Distal Enhancer-Insulator Module of GDF6 is Essential for Cochlear Formation
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 12 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
- 12 samples: 2 × CTCF_CD2_cntrl vs 2 × H3K4me1_CD2_cntrl vs 2 × H3K27ac_CD2_cntrl vs 2 × CD2 iPSC-derived IEO, ATAC-seq, DayGroups 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 GSE329999_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 PRJNA1462350 and SRA study SRP693144. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 8 samples.
How we read this: 4 replicated groups read from 12 sample titles; they account for 8 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.
- GSM9684130 CD2_input
- GSM9684131 CTCF_CD2_cntrl_rep1 CTCF_CD2_cntrl
- GSM9684132 CTCF_CD2_cntrl_rep2 CTCF_CD2_cntrl
- GSM9684133 CTCF_CD2_166_patient_rep1
- GSM9684134 H3K4me1_CD2_cntrl_rep1 H3K4me1_CD2_cntrl
- GSM9684135 H3K4me1_CD2_cntrl_rep2 H3K4me1_CD2_cntrl
- GSM9684136 H3K4me1_CD2_166_patient_rep1
- GSM9684137 H3K27ac_CD2_cntrl_rep1 H3K27ac_CD2_cntrl
- GSM9684138 H3K27ac_CD2_cntrl_rep2 H3K27ac_CD2_cntrl
- GSM9684139 H3K27ac_CD2_166_patient_rep1
- GSM9714908 CD2 iPSC-derived IEO, ATAC-seq, Day 8 CD2 iPSC-derived IEO, A…
- GSM9714909 CD2 iPSC-derived IEO, ATAC-seq, Day 13 CD2 iPSC-derived IEO, A…
- GSE300334 p52:ETS1: a transcriptional complex essential for germinal center formation [ChIP-seq] 15 samples shares essential, formation
- GSE239270 Investigate FOXA2, NKX2-1, CTCF and P300 cistrome and enhancer (H3K27ac and H3k4me1) reprogramming during NEPC transformation by ChIP-seq. 104 samples shares formation
- GSE323311 Human Macrophages Encode Stimulus-Specific Information of Prior Exposures Through Trained Immunity 48 samples shares formation
- GSE264693 Cytokines drive the formation of memory-like NK cell subsets via epigenetic rewiring and transcriptional mechanisms [ATAC-seq] 39 samples shares formation
- GSE325862 BMAL1 regulates circadian rhythms via phase separation–mediated transcriptional hub formation 36 samples shares formation
- GSE330326 NAB2::STAT6 Fusion Proteins Drive Nuclear Condensate Formation and Transcriptional Reprogramming in Solitary Fibrous Tumors 36 samples shares formation
- GSE293201 Ectopic MYC Expression Reprograms Epigenetic Landscapes and Transcription Factor Networks to Drive Differentiation Block and Malignant Transformation in AML [ATAC-seq] 35 samples shares formation
- GSE293474 KMT2D-Mediated H3K4methylation is Essential for GATA1 Transcriptional Activation in Erythropoiesis [ChIP-seq] 24 samples shares essential
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.