GEO DataSets

(Submitter supplied) Purpose: The goal of this study is to provide a detailed transcriptome expression profile of the mouse cornea and evaluate changes in gene expression during mouse corneal development. Methods: RNA-sequencing is used to profile the mouse transcriptome in the pNC isolated at E10.5 and corneas isolated at E14.5 and E16.5. Samples generated in triplicate for sequencing by Illumina Hiseq 4000. Clean reads are mapped to reference gene and GRCm38 by Bowtie2 and HISAT. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL21103

9 Samples

Download data: TXT

(Submitter supplied) Purpose: The goal of this study was to evaluate changes in the transcriptome profile during periocular neural crest differentiation into corneal endothelium and keratocytes. Methods: RNA profiles of chick embryonic day (E3) periocular neural crest, E5 corneal endothelium, and E7 corneal endothelium plus keratocytes were generated in triplicate by deep sequencing using Illumina HS4000. Bowtie2 and HISAT were used to map clean reads to reference gene and genome, respectively. more...

Organism:

Gallus gallus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23499

9 Samples

Download data: TXT

(Submitter supplied) During embryonic development, the mesenchyme surrounding the brain (cranial mesenchyme) gives rise to several structures such as the meninges, calvaria, and the dermis of the scalp. It has been known that the two regions within the cranial mesenchyme, namely, SOM on the basolateral side and EMM on the apical side of the head, have different developmental fates. However, the molecular genetic basis underlying this difference had been unclear. more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

8 Samples

Download data: CSV

(Submitter supplied) We applied previously established in silico whole-embryo body (WB)-subtraction-based approach to identify “lens-enriched” genes. These new RNA-seq datasets on embryonic stages E10.5, E12.5, E14.5 and E16.5 confirmed high expression of established cataract-linked genes and identified several new potential regulators in the lens. Finally, we present lens stage-specific UCSC Genome Brower annotation-tracks; these are publicly accessible through iSyTE (https://research.bioinformatics.udel.edu/iSyTE/) and enable a user-friendly visualization of lens gene expression/enrichment to help prioritize genes from high-throughput data from cataract cases.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

15 Samples

Download data: TXT

(Submitter supplied) Purpose: The purpose of this study is to compare the transcriptome expression profiles of E12.5 and E13.5 Osr2RFP/- and Osr2RFP/+ palatal mesenchyme by using RNA-seq analysis. Methods: Osr2RFP/+ male mice were crossed with Osr2+/- female mice. The embryos were harvested at E12.5 and E13.5. The pair of palatal shelves were dissected from each Osr2-RFP positive embryo. The RFP+ palatal mesenchyme cells were isolated by using fluorescence-activated cell sorting (FACS). more...

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL13112

6 Samples

Download data: XLS

(Submitter supplied) This series represents murine dorsal neural tube bisected along the midline with one half from each embryo used for control and the other half treated with 10-6M RA dissolved in ethanol for 6, 12, 24 or 48 h. For 6 h exposures, the explants were cultured overnight on fibronectin coated 35mm dishes (Biocoat, Becton Dickinson Labware, Bedford, MA) in DMEM with 10% horse serum in order to allow for sufficient outgrowth of neural crest cells. more...

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS773

Platform:

GPL81

27 Samples

Download data: CEL, EXP

Expression profiling of cranial neural crest exposed to 1 uM retinoic acid (RA) at various lengths of time up to 48 hours. Neural crest obtained from 8.5 days postcoitum ICR embryos. Results provide insight into developmental pathways affected upon exposure to teratogenic concentrations of RA.

Organism:

Mus musculus

Type:

Expression profiling by array, transformed count, 2 agent, 4 time sets

Platform:

GPL81

Series:

GSE1588

27 Samples

Download data: CEL, EXP

(Submitter supplied) PURPOSE: To provide a detailed gene expression profile of the normal postnatal mouse cornea. METHODS: Serial analysis of gene expression (SAGE) was performed on postnatal day (PN)9 and adult mouse (6 week) total corneas. The expression of selected genes was analyzed by in situ hybridization. RESULTS: A total of 64,272 PN9 and 62,206 adult tags were sequenced. Mouse corneal transcriptomes are composed of at least 19,544 and 18,509 unique mRNAs, respectively. more...

