Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Rab35 knockdown in primary mouse hepatoblasts

ABSTRACT: To study the role of Rab35 in the formation of bile canaliculi, primary mouse hepatoblasts were acquired, cultured in matrigel, and subjected to Rab35 knockdown by siRNA with scrambled control (4 biol. replicates each, block-randomised). Samples were subjected to S-trap protein digest and label-free quantification by staggered DIA demultiplexed with MSConvert and processed with DIA-NN, followed by differential expression and gene set enrichment analysis.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Mus Musculus (ncbitaxon:10090)

SUBMITTER: Andrej Shevchenko

PROVIDER: MSV000091413 | MassIVE | Mon Mar 06 04:12:00 GMT 2023

SECONDARY ACCESSION(S): PXD040612

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Impact of Cux2 knockdown on gene expression in female mouse liver (Mus musculus)

Project description:We identified genes expressed in mouse liver that are regulated by Cux2, a highly female-specific liver transcription factor whose expression is regulated by sex-dependent plasma GH patterns. Using siRNA to knockdown Cux2 expression in female liver, we show that female specific genes are predominantly repressed by Cux2 knockdown. In contrast, similar numbers of male-biased genes are repressed as are induced by Cux2 knockdown. A scrambled, non-specific siRNA was used as a control. (Published in: TL Conforto et al 2012, Mol Cell Biol. 2012, 32:4611-4627. PubMed PMID: 22966202; PMCID: PMC3486175)

2012-09-10 | GSE37078 | GEO

Ribosome profiling analysis of Neuro2a cells with Ebp1 knockdown

Project description:We perform Ribosome Profiling (Riboseq) analysis of mouse Neuro2a neuronal cultures in Ebp1-siRNA knockdown vs. scrambled-siRNA control conditions in biological triplicate to assess the translation-specific function of Ebp1

2021-03-23 | GSE157423 | GEO

Effects of knockdown of Jmjd6 on human umbilical vein endothelial cells - gene and exon expression

Project description:Human umbilical vein endothelial cells (HUVECs) were incubated for 48 h after transfection of scrambled siRNA or siRNA targeting Jmjd6 . Changes in transcript and exon levels were analyzed.

2012-05-04 | GSE37741 | GEO

FAM13B knockdown in iCMs

Project description:Common human genetic variation near the FAM13B gene are associated with atrial fibrillation as well as with the expression level of FAM13B mRNA in human left atrial appendage tissues. To determine the effects of FAM13B gene expression in human cardiomyocytes derived from induced pluripotent stem cells (iCMs from iCell Cardiomyocytes), we used siRNA targeted against FAM13B to knockdown its gene expression (KD) or an siRNA with a scrambled sequence (SCR). Total RNA was prepared from biological triplicate plates of cells and subjected to bulk RNAseq. 100-bp paired-end sequencing was performed on the Illumina HiSeq 2000. The sequence reads were mapped to the human genome using the STAR aligner (version 2.3.0) to derive a digital count of the expression of genes, which were defined using the Ensembl gene catalog (version 69). Genes were filtered to ensure a CPM (counts per million) > 5 in at least 2 samples, resulting in 11,017 genes. Differential expression analyses of FAM13B KD versus control SCR siRNA in iCMs was performed using the limma-voom approach with false discovery rate control.

2023-12-20 | GSE221262 | GEO

Effect of LIMD1 knockdown on gene expression in Human Bronchial Epithelial Cells (HBECs)

Project description:HBECs were untreated, treated with scrambled siRNA (80nM) or LIMD1 targeting siRNA (80nM) for 72 hours. Total RNA was extracted and gene expression was measured using Illumina HumanHT-12 v4 Expression BeadChip array.

2018-05-22 | GSE114692 | GEO

PBRM1 Knockdown in RCC Cell Lines

Project description:PBRM1 was found to be mutated in a high percentage of clear cell RCCs. We performed knockdown of PBRM1 via siRNA and compared with scrambled control in three different RCC cell lines.

2011-01-20 | GSE22316 | GEO

Effects of knockdown of Jmjd6 on human umbilical vein endothelial cells - gene and exon expression

2012-05-03 | E-GEOD-37741 | biostudies-arrayexpress

Transcriptome changes in bovine oocytes caused by microinjection

Project description:Purpose: In this study, we investigated the effect of microinjection on oocytes transcriptome changes through scrambled siRNA injection. Method: Scrambled siRNA injection followed by RNA-seq of single oocytes. Result:Our result showed 119 transcripts were differentially expressed of which 76 were down-regulated after scrambled siRNA injection.

2019-12-20 | GSE139867 | GEO

Pimary human keratinocyte knockdown with deltaNp63 specific siRNA

Project description:Human ΔNp63-specific siRNA was obtained from Invitrogen (Carlsbad, CA; sense: 5′-ACAAUGCCCAGACUCAAUU-3′; antisense: 5′-AAUUGAGUCUGGGCAUUGU-3′). Scrambled sequence siRNA for the negative control was purchased from Invitrogen. Transfections were performed using Lipofectamine RNAiMAX (Invitrogen) in Opti-MEM (GIBCO) at 40 nmol/L according to the manufacturer's instructions. The culture medium was replaced at 6 h after siRNA transfection. mRNA was extracted from NHEKs transfected with ΔNp63-specific or scramble sequence siRNA at 72 h after transfection. Microarray slides were scanned using a 3D-GENE human 25k (TORAY, Tokyo, Japan) and microarray images were automatically analyzed with AROSTM, version 4.0 (Operon Biotechnologies, Tokyo, Japan).

2020-12-08 | GSE162900 | GEO

Comparative analysis of gene expression after Oct4 or Scrambled siRNA knockdown in HNSCC cell lines

Project description:By employing a global gene expression profiling, we performed analysis of the molecular pathways which are deregulated in head-and-neck cancer cell lines FaDu, Cal33 and UTSCC5 after siRNA mediated knockdown of Oct4 comparing to Scrambled.

2021-07-01 | GSE173161 | 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