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We find that venom composition and arsenal of toxin-producing cells change dramatically between developmental stages of this species.
Interesting that venom changes as the animal grows.
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elifesciences.org elifesciences.org
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holometabolous,
Other insects that are considered holometabolous include some common ones such as: house flies, mosquitoes, gnats, monarch butterflies and some moths. Both the larvae and adults occupy the decaying source at different time frames which allows the interactions between the microbes.
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D. melanogaster do not live alone. Their decaying host resources are also home to many microbes, as well as to other arthropods, including other Drosophila species, all of which they interact with (see Video 1, 2). Some microbes in the decaying material themselves provide food for D. melanogaster, being selectively consumed by larvae or adults
The microbes not only live in this environment, but also serve as a food source for the flies. This explains how the D. melanogaster depend on other organisms in their habitat.
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elifesciences.org elifesciences.org
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taking fully advantage of our algorithm might involve coordination between multiple colleagues in a lab who are constructing plasmids with different expected sequences.
This is something a local core like GCEC can help with
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it could be further reduced by executing time-consuming dynamic programming only for some query-reference pairs that necessitate high levels of accuracy and by introducing parallel computing
Nice, Any other ideas to reduce RAM use?
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theoretical minimum number of reads that is required for the reliable consensus calculation is 30 reads per plasmid
Does this depend on the plasmid length and the preperation kit before sequencing that determines fragmentation?
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plasmid_160905
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ATCC # CRL-11268
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RRID:AB_10915138
DOI: 10.7554/eLife.105264.2
Resource: (BioLegend Cat# 334108, RRID:AB_10915138)
Curator: @scibot
SciCrunch record: RRID:AB_10915138
-
RRID:AB_1210456
DOI: 10.7554/eLife.105264.2
Resource: (Thermo Fisher Scientific Cat# 14-4502-82, RRID:AB_1210456)
Curator: @scibot
SciCrunch record: RRID:AB_1210456
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RRID:AB_2565006
DOI: 10.7554/eLife.105264.2
Resource: (BioLegend Cat# 901501, RRID:AB_2565006)
Curator: @scibot
SciCrunch record: RRID:AB_2565006
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RRID:AB_2573205
DOI: 10.7554/eLife.105264.2
Resource: (Thermo Fisher Scientific Cat# 17-4015-82, RRID:AB_2573205)
Curator: @scibot
SciCrunch record: RRID:AB_2573205
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RRID:AB_891480
DOI: 10.7554/eLife.105264.2
Resource: (Thermo Fisher Scientific Cat# 14-0495-82, RRID:AB_891480)
Curator: @scibot
SciCrunch record: RRID:AB_891480
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RRID:AB_1279055
DOI: 10.7554/eLife.105264.2
Resource: (BioLegend Cat# 328620, RRID:AB_1279055)
Curator: @scibot
SciCrunch record: RRID:AB_1279055
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RRID:AB_10562535
DOI: 10.7554/eLife.105264.2
Resource: (Thermo Fisher Scientific Cat# A10540, RRID:AB_10562535)
Curator: @scibot
SciCrunch record: RRID:AB_10562535
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Addgene, #52961
DOI: 10.7554/eLife.105264.2
Resource: RRID:Addgene_52961
Curator: @dhovakimyan1
SciCrunch record: RRID:Addgene_52961
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Addgene, #133301
DOI: 10.7554/eLife.105264.2
Resource: None
Curator: @dhovakimyan1
SciCrunch record: RRID:Addgene_133301
-
Addgene, #12260
DOI: 10.7554/eLife.105264.2
Resource: RRID:Addgene_12260
Curator: @dhovakimyan1
SciCrunch record: RRID:Addgene_12260
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Addgene, #8454
DOI: 10.7554/eLife.105264.2
Resource: RRID:Addgene_8454
Curator: @dhovakimyan1
SciCrunch record: RRID:Addgene_8454
-
Addgene, #52963
DOI: 10.7554/eLife.105264.2
Resource: RRID:Addgene_52963
Curator: @dhovakimyan1
SciCrunch record: RRID:Addgene_52963
Tags
- RRID:Addgene_12260
- RRID:AB_10915138
- RRID:AB_1210456
- RRID:AB_2621341
- RRID:AB_10562535
- RRID:AB_258284
- RRID:AB_891480
- RRID:AB_262044
- RRID:AB_1279055
- DOI:10.7554/eLife.105264.2
- RRID:AB_2633282
- RRID:AB_439702
- RRID:Addgene_52961
- RRID:Addgene_133301
- RRID:Addgene_8454
- RRID:AB_258315
- RRID:AB_2534072
- RRID:Addgene_52963
- RRID:AB_390917
- RRID:AB_2565006
- RRID:AB_2546029
- RRID:AB_2573205
Annotators
URL
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elifesciences.org elifesciences.org
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The Jackson Laboratory, Stock # 013044
DOI: 10.7554/eLife.100488.2
Resource: (IMSR Cat# JAX_013044,RRID:IMSR_JAX:013044)
Curator: @inessasarian
SciCrunch record: RRID:IMSR_JAX:013044
-
The Jackson Laboratory, Stock # 022730
DOI: 10.7554/eLife.100488.2
Resource: (IMSR Cat# JAX_022730,RRID:IMSR_JAX:022730)
Curator: @inessasarian
SciCrunch record: RRID:IMSR_JAX:022730
-
Ab167453 Abcam
DOI: 10.7554/eLife.100488.2
Resource: (EnCor Biotechnology Cat# RPCA-mCherry, RRID:AB_2571870)
Curator: @inessasarian
SciCrunch record: RRID:AB_2571870
-
A10262 Invitrogen
DOI: 10.7554/eLife.100488.2
Resource: (Thermo Fisher Scientific Cat# A10262, RRID:AB_2534023)
Curator: @inessasarian
SciCrunch record: RRID:AB_2534023
-
The Jackson Laboratory, Stock # 000664
DOI: 10.7554/eLife.100488.2
Resource: RRID:IMSR_JAX:000664
Curator: @inessasarian
