Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Gene expression changes in dorsal dermal fibroblasts after beta-catenin deletion in vivo

ABSTRACT: Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at E10.5 in dermal fibroblasts. Method: Skin tissues were treated in 0/25% trypsin for 15 min at 37 degrees C to obtain single cells for FACS sorting and collected in RNA later. RNA was extracted with Karcturus pico pure kit. The RT and amplification was done using Nugen's ovation RNA-seq system V2. Libraries for sequencing were prepared with Illumina TruSeq kit. Transcriptome of FACS sorted E13.5 Engrailed1; RRYFP lineage-marked dorsal dermal fibroblasts was generated next-gen sequencing, in triplicate, using Illumina HiSeq machine. The sequence reads that passed quality filters were analyzed by TopHat followed by Cufflinks. qRT–PCR validation was performed using TaqMan and SYBR Green assays Results: We mapped about 33-49 million sequence reads per sample and obtained 76-79% of uniquely mapped percentage. We assembled the reads to the mouse ref genome (build mm10).

ORGANISM(S): Mus musculus

PROVIDER: GSE75944 | GEO | 2016/06/16

SECONDARY ACCESSION(S): PRJNA305757

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Differences between fibroblasts derived from normal and IPF lungs

Project description:Objective: To evaluate the characteristics of IPF lungs in fibroblasts, we performed RNA-Sequencing of fibroblasts derived from normal and IPF lungs Method:　NHLF（Normal human lung fibroblast）　and DHLF-IPF (DIPF; Diseased human lung fibroblasts derived from idiopathic pulmonary fibrosis)　were purchased from Lonza (Walkersville, MD, USA) .Total RNA was extracted from fibroblasts (NHLF and DIPF) using an RNeasy® Mini Kit (#74106; Qiagen, Valencia, CA, USA). Preparation of a next-generation sequencing library was performed using a SMARTer® Stranded Total RNA Sample Prep Kit–Pico Input Mammalian (TaKaRa, Shiga, Japan). Sequencing was performed on an Illumina HiSeq 2500 platform in 75-base single-end mode with Illumina Casava 1.8.2 software for base calling. Sequenced reads were mapped to the human reference genome sequence (hg19) using TopHat v.2.0.13 software, in combination with Bowtie 2 v.2.2.3 and SAMtools v.0.1.19. Result: Of the 26,257 genes analyzed, for NHLF and DHLF-IPF (DIPF), FPKM was required to be greater than or equal to 0.3. Under these conditions, 764 genes were up regulated inDHLF-IPF (DIPF) and 691 genes were down regulated.

2021-10-06 | GSE185259 | GEO

Next Generation Sequencing Facilities Quantitative Analysis of Wild type CD8+ T cells with 0.3T static magnetic field or not

Project description:Purpose:Next Generation Sequencing applying for compare the CD8+ T cells with 0.3T static magnetic field (SMF) or not transcriptome, included pathway-enrichment analysis and genes expression of interests Methods:CD8+ T cells were isolated from splenocytes in 8 week old wild type mice through STEMCELL Technologies negative selection kit. FACS sort CD8+ T cells after 3 days with CD3/CD28 costimulation at 0.3T static magnetic field or not. RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100. Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. Libraries were sequenced using an Illumina HiSeq X Ten sequencer. Resluts: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to further analyse Conclusions:Our study represents the detailed analysis of CD8+ T cells with 0.3T static magnetic field or not transcriptomes

2020-09-08 | GSE113858 | GEO

Next Generation Sequencing Facilities Quantitative Analysis of Wild type iNKT cells at stage2 and stage3 transcriptomes

Project description:Purpose:Next Generation Sequencing applying for compare the iNKT cells at stage2 and stage3 distict transcriptome, included pathway-enrichment analysis and genes expression of interests Methods:iNKT cells at stage2 and stage3 were isolated from thymus in 6 week old wild type mice by cell sorting. RNA was extracted, purified and checked for integrity using an Agilent Bioanalyzer 2100. Libraries were generated for sequencing using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian. Libraries were sequenced using an Illumina HiSeq X Ten sequencer. Resluts: Using an optimized data analysis workflow, we mapped about 30 million sequence reads per sample to further analyse Conclusions:Our study represents the detailed analysis of iNKT cells at stage2 and stage3 transcriptomes, with biologic replicates

