Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 38 samples
- What it is
- ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
- Organism
- Mus musculus (mouse)
- Samples
- 38 samples: 18 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
- Lysosomal catabolic activity promotes the exit of murine totipotent 2-cell state by silencing early-embryonic retrotransposonsDevelopmental 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 GSE247083_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: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.
Also filed as BioProject PRJNA1036191 and SRA study SRP470364. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 38 samples.
How we read this: 18 replicated groups read from 38 sample titles; they account for 38 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.
- GSM7883013 FlcnKD_mESC_Tfeb_1 FlcnKD_mESC_Tfeb
- GSM7883014 FlcnKD_mESC_Tfeb_2 FlcnKD_mESC_Tfeb
- GSM7883015 FlcnKD_i2CLC_Tfeb_1 FlcnKD_i2CLC_Tfeb
- GSM7883016 FlcnKD_i2CLC_Tfeb_2 FlcnKD_i2CLC_Tfeb
- GSM7883017 FlcnKD_mESC_Tfe3_1 FlcnKD_mESC_Tfe3
- GSM7883018 FlcnKD_mESC_Tfe3_2 FlcnKD_mESC_Tfe3
- GSM7883019 FlcnKD_i2CLC_Tfe3_1 FlcnKD_i2CLC_Tfe3
- GSM7883020 FlcnKD_i2CLC_Tfe3_2 FlcnKD_i2CLC_Tfe3
- GSM7883021 DMSO_i2C_1 DMSO_i2C
- GSM7883022 DMSO_i2C_2 DMSO_i2C
- GSM7883023 Vacuolin-1_i2C_1 Vacuolin-1_i2C
- GSM7883024 Vacuolin-1_i2C_2 Vacuolin-1_i2C
- GSM7883025 sgSV40_i2C_1 sgSV40_i2C
- GSM7883026 sgSV40_i2C_2 sgSV40_i2C
- GSM7883027 sgFlcn_i2C-1 sgFlcn_i2C
- GSM7883028 sgFlcn_i2C-2 sgFlcn_i2C
- GSM7883029 sgSV40_DMSO_i2C_1 sgSV40_DMSO_i2C
- GSM7883030 sgSV40_DMSO_i2C_2 sgSV40_DMSO_i2C
- GSM7883031 sgSV40_Vacuolin-1_i2C_1 sgSV40_Vacuolin-1_i2C
- GSM7883032 sgSV40_Vacuolin-1_i2C_2 sgSV40_Vacuolin-1_i2C
- GSM7883033 FlcnKO_DMSO_i2C_1 FlcnKO_DMSO_i2C
- GSM7883034 FlcnKO_DMSO_i2C_2 FlcnKO_DMSO_i2C
- GSM7883035 FlcnKO_Vacuolin-1_i2C_1 FlcnKO_Vacuolin-1_i2C
- GSM7883036 FlcnKO_Vacuolin-1_i2C_2 FlcnKO_Vacuolin-1_i2C
- GSM7883037 WT-4C-1 WT-4C
- GSM7883038 WT-4C-2 WT-4C
- GSM7883039 Vacuolin-1-4C-1 Vacuolin-1-4C
- GSM7883041 WT-E2C-1 WT-E2C
- GSM7883042 WT-E2C-2 WT-E2C
- GSM7883043 WT-E2C-3 WT-E2C
- GSM7883044 Vacuolin-1-E2C-1 Vacuolin-1-E2C
- GSM7883045 Vacuolin-1-E2C-2 Vacuolin-1-E2C
- GSM7883046 Vacuolin-1-E2C-3 Vacuolin-1-E2C
- GSM7883047 siGFP-4C-1 siGFP-4C
- GSM7883048 siGFP-4C-2 siGFP-4C
- GSM7883049 siFlcn-4C-1 siFlcn-4C
- GSM7883050 siFlcn-4C-2 siFlcn-4C
- GSM8260474 Vacuolin-1-4C-2 Vacuolin-1-4C
- GSE247082 Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons [RNA-seq] 30 samples shares 2-cell, retrotransposons, early-embryonic, totipotent, lysosomal, catabolic, silencing, activity
- GSE247081 Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons [CUT&Tag] 8 samples shares 2-cell, retrotransposons, early-embryonic, totipotent, lysosomal, catabolic, silencing, activity
- GSE222656 RNA-seq and Cut & Tag analyses of mouse 2-cell embryos in which lamin B1 dissociation from the nuclear envelope is inhibited 40 samples shares 2-cell
- GSE278720 Single-embryo RNA-seq analysis in LAD disrupted 2-cell embryos. 87 samples shares 2-cell
- GSE253944 The disruption of CtBP regulates DUX-dependent and -independent genetic program for the 2-cell-like state in murine embryonic stem cells [RNA-seq and RRBS] 40 samples shares 2-cell
- GSE300864 Single-embryo and single-blastomere RNA-seq analysis of 2-cell and 4-cell mouse embryos 39 samples shares 2-cell
- GSE283389 Functional dissection of enhancers in 2-Cell embryo with an in vitro model. 37 samples shares 2-cell
- GSE269417 Single embryo total RNA sequencing to map the effect of maternal SETDB1 on the 2-celll and 8-cell transcriptome 37 samples shares 2-cell
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.