SciCrunch record: RRID:IMSR_JAX:000664
-
The Jackson Laboratory, Stock # 031629
DOI: 10.7554/eLife.100488.2
Resource: (IMSR Cat# JAX_031629,RRID:IMSR_JAX:031629)
Curator: @inessasarian
SciCrunch record: RRID:IMSR_JAX:031629
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#51503
DOI: 10.7554/eLife.100488.2
Resource: RRID:Addgene_51503
Curator: @inessasarian
SciCrunch record: RRID:Addgene_51503
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-
elifesciences.org elifesciences.org
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Invitrogen A78945
DOI: 10.7554/eLife.99848.3
Resource: (Thermo Fisher Scientific Cat# A78945, RRID:AB_2910652)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2910652
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Synaptic Systems, Cat. No. 226 017
DOI: 10.7554/eLife.99848.3
Resource: (Synaptic Systems Cat# 226 017, RRID:AB_2864765)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2864765
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IDR
DOI: 10.7554/eLife.99848.3
Resource: Image Data Resource (IDR) (RRID:SCR_017421)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_017421
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elifesciences.org elifesciences.org
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MNE
DOI: 10.7554/eLife.99478.2
Resource: MNE software (RRID:SCR_005972)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_005972
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Psychophysics Toolbox
DOI: 10.7554/eLife.99478.2
Resource: Psychophysics Toolbox (RRID:SCR_002881)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002881
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-
elifesciences.org elifesciences.org
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OpenCV
DOI: 10.7554/eLife.99140.2
Resource: OpenCV (RRID:SCR_015526)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_015526
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Python
DOI: 10.7554/eLife.99140.2
Resource: Python Programming Language (RRID:SCR_008394)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_008394
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-
elifesciences.org elifesciences.org
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PostgreSQL v15
DOI: 10.7554/eLife.98759.2
Resource: PostgreSQL (RRID:SCR_021067)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_021067
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elifesciences.org elifesciences.org
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CellChat
DOI: 10.7554/eLife.98558.2
Resource: CellChat (RRID:SCR_021946)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_021946
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BioConductor
DOI: 10.7554/eLife.98558.2
Resource: Bioconductor (RRID:SCR_006442)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_006442
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limma
DOI: 10.7554/eLife.98558.2
Resource: LIMMA (RRID:SCR_010943)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_010943
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QuPath software
DOI: 10.7554/eLife.98558.2
Resource: QuPath (RRID:SCR_018257)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_018257
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R software
DOI: 10.7554/eLife.98558.2
Resource: R Project for Statistical Computing (RRID:SCR_001905)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001905
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Mapix
DOI: 10.7554/eLife.98558.2
Resource: Mapix (RRID:SCR_002723)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002723
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Cytoscape
DOI: 10.7554/eLife.98558.2
Resource: Cytoscape (RRID:SCR_003032)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_003032
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STRING
DOI: 10.7554/eLife.98558.2
Resource: STRING (RRID:SCR_005223)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_005223
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Tibco Spotfire
DOI: 10.7554/eLife.98558.2
Resource: Spotfire (RRID:SCR_008858)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_008858
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GraphPad Prism
DOI: 10.7554/eLife.98558.2
Resource: GraphPad Prism (RRID:SCR_002798)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002798
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elifesciences.org elifesciences.org
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TrakEM2
DOI: 10.7554/eLife.97964.2
Resource: TrakEM2 (RRID:SCR_008954)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_008954
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CATMAID
DOI: 10.7554/eLife.97964.2
Resource: CATMAID (RRID:SCR_006278)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_006278
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elifesciences.org elifesciences.org
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Prism
DOI: 10.7554/eLife.97364.2
Resource: GraphPad Prism (RRID:SCR_002798)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002798
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elifesciences.org elifesciences.org
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Autodock
DOI: 10.7554/eLife.97341.2
Resource: None
Curator: @areedewitt04
SciCrunch record: RRID:SCR_012746'
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Pymol
DOI: 10.7554/eLife.97341.2
Resource: PyMOL (RRID:SCR_000305)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_000305
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YASARA
DOI: 10.7554/eLife.97341.2
Resource: YASARA (RRID:SCR_017591)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_017591
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Origin
DOI: 10.7554/eLife.97341.2
Resource: Origin (RRID:SCR_014212)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_014212
