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Links from GEO DataSets

Items: 20

1.

Expression data from additional molar germs at stages of early development in miniature pigs

(Submitter supplied) We identified the spatiotemporal pattern of cascade initiation of additional molars in miniature pig,where second molar (M2) initiated from the posterior-free end of the dental lamina over the first molar (M1) at E60 when M1 progressed to the late bell stage. Similarly, third molar (M3) budded off from the posterior-free end of the dental lamina over M2, which reached bell stage at PN20. However, the molecular mechanisms of the regulatory network during sequential formation of additional molars remain poorly characterized in diphyodont mammals. more...
Organism:
Sus scrofa
Type:
Expression profiling by array
Platform:
GPL3533
9 Samples
Download data: CEL
Series
Accession:
GSE77006
ID:
200077006
2.

RNA-Sequencing for Additional Molar Germs Transcriptomes at Stages of Early Development in Miniature Pigs

(Submitter supplied) The molecular mechanisms of the regulatory network of mRNAs and long non-coding RNAs during sequential formation of additional molars remain poorly characterized in diphyodont mammals. The diphyodont miniature pig has proved to be a valuable model for studying human molar morphogenesis. Here, we performed RNA-seq on miniature pigs at three molar developmental stages to examine their differential gene expression profiles and potential regulatory networks during additional molar morphogenesis. more...
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11429
5 Samples
Download data: FA, TXT
Series
Accession:
GSE79507
ID:
200079507
3.

Expression data from early diphyodont morphogenesis in minature pig

(Submitter supplied) The miniature pig is diphyodont, making it a valuable alternative model for understanding human tooth development and replacement. However, little is known about gene expression and function during swine odontogenesis. The goal of this study is to undertake the survey of differential gene expression profiling with Affymetrix Porcine GeneChip and functional network analysis during morphogenesis of diphyodont dentition in miniature pigs. more...
Organism:
Sus scrofa
Type:
Expression profiling by array
Platform:
GPL3533
3 Samples
Download data: CEL
Series
Accession:
GSE53182
ID:
200053182
4.

Integrated Analysis of LncRNA-mRNA Co-Expression in the Extracellular Matrix of Developing Deciduous Teeth in Miniature Pigs

(Submitter supplied) Miniature pigs, a valuable alternative model for understanding human tooth development, have deciduous teeth from all four tooth families that are replaced once by permanent molars. The extracellular matrix (ECM) supports cells and maintains the integrity of tooth germs during tooth development. However, details on the role of the ECM in tooth development are poorly understood. Here, we performed long non- coding RNA (lncRNA) and messenger RNA (mRNA) expression profiles in the ECM components of deciduous tooth germs by RNA sequencing in miniature pigs. more...
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19176
9 Samples
Download data: TXT
Series
Accession:
GSE122516
ID:
200122516
5.

Long non-coding RNAs in psoriatic and healthy skin

(Submitter supplied) In this study, we used RNA-sequencing to profile the long non-coding RNA (lncRNA) transcriptome in lesional skin from psoriasis patients before (PP) and after treatment (PT) with adalimumab and in normal skin from healthy individuals (NN). For this we sequenced total RNA from 18 psoriasis patients (before and after treatment) and 16 healthy controls. We created our own reference set of long non-coding RNAs by merging three long non-coding RNA reference data sets. more...
Organism:
Homo sapiens
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16791
52 Samples
Download data: TXT
6.

Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally bred normal piglets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing
Platform:
GPL11429
2 Samples
Download data: WIG, XLS
Series
Accession:
GSE70005
ID:
200070005
7.

Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally bred normal piglets (MeDIP-Seq)

(Submitter supplied) Somatic cell nuclear transfer has brought considerable chances to breed excellent breeds and protect endanger animals, while also produced numerous fail embryos and abnormal individuals due to inefficient epigenetic modification at the same time. To understand some mechanisms of abnormal piglets with phenotypes such as macroglossia, standing and walking disabilities in our study and find some differences between abnormal piglets and conventionally bred normal piglets, DNA methylation profile and genome-wide gene expression were conducted in two groups, using methylated DNA immunoprecipitation binding highthroughput sequencing (MeDIP-Seq) and RNA sequencing(RNA-Seq). more...
Organism:
Sus scrofa
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11429
1 Sample
Download data: WIG
Series
Accession:
GSE70004
ID:
200070004
8.