2018-08-10 | GSE107642 | GEO

Comprehensive analysis of soluble RNAs in human embryo culture media

Project description:Spent culture media was collected on day 5 after in vitro fertilization from 5 human blastocysts that were subsequently transferred or frozen. Corresponding blank culture media from the same lot were cultured alongside the embryos and used as negative controls along with PBS. The samples were prepared for total RNA sequencing using SMARTer® Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian (Takara) and for small RNA sequencing using the QIAseq RNA Library Prep kit (Qiagen). Prepared libraries were sequenced as 100 bp paired end on an Illumina HiSeq 4000 sequencer for total RNA and Illumina NextSeq500 sequencer for small RNA. We found that total RNA mapped only 3% of the reads to gene regions in spent culture media and control and only 2% in PBS samples mapped to gene regions. For the small RNA analysis, human annotated miRNAs constituted from 0.1% to 1.4% of the mapped reads and 40% of small RNA reads mapped to the human genome. tiRNAs derived from 5 different mature tiRNA were differentially expressed when comparing conditioned to unconditioned media. We conclude, that in spite of applying state-of-the-art sensitive detection methods no miRNAs were found to be reliably present in the spent culture medium. In contrast, tiRNA fragments appear to be overexpressed in cultured IVF media samples.

2020-09-07 | GSE142380 | GEO

Next Generation Sequencing to understand the pathogenic role of synovial fibroblasts in experimental models of arthritis

Project description:The goal of this study is to define the pathophysiology of synovial fibroblasts in chroninc joint inflammation using NGS-derived synovial transcriptome profiling (RNA-seq) Methods: Synovial fibroblasts were isolated by FACs sorting [CD45-CD31-Popdoplanin+] from the synovium of healthy mice and mice undergoing experimental Collagen-Induced Arthritis (12 weeks old)(CIA). Methods: Whole Transcriptome Profiling of healthy and CIA synovial fibroblasts were generated by deep sequencing, in triplicate, using Illumina NextSeq™ 500 platform. Libraries were prepared using polyA selection (TruSeq stranded mRNA kit). Methods: The sequence reads that passed quality filters were aligned to mouse reference genome (GRCM38) using Hisat2 version 2.1.0. we mapped about 30 million sequence reads per sample (75 bp, paired-end) Methods: Featurecounts version 1.4.6 was used to quantify reads counts. Data quality control, non-expressed gene filtering, median ratio normalization (MRN) implemented in DESeq2 package and identification of differentially expressed (DE) genes were done using the R bioconductor project DEbrowser. Results: Results: We detected several differentially expressed (DE) genes in CIA synovial fibroblasts compared to naïve cells. These included 298 up-regulated genes and 88 down-regulated (>2 fold, adjp <0.05). DE genes reflected the reflecting the hyperplasia and activation observed during chronic joint disease. Pathways associated to DE genes were cell cycle and cell division and inflammatory response. Conclusions: our study shows pathophysiological changes associated to inflammatory synovial fibroblasts in a model of rheumatoid arthritis. Cells were directly isolated from fresh tissue, providing a valuable tool to study stromal inflammation.

2020-11-30 | GSE162306 | GEO

Global gene expression profile of primary cultured keratinocytes with or without stimulation

Project description:Skin tissues from newborn C57BL/6 mice were obtained for primary keratinocyte culture. Cells were then stimulated with or without IL-25 (Biolegend) for 8hrs. Total RNAs were isolated with RNAprep pure Tissue Kit (DP431) and the RNA-seq library was prepared by the Beijing Genomics Institute. Sequence reads were obtained using BGIseq500 (Illumina) and successfully mapped to mouse genome. Reads counts were normalized based on RPKM, fold changes were calculated for all possible comparisons.

