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Transcriptomic profiling by RNA-Seq of MCF-7 cells edited by CRISPR/Cas9 in the FASN locus

ABSTRACT: Transcriptomic profiling by RNA-Seq of MCF-7 cells edited by CRISPR/Cas9 in the FASN locus

PROVIDER: PRJNA597467 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR10763405_1.fastq.gz	Fastqsanger.gz
	SRR10763405_2.fastq.gz	Fastqsanger.gz
	SRR10763406_1.fastq.gz	Fastqsanger.gz
	SRR10763406_2.fastq.gz	Fastqsanger.gz

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Similar Datasets

Transcriptomic profiling by RNA-Seq of MCF-7 cells edited by CRISPR/Cas9 in the FASN locus

Project description:We report a preliminary RNA-Seq data of MCF-7 cells edited in the FASN locus using CRISPR/Cas9. MCF-7 cells were edited by CRISPR/Cas9, screened by Surveyor assay, purified by limiting dilutions, validated by sanger sequencing, and characterized by diverse cellular analyses. Then, RNA from edited cells and non-edited controls were processed by TruSeq-RNA-Library-Prep-Kit and sequenced in a illumina equipment. Reads were aligned to hg38 in Galaxy using RNA-Star and transcripts were counted by FeatureCounts.

2019-12-25 | GSE142562 | GEO

DNA-seq (low-coverage WGS) for validation of CRISPR-Cas9-edited mESCs

Project description:Mouse embryonic stem cells (i.e., mESCs; line ESC 129-B13) were genetically modified using CRISPR-Cas9 to mutate the H3f3b locus, in order to carry homozygous lysine-to-alanine substitution of residues K9, K27 or K79. Two control mESC lines carrying knock-out of the H3f3a gene were used as background for the editing. Low-coverage whole-genome sequencing (~0.8/0.9X) was performed to assess the chromosomal integrity of the edited lines. Genomic DNA was extracted from each mutant and control mESC line and sonicated to obtain fragments of ~150-200bp on average. Fragmented DNA (~0.5-1 ug) was used for library preparation using the NEBNext Ultra II DNA library preparation kit (New England Biolabs). Sequencing was performed on a NextSeq500 platform in single-end mode (75bp reads).

2024-09-04 | E-MTAB-12867 | biostudies-arrayexpress

Targeted DNA-seq of Human HepG2 cells following editing with CRISPR/Cas9

Project description:We performed a large-scale genome-wide characterisation of indels generated following editing with CRISPR/Cas9. We used pools of sgRNAs and performed targeted capture and sequencing of the edited regions in HepG2 cells.

2018-12-13 | E-MTAB-7095 | biostudies-arrayexpress

RNA-seq of engineered K562 cell line by CRISPR/Cas9 generation of t(7;12)(q36;p13) chromosomal translocation

Project description:We recreated the t(7;12) translocation in K562 cells by CRISPR/Cas9 to understand its effects on haematopoietic cells, which is of relevance to understand how this cytogenetic abnormalities causes and promotes acute leukaemia in infants. Wild-type K562 were edited by electroporation of ribonucleoprotein complexes consisting of Cas9 enzyme and two guide RNAs targeting patient-specific breakpoint loci. K562 electroporated with Cas9 enzyme only were used as control. Edited K562 harbouring the t(7;12) were single-cell cloned to obtain homogeneous populations (hereby referred to as K562-t(7;12)). We performed RNA sequencing analysis of K562-t(7;12) compared to K562 control to uncover transcriptional changes associated with the translocation.

2022-09-06 | E-MTAB-11851 | biostudies-arrayexpress

NGS data of Nicotiana benthamiana 16c plants after CRISPR/Cas9 gene editing

Project description:Provided data came from a detailed study on Nicotiana benthamiana 16c plants where we use Tobacco Rattle Virus (TRV) as a molecular switch to change the chromatin state of a reporter gene (P35S::GFP) from an actively transcribed to a transcriptionally silenced state. Our approach enables us to interrogate different chromatin states of the same locus with the same set of CRISPR/Cas9 genome editing reagents and systematically describe the effect of chromatin state on the frequency and type of mutations induced at various Cas9 targets in a huge set of independently edited cells.

