Assays

Results from lipidomics analyses performed in cod liver microsomes of cod exposed to PAH and PFAS mixtures.

Some results from proteomics analyses of cod liver exposed to PAH and PFAS

Concentration of the egg yolk precursor protein vitellogenin in cod plasma

Gene expression of cyp1a and acox1 measured by qPCR in liver of Atlantic cod exposed to PAHs and PFASs

Semi-quantitative determination of Cyp1a protein amount in cod liver, using the ELISA method.

Measurement of DNA fragmentation using the Comet Assay, in white blood cells of Atlantic cod exposed to PAHs and PFASs

Measurements of PAH metabolites in bile (1-OH-napthalene, 2-OH-naphthalene, 1-OH-phenanthrene, 1-OH-pyrene) and PFAS compounds in liver (PFOS, PFOA, PFNA, PFTrDa)
in Atlantic cod exposed to mixtures of PAHs and PFASs.

Includes physiological informations regarding the fish samples: Weight, length, gender, date sampled, comments regarding physical apperance, in addition to calculations of condition factor (K), hepatosomatic index (HSI) and gonadosomatic index (GSI).

Enzyme activity of the oxidative stress enzymes glutathione S-transferase (Gst) and catalase (Cat) measured in cod liver

Assay: _A_02.4_STAR
Short Name: 02.4_STAR
Assay Class: DRY
Assay Type: STAR
Title: mapping reads back to evigene .tr output
Description: mapping reads back to evigene .tr output using STAR to check the percentage of reads that map
pISA Assay creation date: 2019-10-22
pISA Assay creator: Marko Petek
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

please add your model here - associated to this assay

Data for global pH monitoring for precipitation experiments included in the publication: Microbial-induced calcium carbonate precipitation An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution
Included data: Calibration data and pH time evolution

Optical microscopy experiments for precipitation process.
Images name have the format capture-yearmonthdayhourminutesecond

Data for Raman spectroscopy shown in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution.

Included are the Raman data for precipitation after 1 minute recton time, 3 minutes reaction time and 15 minutes reaction time.

Data for local pH monitoring precipitation experiments in publication: Microbial-induced calcium carbonate precipitation An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution.
Included are the calibration data, the signal from Channel 1 (representing signal from dye SR101) and Channel 3 (representing signal from pH dye R6G-EDA) and Channel 5 (brightfield images).
Resolution is 512x512 pixel, images are recorded every 15 seconds. Data collection startet
...

Data for local pH monitoring expreiments for the dissolution part in publication: Microbial-induced calcium carbonate precipitation: An experimental toolbox for in situ and real-time investigation of micro-scale pH evolution.
Included is data for the calibration, and from the dissolution experiment (Channel 1 data (signal from dye SR101) Channel 3 data (sigenl from dye R6G-EDA, and Channel 5 data (brightfield data)). Resolution is 512x512 pixel, images are recorded every 10sec. Data collection
...

Short Name: 07_Desiree-mapping
Assay Class: DRY
Assay Type: mapping
Title: Desiree mapping
Description: Mapping of Desiree samples (drought stress) to Desiree and Phureja transcriptomes
pISA Assay creation date: 2020-03-11
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Short Name: 05_MSA_3cvs-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: MSA 3cv and GFF-merged
Description: Multiple sequence alignment of Desiree, PW363, Rywal and ITAG/PGSC
pISA Assay creation date: 2020-03-10
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Short Name: cdhit_3cvs-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC
Description: cdhit-est and cdhit-2d on 3cv and ITAG/PGSC
pISA Assay creation date: 2020-03-09
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Short Name: 09_annotation-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: Pan-transcriptome fasta files annotation
Description: Annotation of pan-transcriptome and re-annotation of cultivar-specific transcriptomes
pISA Assay creation date: 2020-03-11
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Supplementary Information linked together

Short Name: 08_centrifuge_3cvs-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: Centrigufe pan-transcriptome sequence classification
Description: Classify cv rep transcripts and pan-transcriptome singletons based on taxonomy
pISA Assay creation date: 2020-03-11
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Short Name: 06_tr_rep-transrate
Assay Class: DRY
Assay Type: transrate
Title: Cultivar representative transcriptome transrate
Description: Transrate on cultivar specific representatives, GFF merged as a reference for CRRB
pISA Assay creation date: 2020-03-11
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Short Name: 03_components_3cvs-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: components
Description: representative and alternative pan-transcriptome CDS and polypeptide fasta files
pISA Assay creation date: 2020-03-10
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data:

Short Name: 04_BUSCO_3cvs-GFFmerged
Assay Class: DRY
Assay Type: GFFmerged
Title: BUSCOs
Description: BUSCO on ITAG, PGSC, ITAG/PGSC merged, pan-transcriptome representatives, pan-transcriptome alternatives, and pan-transcriptome
pISA Assay creation date: 2020-03-10
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data: