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Degradome-seq of maize

ABSTRACT: Degradome-seq of maize

PROVIDER: PRJNA733133 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14664854.fastq.gz	Fastqsanger.gz
	SRR14664855.fastq.gz	Fastqsanger.gz

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Degradome-seq of maize

Project description:Degradome-seq of maize

2021-09-21 | GSE175630 | GEO

Degradome sequencing were performed on maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV).

Project description:The maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV) were inoculated with SCMV (SC, SM) and phosphate buffer (MC, MM), respectively to subjected to degradome sequencing.

2024-08-01 | GSE234274 | GEO

Whole-transcriptome RNA sequencing and degradome sequencing were performed on maize inbred lines Chang7-2 (resistant to SCMV) and Mo17 (susceptible to SCMV).

2024-08-01 | GSE233952 | GEO

Incompletely fused carpels ovary development revealed by miRNAs and target genes analysis in maize. (smallRNA-Seq and degradome-Seq)

Project description:To identify miRNAs involved in carpels fusion development in maize, four independent small RNA libraries and two degradome libraries from WT and IFC ovaries were constructed at the carpels fusion deficiency just being observed. A total of 162 known miRNAs distributed in 33 faimilies were identified, of which 20 known miRNAs were differentially expressed. In addition, 19 novel miRNAs were shown difference in expression levels between IFC and WT ovaries. By degradome analysis, totals of 113 and 78 target genes were predicted for known and novel miRNAs, respectively. 24 (60%) target genes of the differentially expressed known miRNAs coded for transcription factors, among which target genes encoding auxin response factors (ARF), TB1-CYC-PCFs (TCP), APETALA2 (AP2), growth regulating factor (GRF), MYB, NAC and NF-YA were classified as Class I. These target genes showed opposite expression patterns with their corresponding miRNAs according to quantitative real-time PCR results. The results suggested that the incomplete carpels fusion may partly due to the differential expression of these miRNAs and their target genes

2017-06-13 | GSE80998 | GEO

degradome sequence data

Project description:To identity the targets of miRNAs, we bundled 12 samples from different developing satages into four mixture samples. These samples were used to cosntruct degradome libraries and preform degradome sequencing on Illumina Hi-seq 2000 analyzer. More than 44.98 millions clean reads were obtained and 33.52 million reads were mapped to the soybean cDNA. The mapped reads were used to identity miRNA targets by CleaveLand4 pipeline. 4 degradome mixed samples, no replicates, but every degradome data consists of two parts data. Please note that every degradome sample has two processed and two raw data files. To have enough data, additional sequencing was performed from each sample library. And each sample raw data was processed separately (tissue_name*degradome.txt) and also combined (all_degradome*.txt).

2017-05-01 | E-GEOD-72903 | biostudies-arrayexpress

blueberry degradome

Project description:blueberry degradome

| PRJEB23598 | ENA

blueberry degradome

Project description:blueberry degradome

| PRJEB23597 | ENA

ChIP-seq of maize transcription factor LOB30

Project description:Maize LOB30 (Zm00001d036435) is a transcription factor and is specifically expressed in anthers. Our previous RNA-seq data showed that expression of some genes were upregualted in maize lob30 mutant maize anthers. To confirm these genes are the downstrem target genes, we generated proLOB30: GFP-LOB30 transgenic maize lines, collected stage 9 to stage10 anther materials and performed ChIP-seq using the GFP antibody.

2023-01-20 | GSE220176 | GEO

degradome sequence data

2017-05-01 | GSE72903 | GEO

Identification of miRNAs and their target genes associated with improved corn seed vigor induced by gibberellin (GA3) through small RNAs and degradome sequencing

Project description:Background: High seed vigor is crucial for agricultural production owing to its potential in high quality and yield of crops. A better understanding of the underlying mechanisms is highly necessary. Results: To better understand the involvement and regulatory mechanism of miRNAs correlated with maize seed vigor, small RNAs and degradome sequencing of two inbred lines Yu537A and Yu82 were performed. A total of 791 mature miRNAs were obtained with different expressions, among of which 505 miRNAs were newly identified and the rest miRNAs were more or less reported before by comparing the miRNAs with the sequences in miRbase database. Analysis of miRNA families showed maize seeds contain fewer miRNA families and larger miRNA families compared with animals, indicating that functions of miRNAs in maize seeds were more synergistic than animals. Degradome sequencing was used to identify the targets of miRNAs and the results showed a total of 6196 targets were obtained. Function analysis of diﬀerentially expressed miRNAs and targets showed Glycan degradation and galactose metabolism were closely correlated with improved corn seed vigor. Conclusions: These findings provide valuable information to understand the involvement of miRNAs with corn seed vigor and these putative genes will be valuable resources for improving the seed vigor in future corn breeding.

2022-09-08 | GSE196738 | GEO

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