Swate template Imaging extraction
v1.0.3 released on 01/01/0001
145 Downloads
Template Content
Building Blocks + example values
| Input [Source Name] | Parameter [microscopy sample preparation] | Term Source REF (DPBO:1000143) | Term Accession Number (DPBO:1000143) | Characteristic [prepared organism part] | Term Source REF (DPBO:1000145) | Term Accession Number (DPBO:1000145) | Parameter [generic experimental condition] | Term Source REF (MS:1001814) | Term Accession Number (MS:1001814) | Parameter [antibody] | Term Source REF (DPBO:1000117) | Term Accession Number (DPBO:1000117) | Parameter [staining] | Term Source REF (OBI:0302887) | Term Accession Number (OBI:0302887) | Parameter [channel] | Term Source REF (DPBO:1000113) | Term Accession Number (DPBO:1000113) | Parameter [Gene Identifier] | Term Source REF (NCIT:C48664) | Term Accession Number (NCIT:C48664) | Parameter [gene name] | Term Source REF (MS:1000934) | Term Accession Number (MS:1000934) | Parameter [genome reference sequence] | Term Source REF (DPBO:0000026) | Term Accession Number (DPBO:0000026) | Parameter [microscope slide] | Term Source REF (OBI:0400170) | Term Accession Number (OBI:0400170) | Parameter [Cover Slip] | Term Source REF (NCIT:C126370) | Term Accession Number (NCIT:C126370) | Parameter [liquid layer] | Term Source REF (ENVO:01001273) | Term Accession Number (ENVO:01001273) | Parameter [material fixation] | Term Source REF (DPBO:1000144) | Term Accession Number (DPBO:1000144) | Parameter [cover slip preparation (procedure)] | Term Source REF (SCTID:71661000) | Term Accession Number (SCTID:71661000) | Parameter [high content screening stage] | Term Source REF (EFO:0007555) | Term Accession Number (EFO:0007555) | Parameter [screening library] | Term Source REF (OBI:0100064) | Term Accession Number (OBI:0100064) | Parameter [library version] | Term Source REF (DPBO:1000116) | Term Accession Number (DPBO:1000116) | Parameter [manufacturer] | Term Source REF (OBI:0000835) | Term Accession Number (OBI:0000835) | Parameter [microtiter plate] | Term Source REF (OBI:0000192) | Term Accession Number (OBI:0000192) | Parameter [well] | Term Source REF (DPBO:1000101) | Term Accession Number (DPBO:1000101) | Parameter [well Number] | Term Source REF (DPBO:1000102) | Term Accession Number (DPBO:1000102) | Parameter [siRNA identifier] | Term Source REF (DPBO:1000103) | Term Accession Number (DPBO:1000103) | Parameter [sense sequence] | Term Source REF (DPBO:1000109) | Term Accession Number (DPBO:1000109) | Parameter [antisense sequence] | Term Source REF (DPBO:1000110) | Term Accession Number (DPBO:1000110) | Parameter [reagent design genome reference version] | Term Source REF (DPBO:1000136) | Term Accession Number (DPBO:1000136) | Parameter [compound name] | Term Source REF (DPBO:1000104) | Term Accession Number (DPBO:1000104) | Parameter [compound identifier] | Term Source REF (DPBO:1000105) | Term Accession Number (DPBO:1000105) | Parameter [compound class] | Term Source REF (DPBO:1000106) | Term Accession Number (DPBO:1000106) | Parameter [dose] | Term Source REF (OBI:0000984) | Term Accession Number (OBI:0000984) | Parameter [time] | Term Source REF (PATO:0000165) | Term Accession Number (PATO:0000165) | Parameter [ORF identifier] | Term Source REF (data:2795) | Term Accession Number (data:2795) | Parameter [control type] | Term Source REF (DPBO:1000111) | Term Accession Number (DPBO:1000111) | Parameter [control specification] | Term Source REF (DPBO:1000137) | Term Accession Number (DPBO:1000137) | Parameter [quality control] | Term Source REF (DPBO:1000112) | Term Accession Number (DPBO:1000112) | Parameter [quality control comments] | Term Source REF (DPBO:1000138) | Term Accession Number (DPBO:1000138) | Output [Sample Name] |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| remove leaflets from shoot | shoot without leaves | compound treatment | Nup107-aa33-51 antibody | DAPI | DAPI:nuclei;TRITC:HA_Flag tagged protein | ENSG00000117399 | RuBisCo | GRCh37, Ensembl release 61, Feb 2011 | Sigma-Aldrich, microscope plain, size 25 mm × 75 mm | BRAND® L × W 18 mm × 18 mm, square; Sigma-Aldrich | water | 50% v/v ethanol, 3.7% v/v formaldehyde, 5% v/v acetic acid | nailpolish | primary screen | haploid deletion library | Bioneer haploid deletion library v.2 modified to generate a GFP-tubulin expressing library (Dixon et al., 2008). | Ambion | JL_120731_S6A | A1 | 1 | s2748 | CGAAAUGACUAUUACCUGATT | UCAGGUAAUAGUCAUUUCGGA | GRCh37, Ensembl release 61, Feb 2011 | DL-alpha-Methyl-p-tyrosine | 78875 | Neurotransmission | 10 nanogram per milliliter | 1 hour | 9994 | empty well | checks for transfection | pass | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| extract archargonia from gametophyte | antibody target | Alexa Fluor 546 conjugated secondary antibody | GFP:endogenous alpha tubulin 2;Cascade blue:growth media | PSORS1C3 | secondary screen | compound library | LOPAC-1280 compound library | Sigma | 1921 | C3 | s20068 | CGGAAGCAGUUCCAACUUUtt | AAAGUUGGAACUGCUUCCGtt | N-Acetyl-L-Cysteine | 78955 | Glutamate | 168 | positive control | gives strong phenotype | fail | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| validation screen | siRNA library | 6-Methoxy-1,2,3,4-tetrahydro-9H-pyrido[3,4b] indole | negative control | wild type | no cells | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| HA-Flag protein fusion library | non-targeting siRNA | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| no treatment |