Genome-wide gene expression and DNA methylation reveals Genetic and Epigenetic differences in cloned piglets and conventionally bred normal piglets (RNA-Seq)

(Submitter supplied) Somatic cell nuclear transfer has brought considerable chances to breed excellent breeds and protect endanger animals, while also produced numerous fail embryos and abnormal individuals due to inefficient epigenetic modification at the same time. To understand some mechanisms of abnormal piglets with phenotypes such as macroglossia, standing and walking disabilities in our study and find some differences between abnormal piglets and conventionally bred normal piglets, DNA methylation profile and genome-wide gene expression were conducted in two groups, using methylated DNA immunoprecipitation binding highthroughput sequencing (MeDIP-Seq) and RNA sequencing(RNA-Seq). more...
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11429
1 Sample
Download data: XLS
Series
Accession:
GSE70002
ID:
200070002
9.

Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
Organism:
Sus scrofa
Type:
Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
Platform:
GPL11429
4 Samples
Download data: TXT, WIG
Series
Accession:
GSE51477
ID:
200051477
10.

Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets (MeDIP-seq)

(Submitter supplied) Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. more...
Organism:
Sus scrofa
Type:
Methylation profiling by high throughput sequencing
Platform:
GPL11429
2 Samples
Download data: WIG
Series
Accession:
GSE51476
ID:
200051476
11.

Dysregulation of genome-wide gene expression and DNA methylation in abnormal cloned piglets (RNA-Seq)

(Submitter supplied) Backgroud:Epigenetic modifications (especially altered DNA methylation) resulting in altered gene expression may be one reason for development failure or the abnormality of the cloned animals, but the underlying mechanism of the abnormal phenotype in the cloned piglets remains unrevealed. Some cloned piglets in our study showed abnormal phenotypes such as big tongue (longer and thicker), limp, and exomphalos, which is similar to the human BWS syndrome. more...
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL11429
2 Samples
Download data: TXT
Series
Accession:
GSE51282
ID:
200051282
12.

Chickpea Transcriptome Atlas - I

(Submitter supplied) In this study, we aim to present a global view of transcriptome dynamics during flower development in chickpea. We generated around 234 million high-quality reads for eight flower development stages (ranging from 16 to 40 million reads for each stage) and 91 million high-quality reads from three vegetative tissues using Illumina high-throughput sequencing GAII platform. Because of non-availability of reference genome sequence, we mapped the reads to chickpea transcriptome comprised of 34,760 transcripts for estimation of their transcriptional activity in different tissue samples. more...
Organism:
Cicer arietinum
Type:
Expression profiling by high throughput sequencing
Platform:
GPL16348
11 Samples
Download data: TXT
Series
Accession:
GSE42679
ID:
200042679
13.

Identifying CHIR99021 and AICAR-regulated genes in the J1 mESCs

(Submitter supplied) It has been demonstrated that CHIR99021 promotes self-renewal of mouse embryonic stem cells, however, the target genes of CHIR99021 is not fully understood. AICAR is the activator of AMP-activated protein kinase. It is reported that AICAR plays important role in mouse embryonic stem cells, however the moleculor mechanism of this phenomenon is unknown. To better understand the downstream target genes of CHIR99021 and AICAR, we performed Microarray analyses to identify their downstream targets. more...
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL10787
9 Samples
Download data: TXT
Series
Accession:
GSE40959
ID:
200040959
14.

Long non-coding RNAs and mRNAs profiling during spleen development in pig

(Submitter supplied) We describe a total 222.19 Gb of pig RNA-seq sequences generated from the 18 libraries
Organism:
Sus scrofa; Sus scrofa domesticus
Type:
Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL24207 GPL22918
18 Samples
Download data: TXT
Series
Accession:
GSE106381
ID:
200106381
15.

