Assays

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548 Assays visible to you, out of a total of 1034

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:

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:

Contributor: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

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:

Contributor: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: Snapshot 1

DOI: 10.15490/fairdomhub.1.assay.1263.1

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:

Contributor: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

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:

Contributor: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

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: 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:

Contributor: Andrej Blejec

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

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:

Short Name: 01_GC_content-count
Assay Class: DRY
Assay Type: count
Title: GC content and sequence length
Description: A, C, T, G content and sequence length
pISA Assay creation date: 2020-03-09
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata:
Data: ../input/path_to_files.txt

please add your model here - associated to this assay

No description specified

Contributor: Theresa Bender

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

No description specified

Contributor: Theresa Bender

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

No description specified

Contributor: Theresa Bender

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

No description specified

Contributor: Harald Kusch

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Transcriptome analysis suggests a compensatory role of the cofactors coenzyme A and NAD+ in medium-chain acyl-CoA dehydrogenase knockout mice. Expression profiling by high throughput sequencing

Contributor: PoLiMeR_user Martines_data

Assay type: Transcriptomics

Technology type: Rna-seq

Snapshots: No snapshots

Plant material
The same plant material used for transcriptome analysis in (Flis et al., 2016) was the basis of our proteome study. Briefly, Arabidopsis thaliana Col-0 plants were grown on GS 90 soil mixed in a ratio 2:1 (v/v) with vermiculite. Plants were grown for 1 week in a 16 h light (250 μmol m−2 s−1, 20 °C)/8 h dark (6 °C) regime followed by an 8 h light (160 μmol m−2 s−1, 20 °C)/16 h dark (16 °C) regime for one week. Plants were then replanted with five seedlings per pot, transferred for
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Contributor: Finn Bacall

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

Here would be the results from the Analysis part of the Simulation foundry. For the newest version, which was improved based on reviewers comments to represent best practices, of the Simulation Foundry for Methanol-Water mixtures no such results exist yet.

Contributor: Gudrun Gygli

Biological problem addressed: various analyses of molecular dynamics simulations

Snapshots: No snapshots

No description specified

Contributor: Dominik Brilhaus

Assay type: RNA-seq Profiling

Technology type: Illumina HiSeq

Snapshots: No snapshots

No description specified

Contributor: Anne-Marie Galow

Biological problem addressed: Model Analysis Type

Snapshots: No snapshots

Assay: _A_03.1_filtering
Short Name: 03.1_filtering
Assay Class: DRY
Assay Type: filtering
Title: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
Description: Filtering according to biological evidence; removal of contaminants, chimeras and suspicious constructs
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

No description specified

Contributor: Jurgen Haanstra

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

No description specified

Contributor: Jurgen Haanstra

Assay type: Experimental Assay Type

Technology type: Technology Type

Snapshots: No snapshots

No description specified

Contributor: Jurgen Haanstra

Assay type: Cell Count

Technology type: Technology Type

Snapshots: No snapshots

Assay: _A_02.2_assembly-contribution-count
Short Name: 02.2_assembly-contribution-count
Assay Class: DRY
Assay Type: count
Title: assembly contribution count
Description: assembly contribution count, input/output tr2aacds
pISA Assay creation date: 2019-10-22
pISA Assay creator: Maja Zagorscak
Phenodata: None
Featuredata: None
Data: see ./input/path_to_files.txt

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