Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1305499 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:By a robust unbiased ChIP-seq approach, we demonstrated that CRISPR/Cas9 had crRNA-specific off-target binding activities in human genome. However, most of those binding off-targets could not be efficiently cleaved both in vivo and in vitro which suggested the cleavage off-target activity of CRISPR/Cas9 in human genome is very limited. We provided a valuable tool to further investigate the molecular mechanism of CRISPR/Cas9 and to optimize its in vivo targeting sgRNA binding sites were identified with ChipSeq by using GFP antibody (there are 2 replicates for egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in Hek293T cells, one egfa-t1 sgRNA,emx1 sgRNA and control without sgRNA in HeLaS3 cells)
2014-06-18 | E-GEOD-58511 | biostudies-arrayexpress
Project description:To examine the genome-wide gene regulation due to the common seed sequence of the members of miR-302/3272/3273/520 family miRNAs and dsEcad640, we performed microarray profiling of gene expression by the transfection of chemically synthesized dsEcad640, miR-302a,miR-372, miR-373, miR-520c,and miR-520f duplexes into PC-3 cells. Chemically synthesized dsEcad640, miR-302a, miR-372, miR-373, miR-520c,and miR-520f duplexes were transfected into PC-3 cells. At 24 hours after transfection,the total RNA was extracted using the RNeasy Mini Kit (Qiagen). As a control, mock transfected cells treated with transfection reagent without siRNA and miRNA were used.Transfection was carried out four times independently, and the RNA quality was examined using Bioanalyzer (Agilent). Mixed RNA samples (150 ng total) of four experiments were used for the microarray analysis. After cDNA was synthesized with the Agilent One Color Spike Mix Kit, cRNA was prepared using the Quick Amp Labeling Kit (Agilent), labeled with Cy-3, and purified with the RNeasy Mini Kit (Qiagen).The cRNA was hybridized against the Agilent Whole Human Genome Microarray (4 × 44 K multipack format) at 65°C for 17 hours, then washed with Gene Expression Wash Buffer 1 and Wash Buffer 2 (Agilent) in 0.005% Triton X-102. The microarray slide was scanned using the DNA Microarray Scanner (Agilent) and quantified using Feature Extraction Software (Agilent).
2011-10-13 | E-GEOD-32999 | biostudies-arrayexpress
Project description:Human cancer cell lines indicated in the file names, with stably overexpressed Cas9 nuclease, were transfected with (C) control sgRNA or (P) TP53-specific sgRNA, (K) KRAS-specific sgRNA or (M) CMYC-specific sgRNA. Each experiment was done by transfection of sgRNA pair - control (C) or causing a NHEJ-mediated knock-out of the target genes (P, K or M). Samples for proteomics were collected 48h post sgRNA transfection without selection, in three biological replicates each (indicated with numbers 1-3). In cell lines with three activated oncogenes, three separate oncogene-targeting transfections were carried out.
2024-10-17 | PXD037398 | Pride
Project description:Sequencing was performed to assess the ability of Nanopore direct cDNA and native RNA sequencing to characterise human transcriptomes. Total RNA was extracted from either HAP1 or HEK293 cells, and the polyA+ fraction isolated using oligodT dynabeads. Libraries were prepared using Oxford Nanopore Technologies (ONT) kits according to manufacturers instructions. Samples were then sequenced on ONT R9.4 flow cells to generate fast5 raw reads in the ONT MinKNOW software. Fast5 reads were then base-called using the ONT Albacore software to generate Fastq reads.
2019-03-14 | E-MTAB-7778 | biostudies-arrayexpress
Project description:Sequencing of Arabidopsis ECT 234 triple mutant by ONT DRS
| PRJEB85859 | ENA
Project description:Sequencing of Arabidopsis cpsf30-yth and oxt6 by ONT DRS
| PRJEB85860 | ENA
Project description:A dataset containing whole blood samples used as quality control digestion replicates. Samples were automatically processed on i7 automated liquid handling system (Beckman Coulter). Briefly, proteins were extracted and denatured with a buffer composed of TFE (2,2,2-Trifluoroethanol), DTT and ammonium bicarbonate prior being alkylated, reduced and digested with trypsin. Obtained tryptic peptides were desalted by SPE (Solid Phase Extraction) on C18 stationary phase. Pooled whole blood and plasma samples were used as digestion control replicates (DRs). 5 DRs were added to each digestion plate to be digested with the cohort data. DIA-MS analysis was performed on an Orbitrap Exploris 480 (Thermo Fisher) instrument using MS-MS settings with tryptic peptides separated by EVOSEP One LC System (Evosep) over a 60-minute gradient. During LC-MS acquisition, the 5 DRs are run at the beginning of each batch.
| MSV000095743 | MassIVE
Project description:A dataset containing native plasma samples used as quality control digestion replicates. Samples were automatically processed on i7 automated liquid handling system (Beckman Coulter). Briefly, proteins were extracted and denatured with a buffer composed of TFE (2,2,2-Trifluoroethanol), DTT and ammonium bicarbonate prior being alkylated, reduced and digested with trypsin. Obtained tryptic peptides were desalted by SPE (Solid Phase Extraction) on C18 stationary phase. Pooled whole blood and plasma samples were used as digestion control replicates (DRs). 5 DRs were added to each digestion plate to be digested with the cohort data. DIA-MS analysis was performed on an Orbitrap Exploris 480 (Thermo Fisher) instrument using MS-MS settings with tryptic peptides separated by EVOSEP One LC System (Evosep) over a 60-minute gradient. During LC-MS acquisition, the 5 DRs are run at the beginning of each batch.
| MSV000095744 | MassIVE
Project description:Estrogen Receptor a (ERa) bindning to DNA was profiled by ChIP-seq in MCF-7 and T47D cells transduced with either control sgRNA, or sgRNA targeting a specific enhancer region (enhancer588). ERa in MCF-7 and T47D control or enhancer588-targeted cells
2015-12-14 | E-GEOD-75779 | biostudies-arrayexpress
Project description:HNRNPC and m6A RNA methylation control oncogenic transcription and metabolism in T-cell leukemia- ONT DRS study
| PRJNA1222816 | ENA