Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of responsive probes for mRNA transcripts of the pig (S. scrofa) genome

ABSTRACT: Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). Starting from these sequences, the microarray probes were computed using 6 different algorithms (YODA, Picky, ArrayOligoSelector, OligoPicker, OligoFaktory, CommOligo). Two probes in the most 3’ end was tested for their specificity and performance. For any transcript with a replicated tested probe, we used the most responsive and specific in an hybridization trial with a pool of mRNAs from 20 tissues to construct the definitive gene expression microarray for the pig. Definitive 90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl transcripts, 11,363 replicated probes specific for the UniGene clusters of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters (GEO: GPL13259).

ORGANISM(S): Sus scrofa

PROVIDER: GSE28636 | GEO | 2014/03/31

SECONDARY ACCESSION(S): PRJNA143079

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

Identification of responsive probes for mRNA transcripts of the pig (S. scrofa) genome

Project description:Pig mRNAs Ensembl transcripts (Ver. 56) and UniGene (Ver. 38) sequences were used to produce a dedicated microarray platform to analyze mRNAs gene expression. Based on sequence similarity we rejected UniGene features that overlapped more than 40% with an Ensembl transcript. After this filter we obtained 40,267 UniGene clusters and 19,603 Ensembl transcripts (protein coding + pseudogenes + retrotransposed elements). Starting from these sequences, the microarray probes were computed using 6 different algorithms (YODA, Picky, ArrayOligoSelector, OligoPicker, OligoFaktory, CommOligo). Two probes in the most 3M-bM-^@M-^Y end was tested for their specificity and performance. For any transcript with a replicated tested probe, we used the most responsive and specific in an hybridization trial with a pool of mRNAs from 20 tissues to construct the definitive gene expression microarray for the pig. Definitive 90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl transcripts, 11,363 replicated probes specific for the UniGene clusters of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters (GEO: GPL13259). Microarray was probed with a pool of RNAs from 20 different tissues (superior vena cava, adipose tissue, lung, spleen, stomach, liver, intestine, kidney, descending aorta, left atrium, left ventricle, skeletal muscle, pulmonary aorta, skin, tongue, ascending aorta, arterial white cells blood, venal white cells blood, coronary valve, lymph node). Moreover each tissue sample was performed by a pool of 3 different adult pigs because they was not inbred.

2014-03-31 | E-GEOD-28636 | biostudies-arrayexpress

Messenger RNA transcript expression in the pig (S. scrofa)

Project description:90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl (Ver. 56) Transcripts (protein coding + pseudogenes + retrotransposed elements), 11,363 replicated probes specific for the UniGene clusters (Ver. 38) of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters. These microarrays were used to study gene expression in 14 different pig tissues (Atrium Sinister; Skin; Liver; W_B_A: White Blood Cells from Arteriosum blood; W_B_V: White Blood Cells from Venosum blood; Lymph Node; Tongue; Spleen; Skeletal Muscle; Lung; Kidney; Stomach; Adipose Tissue; Ventricle Sinister). Gene expression was correlated with the micro-RNA expression in the same tissues.

2014-03-31 | GSE27853 | GEO

mRNA-cardiocirculatory

Project description:90K Combimatrix gene expression microarrays were composed by 17,048 replicated probes and 963 not replicated specific for the Ensembl (Ver. 56) Transcripts (protein coding + pseudogenes + retrotransposed elements), 11,363 replicated probes specific for the UniGene clusters (Ver. 38) of length comprised between 778 nt and 1,348 nt, and 28,790 single probes specific for the remaining UniGene clusters. These microarrays were used to study gene expression in 9 different pig tissues involved in the cardiocirculatory system (Left Atrium; Right Ventricle, Inferior Vena Cava, Superior Vena Cava, Ascending Aorta, Descending Aorta, Pulmonary Artery, Coronary Artery, Leaflet of Pulmonary Artery). Gene expression was correlated with the micro-RNA expression in the same tissues, also deposited at ArrayExpress under accession number E-MTAB-1938 (https://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-1938).

2014-04-30 | E-MTAB-1941 | biostudies-arrayexpress

Messenger RNA transcript expression in the pig (S. scrofa)

2014-03-31 | E-GEOD-27853 | biostudies-arrayexpress

Whole transcriptome analyses of three Berkshire and three Korean native pig fat, liver and muscle tissue using RNA-Seq

Project description:We sequenced the whole mRNA of six pig (Sus scrofa) fat, liver and muscle tissues, generating a total of 1.3 billion short reads with 90-bp pair-end sequences from 24 samples. Comparing with current genome annotation, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) unigene clusters did not match any current equine gene model. We identified 189,973 single nucleotide variations (SNVs) from the aligned sequences against the horse reference. Most SNVs (171,558 SNVs; 90.31%) were novel compared with over 1.1 million equine SNPs from two databases. Some genes have significantly different expression levels under different environment. We define those identical genes which have different expression levels are ‘differentially expressed’ and carried out differentially expressed gene analysis before and after exercise conditions. We discovered, 62 up- and 80 down-regulated genes in the blood and 878 up- and 285 down-regulated genes in the muscle from the 24 samples. Six out of 28 previously exercise-related known genes, HIF1A, ADRB2, PPARD, VEGF, TNC, and BDNF, were highly expressed in the muscle after exercise. We discovered 56 functionally unknown transcription factors that are probably associated with an early regulatory exercise mechanism from 91 differentially expressed transcription factors. We found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising. whole mRNA sequencing profiles of six pig (Sus scrofa) fat, liver and muscle tissues