2022-05-04 | E-MTAB-10256 | biostudies-arrayexpress

Transcriptomic profiling by RNA-Seq of MCF-7 cells heterozygously depleted in the ARID4B locus by the CRISPR/Cas9 System

Project description:The role of ARID4B in breast cancer development has not been completely elucidated. The aim of this study was to investigate the effect of loss of function mutations generated using the CRISPR/Cas9 system in human breast cancer cells. For this, we characterized the proliferation, viability, and migration rates of different clones with insertions and deletions compared to wild-type cells. We report the transcriptomic profile of mutated MCF-7 clones and negative control.

2023-02-04 | GSE224514 | GEO

CRISPR-Cas9 Editing of TLR4 Improves the Outcome of Cardiac Cell Therapy

Project description:We developed and optimized a new electroporation protocol for CRISPR-Cas9 gene editing. This protocol achieved up to 68% success rate, when applied to isolated hMSCs from the heart and epicardial fat of patients with ischemic heart disease. While cell editing resulted lowered TLR4 expression in hMSCs, it did not affect classical markers of hMSCs and proliferation rate. Advanced protein mass spectrometry analysis revealed that edited cells secreted fewer proteins involved in inflammation and in extracellular matrix organization. The immunomodulatory effect of TLR4 editing was apparent in both free and EV-encapsulated proteins. Furthermore, edited cells expressed less NF-ƙB and secreted lower amounts of extracellular vesicles, pro-inflammatory and pro-fibrotic cytokines than unedited hMSCs. Cell therapy with edited and unedited hMSCs improved survival, left ventricular (LV) remodeling, and cardiac function after myocardial infarction (MI) in mice. Postmortem histologic analysis revealed clusters of edited cells that survived in the scar tissue 28 days after MI. Morphometric analysis showed that implantation of edited cells increased the area of myocardial islands in the scar tissue, reduced the occurrence of transmural scar, increased scar thickness, and markedly decreased expansion index, compared with unedited cells or saline.

2023-05-10 | PXD033253 | Pride

DNA-seq (low-coverage WGS) for validation of CRISPR-Cas9-edited mESCs

Project description:DNA-seq (low-coverage WGS) for validation of CRISPR-Cas9-edited mESCs

| PRJEB61022 | ENA

Transcriptome of erythroid cells derived from human CD34+ cells edited at the BCL11A erythroid enahncer or at the HBG1 and HBG2 promoters using CRISPR-Cas9

Project description:BCL11A represses gamma globin expression by binding to the gamma globin gene (HBG1 and HBG2) promoters. Genome editing of the BCL11A erythroid enhancer in the intron 2 of BCL11A gene or the BCL11A binding site at the HBG1/2 promoters disrupts this pathway and leads to gamma globin induction. Transcriptomic profiling of erythroid cells derived from human CD34+ cells edited at either target site using CRISPR-Cas9 revealed broader transcriptome perturbation when edited at the BCL11A erythroid enhancer.

2024-12-10 | GSE264491 | GEO

RNA-seq of human patient-derived xenograft pancreatic cancer Panc185 sphere-derived cells with the ISG15 gene edited using CRISPR-CAS9 against control spheres.

Project description:The goal of the study was to identify genes and pathways that were altered in the absence of the gene Interferon-Stimulated Gene 16 (ISG15) in human pancreatic ductal adenocarcinoma (PDAC) cancer stem cells. Primary adherent cultures established from patient-derived xenograft passaged in mice were established (Panc185). The ISG15 gene was edited using CRISPR-CAS9 technology and 3 commercially available guide RNAs introduced via lentiviral infection. Control cultures were also established using control guide RNAs. Once a polyclonal population was established and ISG15 loss confirmed, cultures were grown as 3D spheres in ultralow attachment plates to achieve a CSC-enriched culture. Following 5 days in culture as spheres, Total RNA was isolated by the guanidine thiocyanate (GTC) method using standard protocols. PolyA+ RNA fraction was processed as in Illumina’s ‘‘TruSeq RNA Sample Preparation v2 Protocol’’. The resulting purified cDNA library was applied to an Illumina flow cell for cluster generation (TruSeq cluster generation kit v5) and sequenced on the Genome Analyzer IIx with SBS TruSeq v5 reagents by following manufacturer’s protocols. RNA-seq data sets were analyzed using the tool Nextpresso.

2020-04-30 | E-MTAB-8984 | biostudies-arrayexpress

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