The Interferon γ Pathway Enhances Pluripotency and X-Chromosome Reactivation in iPSC Reprogramming
DNA methylation · mouse · 68 samples
- What it is
- DNA methylationChemical marks on DNA that help switch genes on or off.
- Organism
- Mus musculus (mouse)
- Samples
- 68 samples: 52 distinct titles, 16 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed expression table (series matrix) and the array files, from NCBI.
- Paper
- The interferon γ pathway enhances pluripotency and X-chromosome reactivation in iPSC reprogrammingScience advances · 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 GSE236247_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 beta-value tables or raw IDAT files among the supplementary files.
Also filed as BioProject PRJNA989561 and SRA study SRP446786. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 68 sample titles: 52 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.
- GSM7520273 gRNA sequencing - NPC Biol Rep1
- GSM7520274 gRNA sequencing - NPC Biol Rep2
- GSM7520275 gRNA sequencing - Non-Pluripotent Biol Rep1
- GSM7520276 gRNA sequencing - Non-Pluripotent Biol Rep2
- GSM7520277 gRNA sequencing - Early Pluripotent Biol Rep1
- GSM7520278 gRNA sequencing - Early Pluripotent Biol Rep2
- GSM7520279 gRNA sequencing - Late Pluripotent Biol Rep1
- GSM7520280 gRNA sequencing - Late Pluripotent Biol Rep2
- GSM7520281 RNA-seq - ESC Rep 1
- GSM7520282 RNA-seq - ESC Rep 2
- GSM7520283 RNA-seq - NPC Rep 1
- GSM7520284 RNA-seq - NPC Rep 2
- GSM7520285 RNA-seq - day 2 iPSCs control Rep 1
- GSM7520286 RNA-seq - day 2 iPSCs control Rep 2
- GSM7520287 RNA-seq - day 2 iPSCs IFNγ Rep 1
- GSM7520288 RNA-seq - day 2 iPSCs IFNγ Rep 2
- GSM7520289 RNA-seq - day 5 iPSCs control Rep 1
- GSM7520290 RNA-seq - day 5 iPSCs control Rep 2
- GSM7520291 RNA-seq - day 5 iPSCs IFNγ Rep 1
- GSM7520292 RNA-seq - day 5 iPSCs IFNγ Rep 2
- GSM7520293 RNA-seq - day 7 X-GFP negative iPSCs control Rep 1
- GSM7520294 RNA-seq - day 7 X-GFP negative iPSCs control Rep 2
- GSM7520295 RNA-seq - day 7 X-GFP negative iPSCs IFNγ Rep 1
- GSM7520296 RNA-seq - day 7 X-GFP negative iPSCs IFNγ Rep 2
- GSM7520297 RNA-seq - day 7 X-GFP medium iPSCs control Rep 1
- GSM7520298 RNA-seq - day 7 X-GFP medium iPSCs control Rep 2
- GSM7520299 RNA-seq - day 7 X-GFP medium iPSCs IFNγ Rep 1
- GSM7520300 RNA-seq - day 7 X-GFP medium iPSCs IFNγ Rep 2
- GSM7520301 RNA-seq - day 7 X-GFP high iPSCs control Rep 1
- GSM7520302 RNA-seq - day 7 X-GFP high iPSCs control Rep 2
- GSM7520303 RNA-seq - day 7 X-GFP high iPSCs IFNγ Rep 1
- GSM7520304 RNA-seq - day 7 X-GFP high iPSCs IFNγ Rep 2
- GSM7520305 DNA methylation array - Day 5 iPSC control Rep1_BS_OX
- GSM7520306 DNA methylation array - Day 5 iPSC control Rep1_BS
- GSM7520307 DNA methylation array - Day 5 iPSC IFNg Rep1_BS_OX
- GSM7520308 DNA methylation array - Day 5 iPSC IFNg Rep1_BS
- GSM7520309 DNA methylation array - Day 5 iPSC control Rep2_BS_OX
- GSM7520310 DNA methylation array - Day 5 iPSC control Rep2_BS
- GSM7520311 DNA methylation array - Day 5 iPSC IFNg Rep2_BS_OX
- GSM7520312 DNA methylation array - Day 5 iPSC IFNg Rep2_BS
+ 28 more — browse all 68 samples with per-sample file links →
- GSE282319 Long read RNA sequencing reveals a new long non-coding RNA that regulates somatic cell reprogramming and pluripotency 45 samples shares reprogramming, pluripotency
- GSE261139 Tumour-derived Extracellular Vesicle and Particle Reprogramming of Interstitial Macrophages in the Lung Pre-Metastatic Niche Enhances Vascular Permeability and Metastatic Potential 16 samples shares reprogramming, enhances
- GSE324502 Bioinspired, Mitochondria-targeted Single-atom Nanozyme Enhances Bone Regeneration by Reprogramming Stem Cell Energy Metabolism 12 samples shares reprogramming, enhances
- 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
- GSE319397 Particle Reprogramming of the TLR–Ferroptosis Axis and Immunometabolic Pathways Inhibits Myeloid Suppression to Improve Checkpoint Blockade in Prostate Cancer 9 samples shares reprogramming
- GSE268822 Transcriptional landscapes underlying Notch-induced lineage conversion and reprogramming of mammary cells 840 samples shares reprogramming
- GSE256287 Sirtuin 7 regulates dosage compensation and safeguards the female X-chromosome 182 samples shares x-chromosome
- GSE274695 Aging promotes reactivation of the Barr body at distal chromosome regions 175 samples shares reactivation
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.