18 research outputs found
Pvirgatum_v1.1_273_gene_exons_updated_ChrUn_representative.gff3
Pvirgatum_v1.1_273_gene_exons_updated_ChrUn_representative.gff
SNIPE_all_plates_matrix_biallelic_only_nomissing.txt
SNIPE_all_plates_matrix_biallelic_only_nomissing.tx
switchgrass_upland_panel_up_cnv_list.txt
switchgrass_upland_panel_up_cnv_list.tx
Pvirgatum_v1.1_273_hardmasked_ChrUn.fasta
Pvirgatum_v1.1_273_hardmasked_ChrUn.fast
SNIPE_all_plates_matrix_biallelic_only_nomissing.exonic_variant_function
SNIPE_all_plates_matrix_biallelic_only_nomissing.exonic_variant_functio
SNIPE_all_plates_matrix_unfiltered.txt
SNIPE_all_plates_matrix_unfiltered.tx
Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria
<p>Supplementary material as published in <i>Microbial Genomics</i> in the following article: Absence of Genome Reduction In Diverse, Facultative Endohyphal Bacteria</p><p>DOI 10.1099/mgen.0.000101</p
Strand-Specific RNA-Seq Analyses of Fruiting Body Development in <i>Coprinopsis cinerea</i>
<div><p>The basidiomycete fungus <i>Coprinopsis cinerea</i> is an important model system for multicellular development. Fruiting bodies of <i>C</i>. <i>cinerea</i> are typical mushrooms, which can be produced synchronously on defined media in the laboratory. To investigate the transcriptome in detail during fruiting body development, high-throughput sequencing (RNA-seq) was performed using cDNA libraries strand-specifically constructed from 13 points (stages/tissues) with two biological replicates. The reads were aligned to 14,245 predicted transcripts, and counted for forward and reverse transcripts. Differentially expressed genes (DEGs) between two adjacent points and between vegetative mycelium and each point were detected by Tag Count Comparison (TCC). To validate RNA-seq data, expression levels of selected genes were compared using RPKM values in RNA-seq data and qRT-PCR data, and DEGs detected in microarray data were examined in MA plots of RNA-seq data by TCC. We discuss events deduced from GO analysis of DEGs. In addition, we uncovered both transcription factor candidates and antisense transcripts that are likely to be involved in developmental regulation for fruiting.</p></div