Genome-wide binding of ZFPOBI1/TRIM28 and linked H3K9me3 dynamics
ChIP-seq / ATAC-seq (genome binding and open chromatin) · mouse · 20 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
- Mus musculus (mouse)
- Samples
- 20 samples: 6 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 GSE326899_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 PRJNA1447576 and SRA study SRP689008. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 6 replicated groups read from 20 sample titles; they account for 18 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.
- GSM9643183 vector control INPUT
- GSM9643184 vector control HA-ChIP replicate 1 vector control HA-ChIP
- GSM9643185 vector control HA-ChIP replicate 2 vector control HA-ChIP
- GSM9643186 vector control HA-ChIP replicate 3 vector control HA-ChIP
- GSM9643187 vector control TRIM28-ChIP replicate 1 vector control TRIM28-C…
- GSM9643188 vector control TRIM28-ChIP replicate 2 vector control TRIM28-C…
- GSM9643189 vector control TRIM28-ChIP replicate 3 vector control TRIM28-C…
- GSM9643190 vector control H3K9me3_ChIP replicate 1 vector control H3K9me3_…
- GSM9643191 vector control H3K9me3_ChIP replicate 2 vector control H3K9me3_…
- GSM9643192 vector control H3K9me3_ChIP replicate 3 vector control H3K9me3_…
- GSM9643193 HA-ZFPOBI1 OE INPUT
- GSM9643194 HA-ZFPOBI1 OE HA-ChIP replicate 1 HA-ZFPOBI1 OE HA-ChIP
- GSM9643195 HA-ZFPOBI1 OE HA-ChIP replicate 2 HA-ZFPOBI1 OE HA-ChIP
- GSM9643196 HA-ZFPOBI1 OE HA-ChIP replicate 3 HA-ZFPOBI1 OE HA-ChIP
- GSM9643197 HA-ZFPOBI1 OE TRIM28-ChIP replicate 1 HA-ZFPOBI1 OE TRIM28-Ch…
- GSM9643198 HA-ZFPOBI1 OE TRIM28-ChIP replicate 2 HA-ZFPOBI1 OE TRIM28-Ch…
- GSM9643199 HA-ZFPOBI1 OE TRIM28-ChIP replicate 3 HA-ZFPOBI1 OE TRIM28-Ch…
- GSM9643200 HA-ZFPOBI1 OE H3K9me3_ChIP replicate 1 HA-ZFPOBI1 OE H3K9me3_C…
- GSM9643201 HA-ZFPOBI1 OE H3K9me3_ChIP replicate 2 HA-ZFPOBI1 OE H3K9me3_C…
- GSM9643202 HA-ZFPOBI1 OE H3K9me3_ChIP replicate 3 HA-ZFPOBI1 OE H3K9me3_C…
- GSE263249 Genome-wide distribution of H3K9me3, RNA polymerase II, Rloop, DDX55 and HA-tagged DDX55 in WT and DDX55 knockout CD4 naive T cells 23 samples shares h3k9me3, genome-wide
- GSE232398 NKAPL binding sites in mouse testis and the genome-wide occupancy of the SOX30/HDAC3 protein complex and RNA Pol II in the absence of NKAPL 20 samples shares genome-wide, binding
- GSE230527 Genome-wide profiling of Kdm2a binding and H3K36me2 of hypoxia-cultured B cells derived from miR-155-sufficient and -deficient mice [ChIP-seq] 18 samples shares genome-wide, binding
- GSE237640 Identification of the genome-wide binding sites of OCT2 in Reg-1fl/fl- and Reg-1ΔNK-NK cells. [ChIP-Seq] 12 samples shares genome-wide, binding
- GSE261197 Decoding genome-wide DNA binding sites for AR and ERRα in mouse primary hepatocytes 10 samples shares genome-wide, binding
- GSE231845 The H3K9me3 heterochromatin integrity and function are sustained by H3K9me3 methyltransferases-HP1 dependencies [ChIP-Seq] 216 samples shares h3k9me3
- GSE273948 Nuclear polysaccharides maintain H3K9me3-heterochromatin and genomic stability 56 samples shares h3k9me3
- GSE304113 Establishment of sex-specific liver transcriptomes and H3K9me3 profiles during sexual maturity: the impact of maternal obesity [ChIP-seq] 36 samples shares h3k9me3
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.