2018-04-03 | GSE109833 | GEO

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Adar1 B Cell Conditional Knockout Activated B Cells Transcriptomes

Project description:Purpose: to compare the gene expression differences between wild-type activated B cells and Adar1 knockout activated B cells Methods: In vitro activated B cells were sorted using a BD FACSAira sorter, and total RNA was extracted using RNeasy Mini Kit (Qiagen) and poly(A) mRNA was isolated with the poly(A) mRNA Magnetic Isolation Module (NEB). Libraries were prepared using NEBNext Ultra RNA Library Prep Kit for Illumina (NEB) and sequenced on an Illumina Hiseq instrument (Illumina). Sequence reads were filtrated using Cutadapt (V1.9.1), and then mapped to the reference genome sequences (GRCm38.98) using Hisat2 (V2.0.1).

2022-06-15 | GSE196878 | GEO

Quantitative Analysis of OxyS regulatory Transcriptomes

Project description:Purpose: The identification of genes and regulatory pathways by OxyS sRNA in Escherichia coli. Methods: mRNA profiles of OxyS overexpression in wild-type and knockout of hfq strains using Illumina sequencing. Ribosomal RNA depletion from total RNA was performed using Ribo-Zero rRNA Removal Kit (Gram-Negative Bacteria, Illumina) according to manufacturer protocols. Libraries for Illumina sequencing were made with the TruSeq Stranded mRNA Sample Preparation Kit (Illumina) by the manufacturer’s protocol. RNA sequencing was performed on the Illumina HiSeq 2500 platform using a pair-end 50 bp sequencing. The sequence data for the reference genome (E. coli K-12 MG1655) was retrieved from the NCBI database. Quality-filtered reads were aligned to the reference-genome sequence using Bowtie2 software. The relative transcript abundance was measured in fragments in reads per kilobase of exon sequence per million mapped sequence reads (FPKM). All data processing were further performed by CLRNASeq V.1.00 (Chunlab, South Korea). Results: Using an optimized data analysis workflow, about 1 million sequence reads per sample to the E. coli K-12 genome were mapped and identified 4,224 and 4,303 transcripts in wild-type and hfq- strains, respectively. After TMM (Trimmed Mean of M-value) normalization and elmination of <100 reads in control and OxyS overexpression, 3,524 or 2,748 genes in hfq+ or hfq- strain, respetively, were utilized as a set to screening of candidates related to OxyS phenotype. Conclusions: Our study represents the first detailed analysis of OxyS transcriptomes in hfq+ and hfq- strains, generated by RNA-seq technology. The optimized data analysis workflows reported here could comparative investigate the expression profiles of sRNA in different background strains. We conclude that RNA-seq based transcriptome characterization of sRNAs would unravel genetic network in complex biologic functions.

2019-05-31 | GSE110005 | GEO

RNA-seq expression analysis to determine expression profile similarities between fibroblasts, induced endothelial cells from fibroblasts, and human dermal microvascular endothelial cells

Project description:The goal of this study was to determine the similarity between human dermal microvascular endothelial cells, induced endothelial cells from fibroblasts, and fibroblasts through RNA-seq expression analysis. RNA samples from independently induced cultures, plus fibroblast and human dermal microvascular endothelial cultures were converted into individual cDNA libraries using Illumina TruSeq methods and subjected to single-end 50 base-sequence analysis at 20-30 million read depths.

2013-04-14 | GSE45176 | GEO

Analysis of Notch2 conditional knockout (CKO) and wild type mouse hippocampal stem cells

Project description:Regulated genes downsteam of Notch2 Methods: mRNA profiles of adult wild type and Notch2 CKO neural stem cells were generated by deep sequencing, in triplicate. Two libraries were generated for each RNA sample using Nextera XT DNA Library Preparation Kit (Illumina) and sequenced by SmartSeq2 kit (Illumina) on different days. Each sample was sequenced twice in two independent lanes on a Illumina HiSeq 2500. The sequence reads that passed quality filters were mapped to the mouse genome (GRCm38) by Bowtie2 and transcript identification and quantification were performed using HTSeq. qRT–PCR validation was performed using SYBR Green assays. Results: This study identifies Notch2 regulated genes in neurogenic neural stem cells of the adult mouse hippocampus.

2019-09-27 | GSE116773 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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