Assays

Short Name: 06_extr_bact-assembly Assay Class: DRY Assay Type: assembly Title: De novo genome assembly of bacteria Description: De novo genome assembly of bacteria from rcf-extracted shotgun metagenomics reads pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 05_extr_reads-rcf Assay Class: DRY Assay Type: rcf Title: Extract reads for specific taxa using recentrifuge (rcf) Description: Extract reads for specific bacterial taxa using recentrifuge for further use in de novo genome assembly pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 03-Centrifuge Assay Class: DRY Assay Type: Centrifuge Title: Centrifuge classification of DNA reads Description: Taxonomic classification of shotgun gDNA Illumina reads from CPB gut microbiome and visualization using pavian pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data: http://stork/dirindex/fitostorage/fitostorageA/datarepo/ngs_omics/NGS_lde_dna-seq_2018_mpe_CPB-gut-metagenome/data/

Short Name: 02-DNASeq Assay Class: WET Assay Type: DNASeq Title: Shotgun CPB gut microbiome DNA-Seq Description: Sequencing of CPB gut microbiome genomic DNA to determine the offect of dsRNA feeding on the microbial flora pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata:

Short Name: 01-DNAisol Assay Class: WET Assay Type: DNAisol Title: Isolation of gDNA from CPB gut content Description: Isolation of gDNA from CPB gut content pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 07_allReads_meta-assembly Assay Class: DRY Assay Type: assembly Title: De novo assembly of metagenome using metaSPAdes Description: De novo assembly of microbes present in the metagenome using metaSPAdes using all reads without selection but with rigorous filtering and read correction pISA Assay creation date: 2021-01-16 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 04_DE_divers-R Assay Class: DRY Assay Type: R Title: Diversity analysis and differential abundance Description: Metagenomic diversity analyisis using kraken data in R and differential abundance using phyloseq and DESeq R packages. pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Analyst: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 02_CLC-RNASeq Assay Class: DRY Assay Type: RNASeq Title: CLC RNA-Seq data analysis dsEGFP vs water treatment Description: CLC RNA-Seq data analysis dsEGFP vs water treatment pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata: Data:

Short Name: 01_RNA-Seq_dsEGFP-NGS Assay Class: WET Assay Type: NGS Title: Treatment of dsEGFP and water treated samples before sending for RNA-Seq Description: RNA-Seq DNase and cleanup of dsEGFP and water treated CPB larval samples from the june2017 experiment to determine non-specific response of dsRNA consumption pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210115.txt Featuredata:

Files connected to study: _S_02_metagenome_resp

Files connected to study: _S_01_ns-dsRNA_trans

Files connected to investigation: _I_03_Omics