Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis

ABSTRACT: Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis

PROVIDER: PRJNA688899 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	SRR13337056_1.fastq.gz	Fastqsanger.gz
	SRR13337056_2.fastq.gz	Fastqsanger.gz
	SRR13337057_1.fastq.gz	Fastqsanger.gz
	SRR13337057_2.fastq.gz	Fastqsanger.gz
	SRR13337058_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 38

Similar Datasets

Comparative transcriptome analysis reveals genetic basis of the annual Pashmina fiber cycle in Changthangi Pashmina goats

Project description:Identification of genes that regulate fiber cycling in Pashmina goat.

2019-10-15 | GSE117065 | GEO

Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis

Project description:In the present study transcriptomic profiling of skin biopsies containing secondary hair follicles were utilized to identify key genes and signaling pathways involved in hair follicle transition from no-growth phase (telogen) to growth phase (anagen).

2021-01-27 | GSE164100 | GEO

Histone H3 lysine 27 trimethylation (H3K27me3) modulates the fiber initiation in upland cotton

Project description:Histone methylation is one of the most significant epigenetic modifications in plants because it is responsible for regulating and controlling the expression of many important functional genes. Although there have been many studies concerning histone methylation, its specific functions and mechanisms in cotton fiber initiation remain unclear. To determine if the H3K27me3 modification had regulated cotton fiber initiation in upland cotton (Gossypium hirsutum), we performed a comparative analysis on the cleavage under targets and tagmentation (CUT&Tag) between the wild-type cultivar Xu142 and its fibreless mutant Xu142 fl. This research was carried out three time points during the initiation period of cotton fibers, which were -1, 0 and 1 days post-anthesis (DPA). We also used the H3K27me3 antibody in Xu142 and Xu142 fl to examine the differential deposition of H3K27me3. Combing these results with RNA-seq analysis, we discovered a negative correlation between transcription and H3K27me3. We identified 336 genes with opposing trends in H3K27me3 deposition and expression. These genes are involved in various metabolic pathways, including fatty acid biosynthesis, galactose metabolism, plant hormone signal transduction, plant-pathogen interaction, glycolysis-/-gluconeogenesis, phenylpropanoid biosynthesis, and cutin, suberin and wax biosynthesis. Further physiological research revealed that in vitro ovule culture with an RDS 3434 inhibitor could alters the level of H3K27me3 in ovules, thus influencing the process of cotton fiber development. Taken together, these results indicate that H3K27me3 plays an important role in the fiber initiation process of cotton, and demonstrates the H3K27me3 network involved in fiber initiation in cotton ovules. The study also provides a foundation for the future study of genes involved in fiber development.

2024-03-14 | GSE227870 | GEO

Comparative analysis of transcriptome profiles of a lintless-fuzzless mutant XinWX and its near-isogenic line linted-fuzzless mutant XinFLM during fiber initiation development stages

Project description:To gain novel insights into the molecular mechanisms of fiber initiation development,transcription profiling of the lintless-fuzzless mutant (XinWX) and its near-isogenic line,XinFLM (fuzzless-linted mutant) were compared using cDNA microarray technology. The expression profiling was performed at 3 developmental time points: -1, 0, and 1 dpa. fiber initiation development related genes were identified by differentially expressed gene analysis. And these genes could be used as potential candidate genes for manipulation to improve fiber yield. Cotton plants were grown under field condition. Flowers were tagged and cotton bolls were collected during Fiber initiation stages. Total RNA was isolated from ovule and fiber mixtures of XinWX and XinFLM at -1, 0, and 1 dpa. A total of 9 hybridizations with three biological replicates including a swap-dye experiment for each fiber developmental stage were employed.

2015-07-01 | E-GEOD-59208 | biostudies-arrayexpress

Identification of potential key genes and pathways associated with the Pashmina fiber initiation using RNA-Seq and integrated bioinformatics analysis.

