Assays

This Jupyter Notebook assists you in the analysis of initial rate experiments.

For help on installing the classical Jupyter Notebook, see here: https://jupyter.org/install

For documentation about Juypter Notebooks, see here: https://jupyter-notebook.readthedocs.io/en/stable/

There are multiple tutorials online that help you to learn how to use a Jupyter notebook.

The notebook is provided as an .ipynb and as a .pdf file. The plots the script generates with the default input data are also given as ...

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

Short Name: 01_jun20-wet Assay Class: WET Assay Type: wet Title: June 2020 potato field trial Description: June 2020 potato field trial conducted as part of Ecobreed project from KIS coordinated by dr. Jaka Razinger pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Short Name: 01_jun19-wet Assay Class: WET Assay Type: wet Title: June 2019 potato field trial Description: June 2019 potato field trial conducted as part of Ecobreed project from KIS coordinated by dr. Jaka Razinger pISA Assay creation date: 2021-01-15 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Files connected to study: _S_02_2020

Files connected to study: _S_01_2019

Files connected to investigation: _I_02_FieldTrials

Short Name: 08_SelTargetsA-dry Assay Class: DRY Assay Type: dry Title: Bioinformatics analyses for individual selected target genes Description: In depth bioinformatic analysis for each target gene using various tools to predict possible off-target effects and select a fragment sequence for dsRNA synthesis pISA Assay creation date: 2021-01-14 pISA Assay creator: Marko Petek Phenodata: None Featuredata: Data:

Short Name: 01_may2018-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Hatching, weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Short Name: 01_jun2017-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters (using dsRNA produced in vivo in E coli) Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek, Rok Ferenc Phenodata: ../../phenodata_20210113.txt Featuredata: Data:

Short Name: 03_jun2017-qPCR Assay Class: WET Assay Type: qPCR Title: qPCR for target genes Description: Quantitative PCR (qPCR) for selected target genes using the established methodology at NIB. pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: Lab manager: Kristina Gruden Assay chemistry: mixed Assay optimisation protocol (file path, link or citation): Pippeting: liquid handling station Reaction volume: 5 ul qPCR ...

Short Name: 01_jan2017-phenotyping Assay Class: WET Assay Type: phenotyping Title: Measuring feeding trial parameters Description: Weight gain, survival, photos and other phenotypic observations pISA Assay creation date: 2021-05-10 pISA Assay creator: Marko Petek Phenodata: ../../phenodata_20210113.txt Featuredata: Data: