Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

RNA-seq of in Kruppel-like factor 6 Knockout Bovine Mammary Epithelial Cells

ABSTRACT: In our exprement, the kruppel-like factors 6 (KLF6) gene was completely knocked out in BMECs using CRISPR/Cas9.Total RNA was extracted using the TRIzol reagent from KLF6-KO and wild type BMECs. The quality of RNA was assessed by the Agilent 2100 (Agilent, USA). The samples with a minimum RIN value of 7.0 were used for RNA-seq.RNA-seq helps to analyze the changes of functional gene expression levels and metabolic pathway in BMECs after KLF6 gene knockout.

ORGANISM(S): Bos taurus

PROVIDER: GSE165990 | GEO | 2021/02/28

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Transcriptomic profiling and analyses of murine prostate orthografts

Project description:RNA was extracted from the frozen prostate tumours or tissues of P1 prostate tumours (n=3), CP1 prostate tumours (n=3) and CP2 prostate tumours (n=4). RNA quality of RNA extracted was evaluated by RNA integrity number (RIN>7.3), calculated using an Agilent 2100 Bioanalyzer (Agilent Technologies) with the Agilent RNA 6000 Nano Kit.

2022-08-20 | GSE136084 | GEO

Role of KLF6 in shaping macrophage inflammatory response

Project description:Kruppel-like transcription factor 6 (KLF6) is a member of zinc-finger family transcription factors that regulate critical cellular processes including development, differentiation, proliferation, and programmed cell death. Alterations in KLF6 expression or function has been associated with the pathogenesis of numerous human ailments, including inflammatory bowel diseases, cancer, hepatic steatosis, and hepatic fibrosis.

2021-01-06 | GSE136476 | GEO

Loss of proximal tubular Kruppel-like factor 6 (KLF6) is protective against AKI and CKD

Project description:Loss of proximal tubular Kruppel-like factor 6 (KLF6) is protective against AKI and CKD

| PRJNA633101 | ENA

Loss of proximal tubular Kruppel-like factor 6 (KLF6) is protective against AKI and CKD

Project description:Altered cellular metabolism in kidney proximal tubule (PT) cells plays a critical role in the development and progression of acute kidney injury (AKI). The transcription factor Krüppel-like factor 6 (KLF6) is rapidly and robustly induced in the PT after AKI, suggesting an early-inducible injury response gene. PT-specific Klf6 knockdown (Klf6PTKO) are protected from AKI and resulting fibrosis in mice. Combined RNA-sequencing and ChIP-sequencing demonstrated preserved expression of genes encoding branched chain amino acid (BCAA) catabolic enzymes in Klf6PTKO mice, with several of the genes also having KLF6 binding sites close to their transcription start sites. Conversely, inducible KLF6 overexpression suppressed expression of BCAA genes and exacerbated kidney injury and fibrosis in mice. Injured kidney cells could not respond to the BCAA catabolic activator BT2, and injured cells overexpressing KLF6 were less able to utilize BCAA. Thus, targeting KLF6-mediated suppression of BCAA catabolism may serve as key therapeutic target in AKI and kidney fibrosis.

2021-05-18 | GSE150656 | GEO

EEF1D RNAi in Bovine mammary epithelial cell

Project description:To further investigate the transcriptome profiles of EEF1D knocked-down and control BMECs, total RNA from the knocked-down BMECs treated with EEF1D-1357 or EEF1D-1893 shRNA, and the BMECs treated without shRNA, was extracted and purified, reversely transcribed into cDNA, and synthesized into cRNAs labeled with Cy3 using a Quick Amp Labeling Kit (Agilent). Afterwards, the labeled cRNAs (1.65 μg) were hybridized to a piece of Agilent Bovine Gene Expression 4×44K Chip using a Gene Expression Hybridization Kit (Agilent).

2020-11-25 | GSE162088 | GEO

Gene expression signatures for miR-26a over-expression and negative control in hela cells

Project description:To further development of our gene expression approach to microRNA-26a over-expression, we have employed whole mRNA microarray expression profiling as a discovery platform. Hela cells at 70–80% confluence in 6-well plates were transfected using Lipofectamine 2000 (Invitrogen). Negative control mimics or miR-26a mimics (100nM) were transfected in each well. Cell extracts were prepared 48 h after transfection, total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).

2016-08-17 | GSE85684 | GEO

MicroRNA profiling of Acute Lymphoblastic Leukemia (ALL)

Project description:Total RNA was isolated from Peripheral blood (PB) and Bone Marrow (BM) samples using mirVana kit and RNA integrity number (RIN) was determined in Agilent Bioanalyzer (2100) to assess the suitability for microarray assays. Fifty samples were individually analyzed using miRCURY™ LNA arrays version 11.0 (Exiqon, Denmark). The LNA array slides were scanned using Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and image analysis was carried out using ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 14 and normalized using global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm.

2014-07-09 | GSE59199 | GEO

Transcriptomic analysis of Responsive and Non-responsive Human NK cells to Plasmodium falciparum-infected red blood cells

Project description:NK cells are important cells of the innate immune system that respond to malaria infection in human. Howver, NK cell responses to malaria infection vary significantly in the human population. Base on their ability to kill infected red blood cells (iRBC), NK cells from malaria-naive individuals can be classified as responsive or non-responsive. NK cells used for microarray was obtained as follows: 10^6 NK cells were cocultured with either 10^5 iRBC at a starting parasitemia of 0.5% or with the same amount of RBC for 96 hours. Thereafter live NK cells were purified by FACS and RNA extracted via Trizol method. RNA quality was assessed by electrophoretic assay on the Agilent 2100 Bioanalyzer using a Nano chip (Agilent RNA 6000 Nano chip). RNA with a RIN value of >7.0 was used for genome-wide transcriptional analysis by microarray using HumanHT-12 v4 BeadChip (Illumina).

2018-08-30 | E-MTAB-6574 | biostudies-arrayexpress

MicroRNA profiling of Human Breast Cancer

Project description:Total RNA was isolated from epithelial tissues of different grades and stages of human breast cancer samples using mirVana kit and RNA integrity number (RIN) was determined in Agilent Bioanalyzer (2100) to assess the suitability for microarray assays. Sixteen samples were individually analyzed using miRCURY™ LNA arrays version 11.0 (Exiqon, Denmark). The LNA array slides were scanned using Agilent G2565BA Microarray Scanner System (Agilent Technologies, Inc., USA) and image analysis was carried out using ImaGene 8.0 software (BioDiscovery, Inc., USA). The quantified signals were background corrected (Normexp with offset value 10 14 and normalized using global Lowess (Locally Weighted Scatterplot Smoothing) regression algorithm.

2014-08-26 | GSE60725 | GEO

Transcriptome profiling of zebrafish brain under hypoxia

Project description:Adult zebrafish (Tübingen strain, sex not specified) at approximately 1 year of age were analysed. For experiments conducted under low oxygen conditions, nitrogen gas was bubbled through water to deplete oxygen before exposure of individual fish to the medium. Oxygen concentrations were measured using a dissolved oxygen meter (DO 6+, EUTECH instruments, Singapore). The dissolved oxygen level for hypoxia treatment was measured to be 1.20 ± 0.6 mg/l, whereas normal ambient oxygen levels were 6.6 ± 0.45 mg/l. Zebrafish were exposed to the hypoxic medium for 3 hours. Briefly, after each hypoxia trial, the animals were euthanized by hypothermic shock and then decapitated to remove the brain. Total RNA was extracted from samples mentioned above using the QIAGEN RNeasy mini kit (QIAGEN, GmbH, Hilden, Germany) and stored at −80°C before further analysis. RNA concentration was determined with a NanoVue™ UV–vis spectrophotometer (GE Healthcare Life Sciences, Fairfield, USA). RNA integrity and quality were then estimated using an Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA) and the RNA integrity number (RIN) index was calculated for each sample. Only RNAs with a RIN number >7.0 were processed further. Microarray analysis of gene expression was performed using the Zebrafish Gene 1.0 ST Array (Affymetrix Inc. Santa Clara, CA). Briefly, 300ng of total RNA derived from a single adult brain was converted to amplified sense strand cDNA using the Ambion WT Expression Kit (Life Technologies, Carlsbad, CA). The resulting sense cDNA was fragmented and Biotin end-labelled using the Affymetrix Genechip WT Terminal Labeling Kit prior to hybridisation to the array at 45 °C for 16 hours.

2016-08-04 | GSE85149 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data