Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

High Throughput, Efficacious Gene Editing & Genome Surveillance in Chinese Hamster Ovary Cells

ABSTRACT: High Throughput, Efficacious Gene Editing & Genome Surveillance in Chinese Hamster Ovary Cells

PROVIDER: PRJNA555577 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR9717320_1.fastq.gz	Fastqsanger.gz
	SRR9717320_2.fastq.gz	Fastqsanger.gz
	SRR9717330_1.fastq.gz	Fastqsanger.gz
	SRR9717330_2.fastq.gz	Fastqsanger.gz
	SRR9717321_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 44

Similar Datasets

High Throughput, Efficacious Gene Editing & Genome Surveillance in Chinese Hamster Ovary Cells

Project description:Purpose: Chinese hamster ovary (CHO) cells are a common tool utilized in bioproduction and directed genome engineering of CHO cells is of great interest to enhance recombinant cell lines. Until recently, this focus has been challenged by a lack of efficacious, high throughput, and low-cost gene editing modalities and screening methods. In this work, we demonstrate an improved method for gene editing in CHO cells using CRISPR RNPs and characterize the endpoints of Cas9 and ZFN mediated genetic engineering. Methods: Amplicons were first assayed for quality using an Invitrogen Quant-iT dsDNA (Thermo, Cat Q33120) assay and gel electrophoresis to determine DNA concentration and DNA quality. Samples were then used for Sanger sequence based decomposition or processed downstream using NGS. For NGS, libraries were generated using the Illumina TruSeq Nano DNA kit (Illumina, Cat: 20015964). The libraries were sequenced using the Illumina MiSeq platform, with read length of 2x150bp. 4.5Gb of sequencing data was generated per DNA sample. Results: There was a tendency for decomposition to underestimate editing as compared to NGS as the indel size became larger. Despite these results, sequence decomposition was able to reproduce next-generation data in the context of gene editing efficiency across a short amplicon. Conclusions: We took advantage of the differential Indel spectrums induced by both ZFN and CRISPR to validate metrics for assess gene editing and show how deconvolution-based methods, can be utilized in the context of cell line development.

2019-07-20 | GSE134559 | GEO

High throughput, efficacious gene editing & genome surveillance in Chinese hamster ovary cells.

Project description:Chinese hamster ovary (CHO) cells are a common tool utilized in bioproduction and directed genome engineering of CHO cells is of great interest to enhance recombinant cell lines. Until recently, this focus has been challenged by a lack of efficacious, high throughput, and low-cost gene editing modalities and screening methods. In this work, we demonstrate an improved method for gene editing in CHO cells using CRISPR RNPs and characterize the endpoints of Cas9 and ZFN mediated genetic engineering. Furthermore, we validate sequence decomposition as a cost effective, rapid, and accurate method for assessing mutants and eliminating non-clonal CHO populations using only capillary sequencing.

| S-EPMC6922373 | biostudies-literature

A Chinese hamster transcription start site atlas that enables targeted editing of CHO cells

Project description:Gene expression is a key determinant of phenotypes that made Chinese Hamster Ovary (CHO) cells, with their human-like glycosylation profile and high protein titers, one of the most widely used cells for the production of therapeutic proteins and biopharmaceuticals. Engineering CHO gene expression thus holds a key to improve drug quality and cost effective production. However, the success of engineering gene expression or ectopic activation of silent genes to optimize desired pathways requires accurate annotation of the underlying regulatory elements and the transcription start site (TSS). Unfortunately, to date, most TSSs of CHO-expressed genes and the ~50% of hamster genes that are silent in CHO were computationally predicted and are frequently inaccurate. To oust this hurdle, we report revised TSSs annotations for 15,308 Chinese Hamster genes and 4,145 non-coding RNAs based on experimental data from CHO K1 cells and 10 hamster tissues. In the example of the glycosyltransferase gene Mgat3, we further demonstrate how accurate annotations readily facilitate activating silent genes by CRISPRa. Together, we envision that our annotation and data from the Chinese Hamster will provide a rich resource for the CHO community, improve genome engineering efforts and additionally aid comparative and evolutionary studies.

2020-10-06 | GSE159044 | GEO

Chinese Hamster Ovary cell proteins co-purified with recombinant HIV-1 envelopes, part 2

Project description:Chinese Hamster Ovary (CHO) cells are frequently used to produce recombinant HIV envelope protein gp120. In this study, we characterized the CHO proteins that become co-purified with gp120 when lectin affinity chromatography is used. Many of co-purified CHO proteins identified were extracellular matrix components. We verified a method for separating gp120 from these CHO proteins with anion exchange chromatography, and assessed the biochemical activity of gp120 preparations with and without co-purified CHO proteins.

2017-09-04 | PXD006061 | Pride

Chinese Hamster Ovary cell proteins co-purified with recombinant HIV-1 envelopes, part 3

2017-09-04 | PXD006062 | Pride

Chinese Hamster Ovary cell proteins co-purified with recombinant HIV-1 envelopes, part 4

2017-09-04 | PXD006063 | Pride

Chinese Hamster Ovary cell proteins co-purified with recombinant HIV-1 envelopes, part 1

2017-09-04 | PXD006060 | Pride

Chinese Hamster Ovary cell proteins co-purified with recombinant HIV-1 envelopes, part 2

2018-01-25 | MSV000081975 | MassIVE

Chinese Hamster Ovary cell proteins co-purified with recombinant HIV-1 envelopes, part 3

2018-02-14 | MSV000082065 | MassIVE

Chinese Hamster Ovary cell proteins co-purified with recombinant HIV-1 envelopes, part 1