Organism:

Mus musculus

Type:

Expression profiling by SAGE

Platform:

GPL11

2 Samples

Download data

(Submitter supplied) To understand better the factors contributing to keratoconus (KTCN), we used RNA sequencing to perform a transcriptome profile of human KTCN corneas. Over 82% of the genes and almost 75% of the transcripts detected as differentially expressed in KTCN and non-KTCN corneas were confirmed in the replication study using another set of samples. We used these differentially expressed genes to generate a network of KTCN-deregulated genes. more...

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL18460

50 Samples

Download data: GFF3, TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platforms:

GPL17021 GPL19057

10 Samples

Download data: BW

(Submitter supplied) Goal of this study was to examine gene expression changes upon conditional deletion of beta-catenin at e13.5 cranial mesenchyme.

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

7 Samples

Download data: TXT, XLSX

(Submitter supplied) H3K27me3 enrichment in the supraorbital cranial mesenchyme with ectoderm upon the deletion of β-catenin

Organism:

Mus musculus

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL19057

3 Samples

Download data: BW

(Submitter supplied) 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:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

5 Samples

Download data: XLSX

(Submitter supplied) During development, the proximal and distal regions of respiratory tract undergo distinct processes that ultimately give rise to conducting airways and alveoli. To gain insights into the genetic pathways differentially activated in these regions when branching morphogenesis is initiating, we characterized their transcriptional profiles in murine rudiments isolated at embryonic day 11.5. Keywords: parallel sample

Organism:

Mus musculus

Type:

Expression profiling by array

Dataset:

GDS953

Platform:

GPL81

6 Samples

Download data

Transcriptional profiles of distal branching and proximal non-branching regions of lung at embryonic day E11.5. During development, the proximal and distal regions of respiratory tract undergo distinct processes that give rise to conducting airways and alveoli.

Organism:

Mus musculus

Type:

Expression profiling by array, count, 2 tissue sets

Platform:

GPL81

Series:

GSE1423

6 Samples

Download data

(Submitter supplied) Analysis of gene expression changes during mouse salivary gland development using RNA-Seq

Organism:

Mus musculus

Type:

Expression profiling by high throughput sequencing

Platform:

GPL17021

13 Samples

Download data: CSV

(Submitter supplied) Posterior embryonic axis develops from neuromesodermal progenitors which differentiate into neural tube and paraxial mesoderm

Organism:

Mus musculus

Type:

Expression profiling by array

Platform:

GPL1261

12 Samples

Download data: CEL

(Submitter supplied) Stem cell-derived tissues have wide potential for modelling developmental and pathological processes as well as cell-based therapy. However, it has proven difficult to generate several key cell types in vitro, including skeletal muscle. In vertebrates, skeletal muscles derive during embryogenesis from the presomitic mesoderm (PSM). Using PSM development as a guide, we establish conditions for the differentiation of monolayer cultures of human pluripotent stem (hPSC) cells into PSM-like cells without the introduction of transgenes or cell sorting. more...

Organism:

Homo sapiens

Type:

Expression profiling by array

Platform:

GPL16686

9 Samples

Download data: CEL

(Submitter supplied) Here we present an RNAseq analysis of human bone samples, obtained from iliac crest needle biopsies, to yield the first in vivo interrogation of all genes and pathways that may be altered in bone with aging and E therapy in humans.

Organism:

Homo sapiens

Type:

Expression profiling by high throughput sequencing

Platform:

GPL11154

58 Samples

Download data: CSV

(Submitter supplied) The corneal endothelium is composed of a monolayer of corneal endothelial cells (CECs), which is essential for maintaining corneal transparency. Human embryonic stem cells (hESCs) hold the promise of providing an abundant donor source for generating CEC cells for cell replacement therapies. Here we demonstrate that CEC-like cells can be efficiently derived from human ESCs. In addition, we performed global gene expression profiling of stem-cell-derived CEC cells, incorporating with adult CEC cells, fetal CEC cells and other human tissue type data. more...

Organism:

Homo sapiens

Type:

Third-party reanalysis; Expression profiling by high throughput sequencing

Platform:

GPL11154

6 Samples

Download data: TXT