KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 36 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
- 36 samples: 30 distinct titles, 6 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.
- Paper
- KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS diseaseiScience · 2026
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 GSE299850_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 PRJNA1277118 and SRA study SRP591963. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 36 sample titles: 30 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.
- GSM9047355 iTF-iPSCs, untreated, rep1
- GSM9047356 iTF-iPSCs, untreated, rep2
- GSM9047357 iTF-Microglia Day 18, untreated, rep1
- GSM9047358 iTF-Microglia Day 18, untreated, rep2
- GSM9047359 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1
- GSM9047360 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2
- GSM9047361 iTF-iPSCs, untreated, rep1 (ChIP)
- GSM9047362 iTF-iPSCs, untreated, rep2 (ChiP)
- GSM9047363 iTF-Microglia Day 18, untreated, rep1 (ChiP)
- GSM9047364 iTF-Microglia Day 18, untreated, rep2 (ChIP)
- GSM9047365 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (ChIP)
- GSM9047366 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (ChIP)
- GSM9047367 iTF-iPSCs, untreated, rep1 (Input)
- GSM9047368 iTF-iPSCs, untreated, rep2 (Input)
- GSM9047369 iTF-Microglia Day 18, untreated, rep1 (Input)
- GSM9047370 iTF-Microglia Day 18, untreated, rep2 (Input)
- GSM9047371 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (Input)
- GSM9047372 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (Input)
- GSM9047373 iTF-iPSCs, untreated_rep1
- GSM9047374 iTF-iPSCs, untreated_rep2
- GSM9047375 iTF-Microglia Day 18, untreated_rep1
- GSM9047376 iTF-Microglia Day 18, untreated_rep2
- GSM9047377 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h_rep1
- GSM9047378 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h_rep2
- GSM9047379 iTF-iPSCs, untreated, rep1 (RNA-seq)
- GSM9047380 iTF-iPSCs, untreated, rep2 (RNA-seq)
- GSM9047381 iTF-iPSCs, untreated, rep3 (RNA-seq)
- GSM9047382 iTF-iPSCs, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (RNA-seq)
- GSM9047383 iTF-iPSCs, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (RNA-seq)
- GSM9047384 iTF-iPSCs, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep3 (RNA-seq)
- GSM9047385 iTF-Microglia Day 18, untreated, rep1 (RNA-seq)
- GSM9047386 iTF-Microglia Day 18, untreated, rep2 (RNA-seq)
- GSM9047387 iTF-Microglia Day 18, untreated, rep3 (RNA-seq)
- GSM9047388 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep1 (RNA-seq)
- GSM9047389 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep2 (RNA-seq)
- GSM9047390 iTF-Microglia Day 18, LPS 100mg/ml + IFNG 20 ng/ml, 24h, rep3 (RNA-seq)
- GSE299831 KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [RNA-seq] 12 samples shares kolf2, cns, itf-microglia, standardized, microglial, regulatory, platform, networks
- GSE299829 KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [ChIP-seq] 12 samples shares kolf2, cns, itf-microglia, standardized, microglial, regulatory, platform, networks
- GSE299828 KOLF2.1J iTF-Microglia: A standardized platform to study microglial transcriptional regulatory networks in CNS disease [ATAC-seq] 6 samples shares kolf2, cns, itf-microglia, standardized, microglial, regulatory, platform, networks
- GSE300985 A standardized patient-derived glioblastoma organoid platform for evaluating radiotherapy efficacy and overcoming resistance 147 samples shares standardized, platform
- GSE268458 Standardized generation of human iPSC-derived hematopoietic organoids and macrophages utilizing a benchtop bioreactor platform under fully defined conditions 3 samples shares standardized, platform
- GSE73801 DNA methylation data from CNS-PNETs and various other brain tumor samples 593 samples shares cns
- GSE65362 Molecular Classification of Ependymal Tumors across All CNS Compartments, Histopathological Grades, and Age Groups. 562 samples shares cns
- GSE61578 Gene Expression and HD-SNP6.0 data from Primary Testicular (PTL), Primary Central Nervous System Lymphoma (PCNSL) and Primary Mediastinal B-cell Lymphoma (PMLBCL) 260 samples shares cns
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.