Similar Datasets
Project description:IDLV capture for gRNA off-target analysis
| PRJNA552824 | ENA
Project description:RNASeq of Arg2 gRNA or scrambled gRNA CRISPR'd Tregs
| PRJNA588065 | ENA
Project description:RNA-Seq after Cas9-gRNA transfection with different length gRNAs we performed PolyA Selection and RNA-Seq on cells transfected with dCas9-VPR and a gRNA of each length (20nt, 16nt, or 14nt) targeting ACTC1, MIAT, or HBG1/2
2015-07-15 | E-GEOD-70694 | biostudies-arrayexpress
Project description:Transcriptional profiling of zebrafish embryos comparing wild type untreated embryos with embryos injected with morpholino of zf-grna. This assay is used for the determination of expression profiling at 22 hpf under GRN-A deficiency. Two-condition experiment: wild type vs. MO-grnA treated cells. 3 biological replicates: each group contains 200 embryos.
2013-03-28 | E-GEOD-28318 | biostudies-arrayexpress
Project description:Transcriptional profiling of zebrafish embryo comparing wild type untreated embryos with embryos injected with morpholino of zf-grna. This assay is used for determination of expression profiling of trunk muscle at 16, 24, 48, 72 hpf under GRN-A deficiency. Two-condition experiment, wild type vs. MO-grnA treated cells. Biological replicates: each group contains 200 embryos.
2013-06-01 | E-GEOD-38441 | biostudies-arrayexpress
Project description:The genome is organized via CTCF/cohesin binding sites, which partition chromosomes into 1-5Mb topologically associated domains (TADs), and further into smaller contact sub-domains within TADs (sub-TADs; 40-1000kb). Here we examined in vivo an ~80kb sub-TAD, containing the mouse α-globin gene cluster, lying within a ~1Mb TAD. We find that the sub-TAD is flanked by predominantly convergent CTCF/cohesin sites which are ubiquitously bound by CTCF but only interact during erythropoiesis, defining a self-interacting erythroid compartment. Whereas the α-globin regulatory elements normally act solely on promoters downstream of the enhancers, removal of a conserved upstream CTCF/cohesin boundary extends the sub-TAD to the adjacent upstream CTCF/cohesin binding site. The α-globin enhancers now interact with the flanking chromatin, upregulating expression of genes within this extended sub-TAD. Rather than acting solely as a barrier to chromatin modification, CTCF/cohesin boundaries in this sub-TAD regulate both directionality and specificity of enhancer interactions with surrounding promoters.
2017-06-14 | GSE97867 | GEO
Project description:Analyses of mutations within the a-globin cluster which downregulate a-globin expression and cause a-thalassaemia provide the basis for genetic counselling and pre-natal diagnosis of this common form of anemia. Understanding the mechanisms by which such mutations cause a-thalassemia has established many of the principles by which mammalian genes are regulated and how this goes awry in human genetic disease. ATAC-Seq and NG Capture-C data from an individual (NSE) with a unique a-globin genotype involving a deletion of the main alpha-globin enhancer on one allele and the --/SEA mutation on the other help to address how the human a-globin cluster is normally regulated.
2022-05-06 | GSE149793 | GEO
Project description:Mammalian genomes are subdivided into large (50-2000 kb) regions of chromatin referred to as Topologically Associating Domains (TADs or sub-TADs). Chromatin within an individual TAD contacts itself more frequently than with regions in surrounding TADs thereby directing enhancer-promoter interactions. In many cases, the borders of TADs are defined by convergently orientated boundary elements associated with CCCTC-binding factor (CTCF), which stabilises the cohesin complex on chromatin and prevents its translocation. This delimits chromatin loop extrusion which is thought to underlie the formation of TADs. However, not all CTCF-bound sites act as boundaries and, importantly, not all TADs are flanked by convergent CTCF sites. Here, we examined the CTCF binding sites within a ~70 kb sub-TAD containing the duplicated mouse α-like globin genes and their five enhancers (5’-R1-R2-R3-Rm-R4-α1-α2-3’). The 5’ border of this sub-TAD is defined by a pair of CTCF sites. Surprisingly, we show that deletion of the CTCF binding sites within and downstream of the α-globin locus leaves the sub-TAD largely intact. The predominant 3’ border of the sub-TAD is defined by a steep reduction in contacts: this corresponds to the transcribed α2-globin gene rather than the CTCF sites at the 3’-end of the sub-TAD. Of interest, the almost identical α1- and α2-globin genes interact differently with the enhancers, resulting in preferential expression of the proximal α1-globin gene which behaves as a partial boundary between the enhancers and the distal α2-globin gene. Together, these observations provide direct evidence that actively transcribed genes can behave as boundary elements.
2022-06-01 | GSE153208 | GEO
Project description:We confirmed Tyrosinase genome insertions or deletions of the three Tg mice by deep sequencing using MiSeq. These mice generated gene editing mice by using Tol2 transposon to introduce tyrosinase guide RNA (gRNA) into fertilized eggs obtained by crossing LSL (loxP-stop-loxP)-Cas9 mice with CAG-CreER mice.
2023-02-27 | GSE225711 | GEO
Project description:The combination of single-cell RNA sequencing with CRISPR inhibition/activation provides a high-throughput approach to simultaneously study the effects of hundreds if not thousands of gene perturbations in a single experiment. One recent development in CRISPR-based single-cell techniques introduces a feature barcoding technology which allows for the simultaneous capture of mRNA and gRNA from the same cell. This is achieved by introducing a capture sequence, whose complement can be incorporated into each gRNA, and which can be used to amplify these features prior to sequencing. However, with the technology in its infancy, there is little information available on how such experimental parameters can be optimised. To overcome this, we varied the capture sequence, capture sequence position and gRNA backbone to identify an optimal gRNA scaffold for CRISPR-activation gene perturbation studies. We provide a report on our screening approach along with our observations and recommendations for future use.
2021-01-08 | GSE164393 | GEO