Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit
RNA-seq (gene expression) · mouse · 13 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
- 13 samples: 6 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
- Reevaluation by the CRISPR/Cas9 knockout approach revealed that multiple pluripotency-associated lncRNAs are dispensable for pluripotency maintenance while Snora73a/b is essential for pluripotency exitScience China. Life sciences · 2024
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 GSE225240_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 PRJNA934393 and SRA study SRP422612. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 12 samples.
How we read this: 6 replicated groups read from 13 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.
- GSM7042327 WT+1343KO-a14-D0-R2 WT+1343KO-a14-D0
- GSM7042328 WT+1343KO-a14-D8-R2 WT+1343KO-a14-D8
- GSM7042329 WT+1343KO-a14-D16-R2 WT+1343KO-a14-D16
- GSM7042330 WT-D0-R1 WT-D0
- GSM7042331 WT-D8-R1 WT-D8
- GSM7042332 WT-D16-R1 WT-D16
- GSM7042333 WT+1343KO-a14-D0-R1 WT+1343KO-a14-D0
- GSM7042334 WT+1343KO-a14-D8-R1 WT+1343KO-a14-D8
- GSM7042335 WT+1343KO-a14-D16-R1 WT+1343KO-a14-D16
- GSM7042336 WT-D0-R2 WT-D0
- GSM7042337 WT-D8-R2 WT-D8
- GSM7042338 WT-D16-R2 WT-D16
- GSM7042339 16GT_pooled
- GSE225237 Reevaluation by CRISPR-Cas9 approach reveals multiple lincRNAs dispensable for pluripotency maintenance and SNORA73 essential for pluripotency exit (RNA-Seq) 12 samples shares snora73, reevaluation, pluripotency, crispr-cas9, dispensable, maintenance, essential, multiple
- GSE249389 Transcriptional shut-off of MAP kinase signaling enables pluripotency maintenance during diapause [RNA-seq] 32 samples shares pluripotency, maintenance
- GSE298835 Leveraging dynamic cell responses to design new protocols for pluripotency maintenance 21 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
- GSE280128 The LHX1 Gene Regulatory Network Represses Pluripotency and Modulates Multiple Signaling Pathways to Specify the Embryonic Head [Embryo_ATAC-seq] 12 samples shares pluripotency, multiple
- GSE199855 shRNA-mediated silencing of candidate pluripotency regulators in mouse epibladst stem cells 798 samples shares pluripotency
- GSE264615 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [RNA-seq] 123 samples shares pluripotency
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.