ChAHP and ChAHP2 control diverse retrotransposons by complementary activities [RNA-seq]
RNA-seq (gene expression) · mouse · 18 samples
- What it is
- RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
- Organism
- Mus musculus (mouse)
- Samples
- 18 samples: 5 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.
- Paper
- ChAHP2 and ChAHP control diverse retrotransposons by complementary activitiesGenes & development · 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 GSE253067_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.
Also filed as BioProject PRJNA1063745 and SRA study SRP483246. Searching any of these in the dataset finder brings you back here.
Supports a between-group comparison across 18 samples.
How we read this: 5 replicated groups read from 18 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.
- GSM8013156 Total RNAseq in untreated wt mES cells, replicate 1 Total RNAseq in untreat…
- GSM8013157 Total RNAseq in untreated wt mES cells, replicate 2 Total RNAseq in untreat…
- GSM8013158 Total RNAseq in untreated wt mES cells, replicate 3 Total RNAseq in untreat…
- GSM8013159 Total RNAseq after ADNP depletion in wt mES cells, replicate 1 Total RNAseq after ADNP…
- GSM8013160 Total RNAseq after ADNP depletion in wt mES cells, replicate 2 Total RNAseq after ADNP…
- GSM8013161 Total RNAseq after ADNP depletion in wt mES cells, replicate 3 Total RNAseq after ADNP…
- GSM8013162 Total RNAseq in untreated ADNP2 KO mES cells, replicate 1 Total RNAseq in untreat…
- GSM8013163 Total RNAseq after ADNP2 depletion ADNP2 KO mES cells, replicate 1 Total RNAseq after ADNP…
- GSM8013164 Total RNAseq in untreated ADNP2 KO mES cells, replicate 2 Total RNAseq in untreat…
- GSM8013165 Total RNAseq in untreated ADNP2 KO mES cells, replicate 3 Total RNAseq in untreat…
- GSM8013166 Total RNAseq after ADNP2 depletion ADNP2 KO mES cells, replicate 2 Total RNAseq after ADNP…
- GSM8013167 Total RNAseq after ADNP2 depletion ADNP2 KO mES cells, replicate 3 Total RNAseq after ADNP…
- GSM8271782 Total RNAseq in untreated wt mES cells, replicate 1 Total RNAseq in untreat…
- GSM8271783 Total RNAseq in untreated wt mES cells, replicate 2 Total RNAseq in untreat…
- GSM8271784 Total RNAseq in untreated wt mES cells, replicate 3 Total RNAseq in untreat…
- GSM8271785 Total RNAseq after SETDB1 depletion in wt mES cells, replicate 1 Total RNAseq after SETD…
- GSM8271786 Total RNAseq after SETDB1 depletion in wt mES cells, replicate 2 Total RNAseq after SETD…
- GSM8271787 Total RNAseq after SETDB1 depletion in wt mES cells, replicate 3 Total RNAseq after SETD…
- GSE253069 ChAHP and ChAHP2 control diverse retrotransposons by complementary activities 69 samples shares chahp2, retrotransposons, complementary, activities, control, diverse, chahp
- GSE253066 ChAHP and ChAHP2 control diverse retrotransposons by complementary activities [ChIP-seq] 48 samples shares chahp2, retrotransposons, complementary, activities, control, diverse, chahp
- GSE253065 ChAHP and ChAHP2 control diverse retrotransposons by complementary activities [ATAC-seq] 3 samples shares chahp2, retrotransposons, complementary, activities, control, diverse, chahp
- GSE297833 ChAHP Silences SINE Retrotransposons by Inhibiting TFIIIB Recruitment [RNA-seq] 54 samples shares retrotransposons, rna-seq, chahp
- GSE222745 Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [scRNA-Seq] 422 samples shares activities, rna-seq
- GSE247082 Lysosomal catabolic activity governs the exit of the murine totipotent 2-cell state by silencing early-embryonic retrotransposons [RNA-seq] 30 samples shares retrotransposons, rna-seq
- GSE222738 Enhanced activities of OCT4 and SOX2 facilitates epigenetic reprogramming by modulating cell cycle [RNA-Seq] 12 samples shares activities, rna-seq
- GSE95519 Conserved roles for murine mDUX and human DUX4 in activating cleavage stage genes and MERVL/HERVL retrotransposons [RNA-Seq Mouse siRNA] 8 samples shares retrotransposons, rna-seq
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.