2014-09-01 | E-GEOD-45204 | biostudies-arrayexpress

Expression analysis of individual homoeologous wheat genome- and rye genome-specific transcripts in a 2BS.2RL wheat-rye translocation

Project description:To distinguish transcripts expressed from each of the three wheat genomes and those from the rye chromatins, genomic probes generated from diploid progenitors of wheat and rye were synthesized Consensus sequences for probe design were generated from local unigene clusters. EST and cDNA sequences were downloaded from NCBI. A total of 52,589 pairs of probes were designed. Two 60 bp probes were designed from each consensus sequence. The array was manufactured by NimbleGen and synthesized on 12-plex arrays. Two independent biological replicates were used in separate hybridizations. Each biological replicate was a total RNA sample extracted from the whole tissue of two seedlings.

2015-02-24 | E-GEOD-58678 | biostudies-arrayexpress

Microarray analysis to reveal transcriptional differences between a pair of isogenic tobacco cell lines, SL (wild-type) and ALT301 (aluminum-tolerant), under normal growth condition

Project description:Using our microarray data, we identified 1, 303 probes (680 upregulated; 623 downregulated; with known functions) with changes of at least 2-fold in their differential transcript levels with significance (P < 0.05) in ALT301, compared with SL (note that some probes within the 1,303 probes carry the same TIGR ID and/or UniGene ID). Focusing on the genes related to glycolysis, the TCA cycle, and antioxidant systems, we found several genes differentially expressed between the lines.

2021-07-08 | GSE158255 | GEO

RNA sequencing profiles of control and PRPF19 knockdown TIG-3 cells

Project description:Total RNA was purified from TIG-3 cells transfected with siControl or siPRPF19 using miRNeasy Mini Kit (QIAGEN) with RNase-free DNase (QIAGEN). Library preparation, sequencing, and data analysis were performed by DNAFORM (Yokohama, Kanagawa, Japan). Quality and quantity of extracted RNA was assessed by NanoDrop 8000 Microvolume UV-Vis spectrophotometer (Thermo Fisher Scientific) and Agilent RNA 6000 Nano kit of BioAnalyzer 2100 System (Agilent Technologies). RNA-seq library was prepared using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio) following the manufacturer’s instruction. In brief, ribosomal RNA was depleted employed RiboGone which included in the kit. After that, first strand cDNA synthesis was performed using N6 primer. The first-stranded cDNA was purified using equal volume of AMPure XP beads (Beckman Coulter). The purified cDNA was amplified into Illumina-specific RNA-seq libraries by PCR. The libraries were sequenced on a Hiseq sequencer (Illumina) to generate 150 nt paired-end reads. The quality of sequence data was first assessed using FastQC (ver. 0.11.7). Raw sequence reads were then trimmed and quality-filtered with Trim Galore! (ver. 0.4.4), Trimmomatic (ver. 0.36), and cutadapt (ver. 1.16) software. Trimmed reads were mapped to the human reference genome (GRCh38.p10) using STAR (ver. 2.6.1a).

2021-07-20 | GSE168391 | GEO

Whole transcriptome analyses of three Berkshire and three Korean native pig fat, liver and muscle tissue using RNA-Seq

2014-09-01 | GSE45204 | GEO

The long noncoding RNA expression profile of hepatocellular carcinoma identified by microarray analysis

Project description:To explore the potential involvement of lncRNAs in hepatocellular carcinoma (HCC) oncogenesis, we conducted lncRNA and mRNA profiling in 3 pairs of human HCC and adjacent normal tissue (NT) by microarray. With abundant probes accounting for 33,045 lncRNAs and 30,215 coding transcripts in our microarray, the number of lncRNAs and coding transcripts that could be detected here is 10,149 and 14,944, respectively. From the data, thousands of lncRNAs and mRNAs were found to bedifferentially expressed (Fold Change≥2.0) in HCC tissues compared with NT and identified 624 lncRNAs and 1050 mRNAs were differentially expressed in all three HCC tissues.Bioinformatic analysis (gene ontology, pathway and network analysis) was performed for further study of these differentially expressed mRNAs.By qRT-PCR analysis in nineteen pairs HCC and adjacent normal tissues, we found that eightl ncRNAs were aberrantly expressed in HCC compared with corresponding NT, which is consistent with microarray data. Additionally, change trends of seven lncRNAs were basically identical to their nearby coding genes.

2014-02-21 | GSE55191 | 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