R-loop editing by DNA cytosine deaminase APOBEC3B determines activities of estrogen receptor enhancers.
ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 84 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
- 84 samples: 24 conditions, mostly in triplicateGroups 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 GSE193234_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 PRJNA795957 and SRA study SRP354563. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 69 samples.
How we read this: 24 replicated groups read from 84 sample titles; they account for 69 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.
- GSM5777014 Input
- GSM5777015 ssDRIP-seq
- GSM5777016 A_minus_1 A_minus
- GSM5777017 A_minus_2 A_minus
- GSM5777018 A_minus_3 A_minus
- GSM5777019 A_plus_1 A_plus
- GSM5777020 A_plus_2 A_plus
- GSM5777021 A_plus_3 A_plus
- GSM5777022 A_plus_4 A_plus
- GSM5777023 A_plus_5 A_plus
- GSM5777024 M_plus_1 M_plus
- GSM5777025 M_plus_2 M_plus
- GSM5777026 M_plus_3 M_plus
- GSM5777027 Parental
- GSM5777028 input_siNT_DMSO_rep1 input_siNT_DMSO
- GSM5777029 input_siNT_DMSO_rep2 input_siNT_DMSO
- GSM5777030 input_siNT_E2_rep1 input_siNT_E2
- GSM5777031 input_siNT_E2_rep2 input_siNT_E2
- GSM5777032 A3B_SPIseq_siNT_DMSO_rep1 A3B_SPIseq_siNT_DMSO
- GSM5777033 A3B_SPIseq_siNT_DMSO_rep2 A3B_SPIseq_siNT_DMSO
- GSM5777034 A3B_SPIseq_siNT_E2_rep1 A3B_SPIseq_siNT_E2
- GSM5777035 A3B_SPIseq_siNT_E2_rep2 A3B_SPIseq_siNT_E2
- GSM5777036 ssDRIP_input_siA3B_DMSO_rep1 ssDRIP_input_siA3B_DMSO
- GSM5777037 ssDRIP_input_siA3B_DMSO_rep2 ssDRIP_input_siA3B_DMSO
- GSM5777038 ssDRIP_input_siA3B_DMSO_rep3 ssDRIP_input_siA3B_DMSO
- GSM5777039 ssDRIP_input_siA3B_E2_rep1 ssDRIP_input_siA3B_E2
- GSM5777040 ssDRIP_input_siA3B_E2_rep2 ssDRIP_input_siA3B_E2
- GSM5777041 ssDRIP_input_siA3B_E2_rep3 ssDRIP_input_siA3B_E2
- GSM5777042 ssDRIP_input_siNT_DMSO_rep1 ssDRIP_input_siNT_DMSO
- GSM5777043 ssDRIP_input_siNT_DMSO_rep2 ssDRIP_input_siNT_DMSO
- GSM5777044 ssDRIP_input_siNT_DMSO_rep3 ssDRIP_input_siNT_DMSO
- GSM5777045 ssDRIP_input_siNT_E2_rep1 ssDRIP_input_siNT_E2
- GSM5777046 ssDRIP_input_siNT_E2_rep2 ssDRIP_input_siNT_E2
- GSM5777047 ssDRIP_input_siNT_E2_rep3 ssDRIP_input_siNT_E2
- GSM5777048 ssDRIP_siA3B_DMSO_rep1 ssDRIP_siA3B_DMSO
- GSM5777049 ssDRIP_siA3B_DMSO_rep2 ssDRIP_siA3B_DMSO
- GSM5777050 ssDRIP_siA3B_DMSO_rep3 ssDRIP_siA3B_DMSO
- GSM5777051 ssDRIP_siA3B_E2_rep1 ssDRIP_siA3B_E2
- GSM5777052 ssDRIP_siA3B_E2_rep2 ssDRIP_siA3B_E2
- GSM5777053 ssDRIP_siA3B_E2_rep3 ssDRIP_siA3B_E2
+ 44 more — browse all 84 samples with per-sample file links →
- GSE320139 The timing of antenatal glucocorticoids determines the receptor sensitivity in preterm infants 47 samples shares determines, receptor
- GSE254194 Transcriptome-wide identification of 5-methylcytosine by deaminase and reader protein-assisted sequencing 20 samples shares deaminase, cytosine
- GSE44386 NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs 14 samples shares determines, cytosine
- GSE261124 Physical Phase Transition of Mineralocorticoid Receptors Determines Preservation Quality of Donor Hearts for Transplantation 9 samples shares determines, receptor
- GSE44384 NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [RNA-seq] 8 samples shares determines, cytosine
- GSE44385 NSun2-mediated cytosine-5 methylation in Vault non-coding RNA determines its processing into small RNAs [iCLIP] 6 samples shares determines, cytosine
- GSE245125 Depletion of P2X4 receptors alleviates prostate cancer bone metastasis through reducing cancer cell invasiveness and enhancing cell adhesion activities 5 samples shares activities, receptor
- GSE290774 Cancer cells subvert ZNF93 to escape surveillance by L1 epigenetic sentinels and control APOBEC3B 56 samples shares apobec3b
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.