LaminB1 DamID, RNA-seq and Genome-wide analysis of replication timing in RIF1 depleted preimplantation mouse embryos
RNA-seq (gene expression) · mouse · 468 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
- 468 samples: 12 conditions, mostly with about 72 replicates eachGroups 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
- RIF1 controls replication timing in early mouse embryos independently of lamina-associated nuclear organizationDevelopmental cell · 2025
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 GSE262791_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 PRJNA1093385 and SRA study SRP498633. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 400 samples.
How we read this: 12 replicated groups read from the first 400 of 468 sample titles; they account for 400 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.
- GSM8178903 siControl_4C_rep1 siControl_4C
- GSM8178904 siControl_4C_rep2 siControl_4C
- GSM8178905 siControl_4C_rep3 siControl_4C
- GSM8178906 siControl_8C_rep1 siControl_8C
- GSM8178907 siControl_8C_rep2 siControl_8C
- GSM8178908 siControl_8C_rep3 siControl_8C
- GSM8178909 siRif1_4C_rep1 siRif1_4C
- GSM8178910 siRif1_4C_rep2 siRif1_4C
- GSM8178911 siRif1_4C_rep3 siRif1_4C
- GSM8178912 siRif1_8C_rep1 siRif1_8C
- GSM8178913 siRif1_8C_rep2 siRif1_8C
- GSM8178914 siRif1_8C_rep3 siRif1_8C
- GSM8178915 siCon_4C_1 siCon_4C
- GSM8178916 siCon_4C_2 siCon_4C
- GSM8178917 siCon_4C_3 siCon_4C
- GSM8178918 siCon_4C_4 siCon_4C
- GSM8178919 siCon_4C_5 siCon_4C
- GSM8178920 siCon_4C_6 siCon_4C
- GSM8178921 siCon_4C_7 siCon_4C
- GSM8178922 siRif1_4C_1 siRif1_4C
- GSM8178923 siRif1_4C_2 siRif1_4C
- GSM8178924 siRif1_4C_3 siRif1_4C
- GSM8178925 siRif1_4C_4 siRif1_4C
- GSM8178926 siRif1_4C_5 siRif1_4C
- GSM8178927 siRif1_4C_6 siRif1_4C
- GSM8178928 siRif1_4C_7 siRif1_4C
- GSM8178929 siRif1_4C_8 siRif1_4C
- GSM8178930 siRif1_4C_9 siRif1_4C
- GSM8178931 siRif1_4C_10 siRif1_4C
- GSM8178932 siRif1_4C_11 siRif1_4C
- GSM8178933 siRif1_4C_12 siRif1_4C
- GSM8178934 siRif1_4C_13 siRif1_4C
- GSM8178935 siCon_8C_1 siCon_8C
- GSM8178936 siCon_8C_2 siCon_8C
- GSM8178937 siCon_8C_3 siCon_8C
- GSM8178938 siCon_8C_4 siCon_8C
- GSM8178939 siCon_8C_5 siCon_8C
- GSM8178940 siCon_8C_6 siCon_8C
- GSM8178941 siCon_8C_7 siCon_8C
- GSM8178942 siCon_8C_8 siCon_8C
+ 428 more — browse all 468 samples with per-sample file links →
- GSE262789 Single embryo RNA-seq analysis in RIF1 depleted preimplantation mouse embryos 40 samples shares rif1, preimplantation, depleted, rna-seq, embryos
- GSE284010 Novel Single-Cell Multiomics Approach to Analyze Replication Timing and Gene Expression in Mouse Preimplantation Embryos 248 samples shares preimplantation, replication, embryos
- GSE278944 Genome-wide DNA replication profiling and full-length total RNA sequencing from the same single cell [02_Mouse8cell_embryos] 26 samples shares genome-wide, replication, embryos
- GSE156297 RNA-seq, LaminB1 ChIP-seq and in situ Hi-C of double positive thymocytes from control and Suv39h1/Suv39h2 double knockout mice 34 samples shares laminb1, rna-seq
- GSE263902 The translational landscape of mouse oocytes and preimplantation embryos revealed by high-resolution ribosome profiling 272 samples shares preimplantation, embryos
- GSE278949 Genome-wide DNA replication profiling and full-length total RNA sequencing from the same single cell [03_CBMS1_mESC] 168 samples shares genome-wide, replication
- GSE272793 An atlas of small non-coding RNAs in Human Preimplantation Development (Mouse embryo RNA-seq) 132 samples shares preimplantation, rna-seq
- GSE225317 Trophectoderm biopsies of blastocysts for preimplantation genetic testing following in vitro fertilization and embryo culture increases epigenetic dysregulation in a mouse model [RNA-seq] 110 samples shares preimplantation, rna-seq
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.