PHLDA1-PRDM1 mediates the effect of lentiviral vectors on fate-determination of human retinal progenitor cells
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 11 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
- Homo sapiens (human)
- Samples
- 11 samples: 3 × Y79,Mock,RNA-seq, vs 3 × Y79,Scramble,RNA-seq, vs 2 × Y79,Mock,CUT&TAG, vs 2 × Y79,Scramble,CUT&TAG,Groups 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
- PHLDA1-PRDM1 mediates the effect of lentiviral vectors on fate-determination of human retinal progenitor cellsCellular and molecular life sciences : CMLS · 2024
Read the full summary ↓
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 GSE251752_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 PRJNA1055163 and SRA study SRP479280. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 10 samples.
How we read this: 4 replicated groups read from 11 sample titles; they account for 10 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.
- GSM7987327 Y79,Mock,RNA-seq,rep1 Y79,Mock,RNA-seq,
- GSM7987328 Y79,Mock,RNA-seq,rep2 Y79,Mock,RNA-seq,
- GSM7987329 Y79,Mock,RNA-seq,rep3 Y79,Mock,RNA-seq,
- GSM7987330 Y79,Scramble,RNA-seq,rep1 Y79,Scramble,RNA-seq,
- GSM7987331 Y79,Scramble,RNA-seq,rep2 Y79,Scramble,RNA-seq,
- GSM7987332 Y79,Scramble,RNA-seq,rep3 Y79,Scramble,RNA-seq,
- GSM7987333 Y79,IgG,CUT&Tag,rep1
- GSM7987334 Y79,Mock,CUT&TAG,rep1 Y79,Mock,CUT&TAG,
- GSM7987335 Y79,Mock,CUT&TAG,rep2 Y79,Mock,CUT&TAG,
- GSM7987336 Y79,Scramble,CUT&TAG,rep1 Y79,Scramble,CUT&TAG,
- GSM7987337 Y79,Scramble,CUT&TAG,rep3 Y79,Scramble,CUT&TAG,
- GSE297722 Genomic characterization of sub-populations in human pluripotent stem cell-derived retinal progenitor cells that drive retinal layer structure 12 samples shares progenitor, retinal
- GSE248730 BCG vaccination alters the epigenetic landscape of progenitor cells in human bone marrow to influence innate immune responses 42 samples shares progenitor
- GSE276836 ATRX Condensates Formed by Liquid-Liquid Phase Separation Regulate Neural Progenitor Cell Identity 30 samples shares progenitor
- GSE302350 KMT2D-deficiency destabilizes lineage progression in immature neural progenitors 16 samples shares progenitor
- GSE229901 INSM1 governs a neuronal progenitor state that drives glioblastoma in a human stem cell model 15 samples shares progenitor
- GSE270127 Myeloid progenitor dysregulation fuels immunosuppressive macrophages in tumors [dataset 2] 10 samples shares progenitor
- GSE280113 Progenitor effects and unique transcriptomic signatures linked to differentiation phenotype in clonally expanded antigen-specific CD8 T memory stem cells (TSCM) 509 samples shares progenitor
- GSE272993 Combination anti-PD-1 and anti-CTLA-4 therapy generates waves of clonal responses that include progenitor-exhausted CD8 T cells [dataset 1] 360 samples shares progenitor
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.