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| Status |
Public on Nov 04, 2019 |
| Title |
Transcriptome profiling reveals transcriptional and alternative splicing regulation in the early embryonic development of hair follicles in the cashmere goat |
| Organism |
Capra hircus |
| Experiment type |
Expression profiling by high throughput sequencing
Non-coding RNA profiling by high throughput sequencing
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| Summary |
The undercoat fiber of the cashmere goat, from the secondary hair follicle (HF), possesses commercial value. However, very few studies have focused on the molecular details of primary and secondary HF initiation and development in goat embryos. In this study, skin samples at embryonic day 45, 55, and 65 (E45, E55, and E65) were collected and prepared for RNA sequencing (RNA-seq). We found that the HF probably initiated from E55 to E65 by analyzing the functional pathways of differentially expressed genes (DEGs). Most key genes in canonical signaling pathways, including WNT, TGF-β, FGF, Hedgehog, NOTCH, and other factors showed clear expression changes from E55 to E65. We, for the first time, explored alternative splicing (AS) alterations, which showed distinct patterns among these three stages. Functional pathways of AS-regulated genes showed connections to HF development. By comparing the published RNA-seq samples from the E60, E120, and newborn (NB) stages, we found the majority of WNT/β-catenin signaling genes were important in the initiation of HF development, while other factors including FOXN1, GATA3, and DLX3 may have a consistent influence on HF development. Our investigation supported the time points of embryonic HF initiation and identified genes that have potential functions of embryonic HF initiation and development. We further explored the potential regulatory roles of AS in HF initiation, which extended our knowledge about the molecular mechanisms of HF development.
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| Overall design |
Nine samples for RNA sequencing: three skin samples from cashmere goat embryo at embryonic day 45, three skin samples from cashmere goat embryo at embryonic day 55, and three skin samples from cashmere goat embryo at embryonic day 65. Three samples for small RNA sequencing: three skin samples from cashmere goat embryo at embryonic day 45 were mixed together as one sample, three skin samples from cashmere goat embryo at embryonic day 55 were mixed together as one sample, and three skin samples from cashmere goat embryo at embryonic day 65 were mixed together as one sample.
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| Contributor(s) |
Zhang Y, Wang L, Li Z, Chen D, Han W, Su R, Wang R, Wang Z, Zhang Y, Li J |
| Citation(s) |
31780728 |
| Submission date |
Jan 05, 2016 |
| Last update date |
Feb 03, 2020 |
| Contact name |
Dong Chen |
| Organization name |
ABLife, Inc.
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| Department |
Center for Genome Analysis
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| Street address |
388 GaoXin 2nd Road, East Lake Hi-Tech Development Zone
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| City |
Wuhan |
| State/province |
Hubei |
| ZIP/Postal code |
430075 |
| Country |
China |
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| Platforms (1) |
| GPL21299 |
Illumina NextSeq 500 (Capra hircus) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA307666 |
| SRA |
SRP068098 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE76538_cds.fa.gz |
10.5 Mb |
(ftp)(http) |
FA |
| GSE76538_expressed_gene_RPKM.txt.gz |
471.1 Kb |
(ftp)(http) |
TXT |
| GSE76538_expressed_miRNA_TPM.txt.gz |
11.9 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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