S Krishna Kumar 2023 PhD Thesis Supplementary Tables
| dc.contributor.author | Kumar, Shanthanu Krishna | |
| dc.contributor.author | Peck, Gregory | |
| dc.date.accessioned | 2023-08-09T21:43:23Z | |
| dc.date.available | 2023-08-09T21:43:23Z | |
| dc.date.issued | 2023-08-09 | |
| dc.description.abstract | These data files are a supplement in support of a thesis with the following abstract: Methods for processing the data: Pooled libraries were sequenced using HiSeqX 150 bp Pair End sequencing (Psomagen Inc, Rockville MD). Raw RNA-Seq reads were processed to remove adaptors and low-quality sequences using Trimmomatic (version 0.36; Bolger et al. 2014) with parameters ‘SLIDINGWINDOW:4:20 LEADING:3 TRAILING:3 MINLEN:40’ and to remove polyA/T tails using PRINSEQ++ [v1.2; (Cantu et. al. 2019) with parameters ‘-min_len 40 -trim_tail_left 10 -trim_tail_right 10’]. The remaining cleaned reads were aligned to the ribosomal RNA database (Quast et al. 2013) using Bowtie (version 1.1.2; Langmead, 2010) allowing up to three mismatches, and those aligned were discarded. The final cleaned reads were aligned to the ‘Golden Delicious’ double haploid (GDDH13) genome (v1.1; Daccord et al. 2017) using HISAT2 (version 2.1.0; Kim et al. 2019) with default parameters. Based on the alignments, raw read counts for each gene were calculated and then normalized to fragments per kilobase of exon model per million mapped fragments (FPKM). Raw read counts were then fed to DESeq2 to identify differentially expressed genes (DEGs) using a cutoff of adjusted P value < 0.05 and fold change ≥ 2. Gene ontology terms enriched in the lists of genes were identified using Blast2GO (Conesa et al. 2005) with a cutoff of adjusted P value < 0.05. Transcription factors were identified by using the blast tool in the genome database for Rosaceae and homolog comparisons with the Arabidopsis genome (Sook et al. 2018). | en_US |
| dc.description.sponsorship | Hatch Grant Cornell Atkinson Grant Boller Grant | en_US |
| dc.identifier.doi | https://doi.org/10.7298/kksr-7928 | |
| dc.identifier.uri | https://hdl.handle.net/1813/113364 | |
| dc.language.iso | en_US | en_US |
| dc.subject | Differentially expressed genes | en_US |
| dc.subject | enriches genes | en_US |
| dc.subject | gene ontology | en_US |
| dc.title | S Krishna Kumar 2023 PhD Thesis Supplementary Tables | en_US |
| dc.type | dataset | en_US |
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