Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system (BeadChip)
Expression microarray · mouse · 16 samples
- What it is
- Expression microarrayGene activity read on a chip (the older technology that RNA-seq replaced).
- Organism
- Mus musculus (mouse)
- Samples
- 16 samples: 14 distinct titles, 2 of them repeatedGroups are read from the sample names, not from the paper. Check the list below.
- Data you can get
- A processed expression table (series matrix) and the array files, from NCBI.
Direct links to NCBI, 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.
Whole study · RAW.tar
Everything the authors deposited as one archive (GSE64057_RAW.tar), including the raw array or instrument files. Can be large; the picker in step 2 takes just the samples you need.
What the files usually look like: For arrays the series matrix is normally the normalised expression table you want; the raw array files (CEL and similar) are in the RAW.tar.
Also filed as BioProject PRJNA269981. Searching any of these in the dataset finder brings you back here.
How we read this: Read from 16 sample titles: 14 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.
- GSM1563553 Nm dCas9-BAT + sgTbx3-DE
- GSM1563554 Nm dCas9-BAT + sgTbx3-PP
- GSM1563555 Nm dCas9-LSD1 + sgCtrl 1
- GSM1563556 Nm dCas9-LSD1 + sgTbx3-DE
- GSM1563557 Nm dCas9-LSD1 + sgTbx3-PP
- GSM1563558 Nm dCas9-KRAB + sgCtrl 1
- GSM1563559 Nm dCas9-KRAB + sgTbx3-DE
- GSM1563560 Nm dCas9-KRAB + sgTbx3-PP
- GSM1563561 Nm dCas9-KRAB + sgOct4-PP
- GSM1563562 Nm dCas9-KRAB + sgOct4-DE
- GSM1563563 Nm dCas9-KRAB + sgCtrl 2
- GSM1563564 Nm dCas9-BAT + sgOct4-PP
- GSM1563565 Nm dCas9-BAT + sgOct4-DE
- GSM1563566 Nm dCas9-LSD1 + sgOct4-PP
- GSM1563567 Nm dCas9-LSD1 + sgOct4-DE
- GSM1563568 Nm dCas9-LSD1 + sgCtrl 2
- GSE64059 Rapid functional annotation of native enhancers in embryonic stem cells with a Neisseria meningitidis CRISPR-Cas9 system 17 samples shares meningitidis, crispr-cas9, annotation, enhancers, embryonic, neisseria, native
- GSE240327 A set of Sox2-dependent OSN enhancers mediates the immediate response to neural induction and default neural differentiation of embryonic stem cells 40 samples shares enhancers, embryonic
- GSE24164 ChIP-Seq of chromatin marks at distal enhancers in Mouse Embryonic Stem Cells and adult tissues. 25 samples shares enhancers, embryonic
- GSE23907 Histone H3K27ac separates active from poised enhancers and predicts developmental state (gene expression data) 8 samples shares enhancers
- GSE339045 Mega-Enhancers Compartmentalize Transcriptionally Active Long Genes in the Brain 193 samples shares enhancers
- GSE217970 Mapping putative enhancers in mouse oocyte and early embryo reveals TCF3/12 as key folliculogenesis regulators 164 samples shares enhancers
- GSE290849 Acute intervention reveals critical roles of BAF, KMT2D and p300 in MyoD binding on enhancers 143 samples shares enhancers
- GSE294389 BMAL1 and YAP cooperate to hijack enhancers and promote inflammation in the aged epidermis 131 samples shares enhancers
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.