Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

UGDH knockdown in MDA-MB-231

ABSTRACT: Transcriptome profiling (RNA-Seq) to evaluate the connection the metabolic enzyme UGDH on gene expression. The RNA libraries were prepared and sequenced at University of Houston Seq-N-Edit Core per protocols. Total libraries were prepared with Ovation® Universal Plus mRNA-Seq (NuGen) using 200 ng input RNA. The size selection for libraries were performed using SPRIselect beads (Beckman Coulter) and purity of the libraries were analyzed using the High Sensitivity DNA chip on Bioanalyzer 2100 (Agilent). The prepared libraries pooled and sequenced using NextSeq 500 (Illumina), generating ~15 million 2×76 bp paired-end reads per samples. The RNA-seq raw fastq data were processed with RNA-Seq Express app within the Illumina BaseSpace app suite (www.basespace.illumina.com), which performed alignment with STAR aligner, assignment of aligned reads to genes, and differential gene expression with DESeq2 Analysis was performed comparing controls (shNT) against individual knockdowns (shU1 or shU2). Then, results from both analyses were compared for the intersection to identify commonly altered genes.

ORGANISM(S): Homo sapiens

PROVIDER: GSE118772 | GEO | 2018/08/21

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Vascular fate in misidentified pluripotent-derived blood-brain-barrier endothelial cells rescued by transcriptional reprogramming.

Project description:A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were isolated, lysed and barcoded in droplets. Droplets were then disrupted and cDNA was pooled for second strand synthesis. Libraries were generated with direct tagmentation followed by 3’ enrichment and sample indexing using Illumina Nextera library prep kit. Pooled libraries were sequenced on the Illumina NextSeq500 sequencer. Sequencing data were primarily analyzed using the SureCell RNA Single-Cell App in Illumina BaseSpace Sequence Hub.

2019-12-25 | GSE138025 | GEO

Small-RNA high-throughput sequencing of head-and-neck cancer with or without human papilloma virus etiology

Project description:HPV positive head and neck cancer (HNC) are thought to have different etiology from HPV-unrelated HNC. There are indications that HPV positive HNC have better survival and that treatment options could be optimized in this set of tumours. In this study, we sought to evaluate miRNA profiles in the different groups of HNC based on cancer subsite (oral or oropharyngeal) and HPV presence (positive/negative; based on both viral DNA and RNA presence) all in comparison with normal tonsillar tissue from approximately aged subjects. From 61 enrolled patients, 22 were selected for NGS small RNA sequencing using Illumina small RNA library preparation kits and sequencing reagents on Nextseq 500 machine. Only samples with RIN >= 7 were included. manufacturers protocol was followed for library preparation. Indexing was done with indexes 1-22, and final libraries were normalizes to same amount after QBit measurement. Sequencing was done on Nextseq 500 machine and subsequent analyisis in Basespace (illumina). Raw fastq files were subsequently additionally trimmed of adapter sequences using FastQc Basespace app and differential expression evaluated with SmallRNA app. Customized plots were obtained after importing SmallRNA app calculated counts to DeSeq2 package in R and reanalysis therein.

2019-02-20 | E-MTAB-7030 | biostudies-arrayexpress

7d43f91c-87f1-4955-aef2-c5146f0d0893 - samples

Project description:16 DS and Control brain samples were prepared using the 10X Single Cell 3' v3 kit. Pre-fragmented libraries were selectively amplified for APP using custom designed primers.

| EGAD00001008284 | EGA

Mouse wound healing [RNA-seq]

Project description:Purpose: To explore the changes of genes expression in different time points during mouse wound healing. Two wounds tissue from one animal were pooled, three animals were used per time point. The wounds tissue was collected on day 0, 1, 3, 5, 7 after cutting. Skin was cleaned of muscle and fat tissue; total RNA was extracted using the RNeasy mini kits (Qiagen), purified using Direct-zol RNA MiniPrep kit (Zymo Research). Next-generation libraries were prepared using the VAHTS TM mRNA-seq V2 Library Prep Kit for Illumina (Vazyme, #NR601). RNA-seq libraries were run on an Illumina HiSeq X-Ten next-generation sequencer. Analysis of RNA-seq data was done using the DESeq package in R.

