst stem cells 798 samples shares pluripotency
- GSE302715 A tumor-associated macrophage-targeted immunocytokine leveraging T and NK cell synergy for potent cancer immunotherapy [scRNA-seq] 187 samples shares leveraging
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.