Project description:Pashmina goat (Capra hircus) is an economically important livestock species, which habitats the cold arid desert of the Ladakh region (India), and produces a princely animal fiber called Pashmina. The Pashmina goat has a double coat fleece as an adaptation to the very harsh cold winters the outer long coarse hair (guard hair) produced from primary hair follicles and the inner fine Pashmina fiber produced from secondary hair follicles. Pashmina fiber undergoes a circannual and synchronized growth cycle. In the present study, we analyzed transcriptome profiles from 10 different Pashmina goats during anagen and telogen to delineate genes and signaling pathways regulating active (anagen) and regressive (telogen) phases of the follicle growth. During anagen, 150 genes were expressed at significantly higher levels with log (FC) > 2 and padj < 0.05. The RNA seq results were subjected to qRT-PCR validation. Among the nine genes selected, the expression of HAS1, TRIB2, P2RX1. PRG4, CNR2, and MMP25 were significantly higher (p < 0.05) in the anagen phase, whereas MC4R, GIPC2, and CDO1 were significantly expressed (p < 0.05) in the telogen phase which supports and validates the gene expression pattern from the RNA-sequencing. Differentially expressed genes revealed that Pashmina fiber initiation is largely controlled by signaling pathways like Wnt, NF-Kappa, JAK-STAT, Hippo, MAPK, Calcium, and PI3K-Akt. Expression of genes from the Integrin family, Cell adhesion molecules, and ECM-receptors were observed to be at much higher levels during anagen. We identified key genes (IL36RN, IGF2, ITGAV, ITGA5, ITCCR7, CXCL5, C3, CCL19, and CXCR3) and a collagen cluster which might be tightly correlated with anagen-induction. The regulatory network suggests the potential role of RUNX3, NR2F1/2, and GATA family transcription factors in anagen-initiation and maintaining fiber quality in Pashmina goats.

| S-EPMC7815713 | biostudies-literature

Comparative analysis of transcriptome profiles of a lintless-fuzzless mutant XinWX and its near-isogenic line linted-fuzzless mutant XinFLM during fiber initiation development stages

2015-07-01 | GSE59208 | GEO

Castor fiber fiber

Project description:Castor fiber fiber Raw sequence reads

| PRJNA313146 | ENA

Activation of Arabidopsis seed hair development by cotton fiber-related genes

Project description:This experiment was designed to investigate the molecular basis of cotton fiber cell initiation. 32,000 ESTs were sequenced from Gossypium hirsutum L. TM-1 immature ovules (GH_TMO) and developed cotton oligonucleotide microarrays containing ~23,000 unigenes. Transcriptome analyses were performed to compare gene expression changes in laser capture microdissected fiber cell initials (or epidermis) and inner ovules. The gene expression profiles of the fiber cell initials were compared with those of the inner ovules in each developmental stage prior to, right at, and shortly after the initiation of fiber cells. Many genes in various molecular function or biological processes were over- or under-represented between fibers and non-fiber tissues in each developmental stage, suggesting temporal regulation of gene expression during early stages of fiber development. For gene expression studies using a large set cotton oligo-microarray, 4 developmental stages were chosen. To study differential expression during fiber initiation, ovules at -2 DPA, 0 DPA, and 2 DPA were used. One of the fiber elongation stage tissues (7 DPA) was included. In each developmental stage, epidermis was separated from inner ovules and subjected to the hybridization. In addition, epidermis and ovule comparisons were performed individually with 0 DPA as a control point for comparison.

2011-11-02 | E-GEOD-17378 | biostudies-arrayexpress

Identification of genes differentially expressed in 1 dpa and 10 dpa fiber

Project description:A method was developed to isolate RNA from 1 dpa fiber. ESTs derived from this and other cotton mRNAs were sequenced and assembled into contigs. Contigs composed of EST unique to libraries of interest and unique singletons were represented on a microarray. Microarrays were hybridized with labed nucleic acids derived from 10 dpa fiber and 1 dpa fiber to identify genes differentially regulated during fiber initiation and fiber elongation. Genes with known expression in fiber were included to validate the microarray. Analysis of the gene ontology (GO) of differentially expressed genes suported previously reported aspects of fiber initiation such as cell wall remodeling. Transcription factors upregulated in fiber initials and elongating fiber were identified Keywords: cell type comparison

2007-06-26 | GSE6852 | GEO

Genes differentially expressed in fiber 1 day post anthesis (dpa)

Project description:A method was developed to isolate RNA from 1 dpa fiber. ESTs derived from this and other cotton mRNAs were sequenced and assembled into contigs. Contigs composed of EST unique to libraries of interest and unique singletons were represented on a microarray. Microarrays were hybridized with labed nucleic acids derived from whole 1 dpa ovules and 1 dpa fiber to identify genes differentially regulated during fiber initiation. Genes with known expression in fiber were included to validate the microarray. Analysis of the gene ontology (GO) of differentially expressed genes suported previously reported aspects of fiber initiation such as an increase in protein biosynthesis. An increase in the "membrane" was indicated by the GO analysis ans supported by increased staining of fiber initial ER. Analysis of individule genes differentially regulated in fiber initials indicated calcium may play a role in fiber deveopment which was also supported by an increase in calcium in fiber initials. Keywords: comparative hybridization

2007-06-26 | GSE6851 | 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