Nuclear receptor-SINE B1 network modulates expanded pluripotency in blastoids and blastocysts.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 101 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
- 101 samples: 79 distinct titles, 22 of them repeatedGroups 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.
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 GSE294032_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 PRJNA1247918 and SRA study SRP390658. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 101 sample titles: 79 distinct titles with little repetition. 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.
- GSM6437637 EPSC
- GSM6437638 EPSCT09
- GSM6437639 EPT09Bad
- GSM6437640 EPT09_Gd
- GSM6437641 ESC
- GSM6437642 ESCT09
- GSM6437643 siNr1_D2
- GSM6437644 siNT_D2
- GSM6437645 CellTag_Day5_Average_Blastoid__undiluted
- GSM6437646 CellTag_Day5_Bad_Blastoid__undiluted
- GSM6437647 CellTag_Day5_Good_Blastoid__undiluted
- GSM6437648 E14_EP_blastoid_AVG
- GSM6437649 E14_EP_blastoid_BAD
- GSM6437650 E14_EP_blastoid_GOOD
- GSM6727241 H3K27ac_2iES_Input
- GSM6727242 H3K27ac_2iES_Sample
- GSM6727243 H3K27ac_EPSC_Input
- GSM6727244 H3K27ac_EPSC_Sample
- GSM6727245 H3K27ac_NrEPSC_Input
- GSM6727246 H3K27ac_NrEPSC_Sample
- GSM6727247 H3K27ac_NrES_Input
- GSM6727248 H3K27ac_NrES_Sample
- GSM6727249 Nr1h2_2iES_Sample
- GSM6727250 Nr1h2_E2iES_Input
- GSM6727251 Nr1h2_EPSC_Input
- GSM6727252 Nr1h2_EPSC_Sample
- GSM6727253 Nr1h2_NrEPSC_Input
- GSM6727254 Nr1h2_NrEPSC_Sample
- GSM6727255 Nr1h2_NrES_Input
- GSM6727256 Nr1h2_NrES_Sample
- GSM6727257 EP 1
- GSM6727258 EP 2
- GSM6727259 ES 1
- GSM6727260 ES 2
- GSM6727261 NrES 1 1
- GSM6727262 NrES 1 2
- GSM6727263 NrES 16 1
- GSM6727264 NrES 16 2
- GSM6727265 NrESC_Type_III
- GSM6727266 NrESC_Type_II
+ 61 more — browse all 101 samples with per-sample file links →
- 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, modulates, network
- GSE264615 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [RNA-seq] 123 samples shares pluripotency, network
- GSE264614 Emerging cooperativity between Oct4 and Sox2 governs the pluripotency network in mouse early embryos [ATAC-seq] 44 samples shares pluripotency, network
- GSE199855 shRNA-mediated silencing of candidate pluripotency regulators in mouse epibladst stem cells 798 samples shares pluripotency
- GSE309424 SETDB1/HUSH modulates Xist RNA levels during establishment of X chromosome inactivation 292 samples shares modulates
- GSE272353 Genetic context modulates aging and degeneration in the murine retina 201 samples shares modulates
- 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 blastocysts
- GSE226316 TEAD2 mediates the ground-state pluripotency by chromatin looping 103 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.