Molar and incisor development

(Submitter supplied) One of the key questions in developmental biology is how from universally shared molecular mechanisms and pathways, is it possible to generate organs displaying similar or complementary functions, with a wide range of different shapes or tissue organization? The dentition represents a valuable system to address the issues of differential molecular signatures generating specific tooth types. We performed a comparative transcriptomic analysis of developing murine lower incisors, mandibular molars and maxillary molars at the developmental cap stage (E14.5) prior to recognizable tooth shape and cusp pattern.
Organism:
Mus musculus
Type:
Expression profiling by array
Platform:
GPL6246
16 Samples
Download data: CEL, CHP
Series
Accession:
GSE43144
ID:
200043144
16.

Total RNA sequencing in multiple Sus Scrofa tissues reveals novel long non-coding RNAs functioning in skeletal muscle development

(Submitter supplied) Long non-coding RNAs (lncRNAs) play important roles in diverse biological processes. However, the landscape of lncRNAs is largely unclear in Sus scrofa. Here we performed stranded RNA-seq on total RNA libraries from over 100 samples of Sus scrofa tissues. We identified 10,813 lncRNAs in Sus scrofa, of which 9,075 are novel. 57% of these lncRNAs were conserved in both human and mouse. These conserved lncRNAs tend to be more tissue-specific than pig-specific lncRNAs, and enriched in reproducible organs (i.e. more...
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing
Platforms:
GPL10945 GPL11429
13 Samples
Download data: FA, TXT
Series
Accession:
GSE73763
ID:
200073763
17.

Total RNA sequencing of ovary tissues at 49 days post coitus in Large White and Meishan pigs.

(Submitter supplied) We collected the ovary samples at 49 days post coitus in Large White and Meishan adult female pigs, identified the differentially expressed protein coding genes and long non-coding RNAs between these two breeds. three individuals of each breed were harvested as biological replicates.
Organism:
Sus scrofa
Type:
Expression profiling by high throughput sequencing
Platform:
GPL19176
6 Samples
Download data: TXT
Series
Accession:
GSE73593
ID:
200073593
18.

lncRNA expression in C2C12 myoblasts and myotubes

(Submitter supplied) To determine the lncRNA expression profile in C2C12 myoblasts and myotubes, we used mouse lncRNA microarray from Arraystar to examine the expression of lncRNAs in C2C12 myoblasts and myotubes.
Organism:
Mus musculus
Type:
Non-coding RNA profiling by array
Platform:
GPL19286
6 Samples
Download data: TXT
Series
Accession:
GSE101499
ID:
200101499
19.

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Osr2−/− Tooth Mesenchyme Transcriptomes

(Submitter supplied) Mutations in MSX1 cause craniofacial developmental defects, including tooth agenesis, in humans and mice. Previous studies suggest that Msx1 activates Bmp4 expression in the developing tooth mesenchyme to drive early tooth organogenesis. Whereas Msx1−/− mice exhibit developmental arrest of all tooth germs at the bud stage, however, mice with neural crest-specific inactivation of Bmp4 (Bmp4ncko/ncko), which lack Bmp4 expression in the developing tooth mesenchyme, showed developmental arrest of only mandibular molars. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
2 Samples
Download data: TXT
Series
Accession:
GSE81282
ID:
200081282
20.

Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Msx1-/- tooth mesenchyme Transcriptomes

(Submitter supplied) Mutations in MSX1 cause craniofacial developmental defects, including tooth agenesis, in humans and mice. Previous studies suggest that Msx1 activates Bmp4 expression in the developing tooth mesenchyme to drive early tooth organogenesis. Whereas Msx1−/− mice exhibit developmental arrest of all tooth germs at the bud stage, however, mice with neural crest-specific inactivation of Bmp4 (Bmp4ncko/ncko), which lack Bmp4 expression in the developing tooth mesenchyme, showed developmental arrest of only mandibular molars. more...
Organism:
Mus musculus
Type:
Expression profiling by high throughput sequencing
Platform:
GPL13112
4 Samples
Download data: TXT
Series
Accession:
GSE80288
ID:
200080288
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