Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Transcriptomic analyses identify pathways linking developmental atrazine exposure to altered intestine development

ABSTRACT: Purpose: Identify gene expression changes in whole intestines of Xenopus laevis embryos exposed to atrazine (35 mg/L) compared to DMSO controls Methods: NF 39 embryos were exposed to 35 mg/L ATR or DMSO control for 24 hours. After 24 hours of exposure, intestines from embryos of each treatment group were dissected from anesthetized embryos with sharpened forceps. The anterior portion of the embryo (including the head, heart, and foregut) were removed and discarded, leaving only the mid-and hindgut portion of the intestine. Intestines from multiple embryos were removed, combined within a microcentrifuge tube containing TRIzol™ Reagent (Invitrogen) such that each replicate contained 10 intestines (n = 4). RNA extraction was performed using the TRIzol™ Reagent (Invitrogen) according to the manufacturer's instructions, followed by lithium chloride precipitation. Quality and quantity of RNA yield was confirmed on a Thermo Fisher Scientific Nanodrop 1000 and an Agilent 2100 Bioanalyzer. RNA-seq was performed by North Carolina State University’s Genomic Sciences Laboratory with an Illumina poly-A enriched directional RNA library and an Illumina NovaSeq 6000 was used for sequencing (SP 150 bp PE flow cell). Results: We identified 254 significantly differentially expressed genes (p-adj<0.05) between DMSO and atrazine exposed intestines Conclusions: Gene Ontology analysis of the differentially expressed genes revealed an enrichment for pathways involved in cellular stress, EMT, and the cell cycle, along with pathways involved in cellular (glucose)metabolism.

ORGANISM(S): Xenopus laevis

PROVIDER: GSE226434 | GEO | 2024/02/01

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Analysis of gene expression in Mel Z cells grown on plastic (MP).

Project description:RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invitrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

2024-10-08 | GSE221876 | GEO

Analysis of gene expression in Mel Z cells grown on Matrigel in the presence of inhibitor(MMI).

Project description:RNA-Seq procedure was used for analysis of expression in melanoma cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 14.8 millions of reads were generated for each sample.

2024-05-10 | GSE221873 | GEO

Analysis of gene expression in Mel Z cells grown on Matrigel (MM).

2024-05-10 | GSE221872 | GEO

RNA-Seq in HEK293T human cells

Project description:RNA-Seq procedure was used for analysis of expression in HEK293T cells. Cells were separately lysed with Trizol reagent (Invotrogen). Total RNA was extracted from cell lysed with Trizol reagent and PureLink RNA Micro Kit (Invitrogen) according to manufacture instruction. RNA quality was checked with BioAnalyser and RNA 6000 Nano Kit (Agilent). Poly(A)+ RNA was purified with Dynabeads® mRNA Purification Kit (Ambion). Illumina library was prepared from poly(A)+RNA with NEBNextNEBNext® Ultra™II RNA Library Prep Kit for Illumina® (NEB) according to manual. Sequencing was performed on HiSeq1500 with 50 bp read length. At least 10 millions of reads were generated for each sample.

2019-12-03 | GSE130262 | GEO

Transcriptomics analysis of gene expression in normal and FTO, METTL3 deficient Mouse embryo fibroblast 3T3-L1 pre-adipocytes

Project description:RNA was isolated from control and FTO,METTL3 deficient mouse 3T3-L1 cells using the TRIzol (Invitrogen) reagent by following the company manual.Total RNA was isolated from transiently transfected cells with TRI® Reagent (Sigma). mRNA was extracted using biotinylated poly(dT) oligo, followed by further removing of contaminated rRNA using RiboMinus Transcriptome Isolation Kit (K1550-02, Invitrogen). mRNA quality was analyzed by NanoDrop. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2000 (Illumina) in single-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used and samples were multiplexed in two samples per lane.

2015-03-09 | GSE53249 | GEO

Retrieval of inflammation-compromised periodontal ligament stem cells from dysfunction by exosomes derived from P2X7 receptor gene-modified cells

Project description:Exosomes derived from P2X7 gene modified stem cells could enhance the osteogenic differentiation of periodontal ligament stem cells under inflammatory cultural conditions. In order to identify differentially expressed miRNAs between Exs-Ad-P2X7 and Exs-Ad- control, total RNA from exosomes were extracted by TRIzol™ Reagent (Invitrogen) according to the instructions. Then, miRNA profile of Exs-Ad-P2X7 and Exs-Ad-control form 3 different individuals were sequenced by Agilent miRNA Microarray System and further confirmed by real-time PCR.

2020-10-28 | GSE140356 | GEO

m6A peaks in vehicle/entacapone (ENT)-treated inguinal White Adipose Tissue (iWAT) of DIO mouse.

Project description:RNA was isolated from Vehicle/Entacapone(ENT) treated mouse inguinal White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 5 µg of mRNA was used for m6A-IP. The immunoprecipitated m6A modified mRNAs were then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500(Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

2020-11-16 | GSE106996 | GEO

Transcriptomics analysis of gene expression in mouse lung after PM2.5 exposure

Project description:Total RNA was isolated from mouse lung harvested at different stages using TRIzol® Reagent (Ambion). mRNA was extracted with using Dynabeads® mRNA Purification Kit (Ambion) and subjected to TURBO™ DNase (Invitrogen) treatment at 37°C for 30 min and ethanol precipitation. Thus purified mRNA was used for RNA-Seq library construction. Libraries were directly constructed using the KAPA Stranded mRNA-Seq Kit (KAPA) and were sequenced using HiSeq2500 (Illumina) in paired-read mode, creating reads with a length of 125 bp.

2019-10-24 | GSE122492 | GEO

Transcriptomics of siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues

Project description:RNA was isolated from siCTRL, siNSUN2 and ALYREF-RIP HeLa cells, and multiple mouse tissues using the TRIzol (Invitrogen) reagent by following the company manual. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) or HiSeq2500 in paired-read mode, creating reads with a length of 101 or 125 bp. Sequencing chemistry v2 or v4 (Illumina) was used.

2017-04-19 | GSE93750 | GEO

m6A peaks in mouse brain sample.

Project description:RNA was isolated from 4 weeks old Prrc2a flox/flox whole brain using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen) For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.

2019-05-16 | GSE100492 | 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