Ontology highlight
ABSTRACT:
PROVIDER: PRJNA647001 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12276824.fastq.gz | Fastqsanger.gz |
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Project description:RNA-seq from whole V3 maize seedlings (roots and shoots) for the B73 inbred line and A188 x B73 hybrid.
2022-01-27 | GSE175914 | GEO
Project description:Background: Maize plants developed typical gray leaf spot disease (GLS) symptoms initiating at the lower leaves and progressing to upper leaves through the season. Leaf material was collected at 77 days after planting, at which stage there were a large number of GLS disease necrotic lesions on lower leaves (8% surface area on average determined by digital image analysis), but very few lesions and only at chlorotic stage on leaves above the ear (average of 0.2% lesion surface area). Method:To collect material that reflected a difference between C.zeina infected B73 leaves and control B73 leaf material, samples were collected from two lower GLS infected leaves (second and third leaf internode below ear) , and two upper leaves with minimal GLS symptoms (second and third internode above ear), respectively. The two lower leaves from each plant were pooled prior to RNA extraction, and the two upper leaves from each plant were pooled prior to RNA extraction. Upper and lower leaf samples from three maize B73 plants were subjected to RNA sequencing individually. The three maize plants were selected randomly as one plant per row from three rows of ten B73 plants each. Result: A systems genetics strategy revealed regions on the maize genome underlying co-expression of genes in susceptible and resistance responses, including a set of 100 genes common to the susceptible response of sub-tropical and temperate maize.
2016-10-15 | GSE81344 | GEO
Project description:This SuperSeries is composed of the following subset Series:; GSE8174: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Seedling data; GSE8176: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Immature ear data; GSE8179: Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression - Embryo data Experiment Overall Design: Refer to individual Series
2008-06-17 | E-GEOD-8194 | biostudies-arrayexpress
Project description:Here we report genome-wide high resolution allele-specific maps of DNA methylation and histone H3 lysine 27 trimethylation (H3K27me3) in maize endosperm. To investigate the allele-specific DNA methylation pattern of maize endosperm on a genome-wide scale, we performed MethylC-seq for shoot, embryo, and endosperm tissue 12 d after pollination (DAP) of inbred B73, and the endosperm tissue 12 DAP of reciprocal crosses B73 Ã Mo17 (BM) and Mo17 Ã B73 (MB). We also performed additional RNA-seq for samples from 12-DAP and 10-DAP endosperm of both reciprocal crosses between inbreds B73 and Mo17
2013-10-17 | E-MTAB-4206 | biostudies-arrayexpress
Project description:Small RNAs (sRNAs) are hypothesized to contribute to hybrid vigor because they maintain genome integrity, contribute to genetic diversity, and control gene expression. We used Illumina sequencing to assess how sRNA populations vary between two maize inbred lines (B73, Mo17) and their hybrid. We sampled sRNAs from the seedling shoot apex and the developing ear, two rapidly growing tissues that program the greater growth of maize hybrids. We found that parental differences in siRNAs primarily originate from repeat regions. Although the maize genome contains greater number and complexity of repeats compared to Arabidopsis or rice, we confirmed that like these simpler plant genomes, 24-nt siRNAs whose abundance differs between maize parents also show a trend of downregulation following hybridization. Surprisingly, hybrid vigor is fully maintained when 24-nt siRNAs are globally reduced by mutation of the RNA-dependent RNA polymerase2 (RDR2) encoded by modifier of paramutation1 (mop1). We also discovered that 21-22nt siRNAs derived from a number of distinct retrotransposon families differentially accumulate between B73 and Mo17 as well as their hybrid. Thus, maize possesses a novel source of genetic variation for regulating both transposons and genes at a genomic scale, which may contribute to its high degree of observed heterosis. sRNA libraries were derived from RNA isolated from the seedling shoot apex and developing ear tissues from B73, Mo17, B73xMo17 and Mo17xB73. The shoot apex was chosen because it is enriched for meristematic tissue where cell proliferation occurs, rates of organ initiation are determined, and organ size is specified. The developing ear was examined because it is enriched in meristematic tissue and is undergoing rapid growth, and also because the mature ear shows the highest degree of heterosis. Total RNA was isolated and separated on a 15% TBE-Urea polyacrylamide gel. Using a 10-bp ladder, the sRNA fraction representing 10-40-bp was excised. sRNA libraries were prepared according to Lu et al. (2007) or manufacturer's instructitions (Illumina). A combination of Perl scripts and FASTX toolkit scripts were used to remove adapters, collapse identical sequences and count reads per sequence. Supplementary processed data text files contain the distinct sRNA sequences for all of the genotypes analyzed in that experiment. Abundance (reads per million) was calculated for each distinct sequence by dividing the number of reads of distinct sRNA in a library by the total number of sRNA reads for that library and multiplying this by 1 million. Genome builds: B73 genome, maizesequence.org release 4a.53 (October, 2009); Mo17 whole genome shotgun clones.
2012-05-26 | E-GEOD-37411 | biostudies-arrayexpress
Project description:In this research, we perofomred whole proteomic analysis of maize B73 in response to two viruses infection.
2018-12-11 | PXD012022 |
Project description:chip-seq of Immature ear and Shoot of B73 maize
| PRJNA487471 | ENA