2020-06-05 | GSE128193 | GEO

SPANX control of Lamin A/C modulates nuclear architecture and promotes melanoma growth

Project description:Purpose: To investigate mechanisms underlying SPANX knockdown phenotypes, we monitored changes in gene expression profiles in A375 melanoma cells subjected to SPANX KD (RNA-Seq). Methods: RNASeq Libraries were prepared from isolated total RNA using the QuantSeq 3' mRNA-Seq Library Prep Kit FWD for Illumina from Lexogen, (Vienna, Austria). Barcoded libraries were pooled and single end sequenced (1X75) on the Illumina NextSeq 500 using the High output V2.5 kit (Illumina Inc., San Diego CA). Raw data FASTQ files were generated by standstard illumina base calling pipeline and stored in illumina cloud service BaseSpace. Reads were aligned with the STASR aligner. Analyses of differentially expressed genes (DEGs) were subsequently performed using a negative binomial test method (edgeR)10 implemented using SARTools R Package Results: Of 609 genes deregulated by both shRNA, 454 were upregulated and 123 were downregulated. Networks associated with cell division were downregulated following SPANX KD, while those associated with 3-phosphoinositide biosynthesis were upregulated. Notably, IPA analysis identified the cell cycle as the primary pathway deregulated, and further analysis using the reactome database revealed that most of those genes were associated with the G1/S transition.

2020-12-31 | GSE141823 | GEO

RNAseq analysis between hepatocytes isolated from control livers, β1-integrin mutant livers, P21 over-expressed livers and ductal cells.

Project description:RNAseq analysis between cell types. RNA extracted using Qiagen mini total RNA isolation protocols (Qiagen, Germany). Samples were treated with DNase (Ambion), and sample integrity verified on the Agilent Bioanalyser with the RNA Nano chip. Illumina Tru-seq paired end strand specific sequencing (Illumina, USA) was carried out by on a NextSeq-550 sequencer (Edinburgh Clinical Research Facility, Western General Hospital, Edinburgh, Scotland, UK). 500ng of Total RNA underwent ribosomal RNA depletion (rRNA) prior to purification, fragmentation, random hexamer cDNA generation and purification with AMPure XP beads (Beckman-Coulter, USA). Multiple indexing adapters were ligated to ds cDNA with subsequent hybridisation onto flow cells, and DNA fragment enrichment by 15 cycle PCR for sequencing. Completed libraries were quantified by qPCR using the KAPA Illumina Library Quantification Kit (Illumina, USA) before multiplexing in two equimolar pools and running on two flow cells on the Illumina NextSeq 550. The resulting FastQ files were mapped to the reference genome (mm9) using the Tophat alignment tool (V1) on Illumina Basespace software and reads per kilobase per million (RPKM) scores calculated.

2017-07-12 | GSE98034 | GEO

RNAseq analysis between mouse ESCs cultured in serum or plus the EZH2 inhibitor EPZ.

2017-12-01 | GSE101928 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of MED23-knockdown and Control HUVEC Cells Transcriptomes

Project description:Purpose: RNA-seq analysis to evaluate the impact of MED23 knockdown on the transcriptome of HUVEC cells.Methods: Total RNA was isolated with TRIzol from Med23 knockdown HUVECs (n = 3) or control cells (n = 3). cDNA sequencing libraries were prepared with an NEBNext® Ultra™ RNA Library Prep Kit for Illumina. The RNA-Seq FASTQ raw data were trimmed to remove low-quality reads and adapters using Trimmomatic. The trimmed reads were aligned to the mouse reference genome UCSC GRCh37/hg19 with HISAT2. Gene and transcript quantification was performed using Cutdiff. The results of the mapping of the RNA-seq reads, transcript assembly and abundance estimation were reported as fragments per kilobase of exon per million fragments mapped (FPKM).

2021-10-21 | GSE186112 | GEO

Sequencing of First-strand cDNA Library Reveals Full-length Transcriptomes

Project description:We developed a new method of preparing libraries for strand-specific RNA sequencing (ssRNA-Seq). It employs Direct Ligation of Adaptors to First-strand cDNA (DLAF). We compared ssRNA-Seq libraries prepared using either the DLAF and dUTP methods from mouse embryonic stem cells (mES) and libraries were sequenced from one end or both ends. We also conducted a comparison of ssRNA-Seq libraries prepared using DLAF and ScriptSeq v2 kit (Epicenter) from mouse embryonic cortex (mECx).

2015-01-01 | GSE63424 | GEO

Transcriptome analysis in B16F10 and 4T1 cell lines with decitabine treatment [RNA-seq]

Project description:The goal of RNA-seq is to identify the differential expressed genes in the B16F10 and 4T1 cells after Decitabine treatment. Three biological replicates were assigned for each group and in total 12 groups were prepared for RNA-seq libraries with 300 ng mRNA as starting materials using NEXTflex Illumina qRNA-Seq Library Prep Kit (Bioo Scientific). We mapped over 60 million reads per sample to mouse genome (mm10) with RSEM workflow. P-values of differential expression were adjusted for multiple-hypothesis testing using False Discovery Rate (FDR) method.

2024-06-30 | GSE212027 | 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