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elifesciences.org elifesciences.org
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RDKit
DOI: 10.7554/eLife.97330.2
Resource: RDKit: Open-Source Cheminformatics Software (RRID:SCR_014274)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_014274
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PyTorch
DOI: 10.7554/eLife.97330.2
Resource: PyTorch (RRID:SCR_018536)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_018536
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elifesciences.org elifesciences.org
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RAxML
DOI: 10.7554/eLife.96704.2
Resource: RAxML (RRID:SCR_006086)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_006086
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MAFFT
DOI: 10.7554/eLife.96704.2
Resource: MAFFT (RRID:SCR_011811)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_011811
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HMMER
DOI: 10.7554/eLife.96704.2
Resource: Hmmer (RRID:SCR_005305)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_005305
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Pymol
DOI: 10.7554/eLife.96704.2
Resource: PyMOL (RRID:SCR_000305)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_000305
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cryoSPARC
DOI: 10.7554/eLife.96704.2
Resource: cryoSPARC (RRID:SCR_016501)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_016501
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ChimeraX
DOI: 10.7554/eLife.96704.2
Resource: UCSF ChimeraX (RRID:SCR_015872)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_015872
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elifesciences.org elifesciences.org
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Ethovision XT15 (Noldus)
DOI: 10.7554/eLife.95764.3
Resource: EthoVision XT (RRID:SCR_000441)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_000441
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Python
DOI: 10.7554/eLife.95764.3
Resource: Python Programming Language (RRID:SCR_008394)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_008394
-
R
DOI: 10.7554/eLife.95764.3
Resource: R Project for Statistical Computing (RRID:SCR_001905)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001905
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elifesciences.org elifesciences.org
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ImageJ
DOI: 10.7554/eLife.95557.2
Resource: ImageJ (RRID:SCR_003070)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_003070
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IMOD
DOI: 10.7554/eLife.95557.2
Resource: IMOD (RRID:SCR_003297)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_003297
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USCF Chimera
DOI: 10.7554/eLife.95557.2
Resource: UCSF Chimera (RRID:SCR_004097)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_004097
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USCF ChimeraX
DOI: 10.7554/eLife.95557.2
Resource: UCSF ChimeraX (RRID:SCR_015872)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_015872
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MotionCor2
DOI: 10.7554/eLife.95557.2
Resource: MotionCor2 (RRID:SCR_016499)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_016499
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elifesciences.org elifesciences.org
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MAT-LAB
DOI: 10.7554/eLife.94918.2
Resource: MATLAB (RRID:SCR_001622)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001622
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elifesciences.org elifesciences.org
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MATLAB
DOI: 10.7554/eLife.94578.2
Resource: MATLAB (RRID:SCR_001622)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001622
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R
DOI: 10.7554/eLife.94578.2
Resource: R Project for Statistical Computing (RRID:SCR_001905)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_001905
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elifesciences.org elifesciences.org
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GraphPad Prism
DOI: 10.7554/eLife.94334.2
Resource: GraphPad Prism (RRID:SCR_002798)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002798
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Adobe Photoshop CC
DOI: 10.7554/eLife.94334.2
Resource: Adobe Photoshop (RRID:SCR_014199)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_014199
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Sigma-Aldrich, Cat # A6154
DOI: 10.7554/eLife.94334.2
Resource: (Sigma-Aldrich Cat# A6154, RRID:AB_258284)
Curator: @areedewitt04
SciCrunch record: RRID:AB_258284
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Abcam, ab30359
DOI: 10.7554/eLife.94334.2
Resource: (Abcam Cat# ab30359, RRID:AB_726286)
Curator: @areedewitt04
SciCrunch record: RRID:AB_726286
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Abcam, ab56
DOI: 10.7554/eLife.94334.2
Resource: (Abcam Cat# ab56, RRID:AB_304976)
Curator: @areedewitt04
SciCrunch record: RRID:AB_304976
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Abcam, ab166859
DOI: 10.7554/eLife.94334.2
Resource: (Abcam Cat# ab166859, RRID:AB_2801547)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2801547
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elifesciences.org elifesciences.org
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MAB4470, R&D Systems
DOI: 10.7554/eLife.94288.2
Resource: (R and D Systems Cat# MAB4470, RRID:AB_1293549)
Curator: @areedewitt04
SciCrunch record: RRID:AB_1293549
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ab124937, Abcam
DOI: 10.7554/eLife.94288.2
Resource: (Abcam Cat# ab124937, RRID:AB_11000960)
Curator: @areedewitt04
SciCrunch record: RRID:AB_11000960
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MAB66861, R&D Systems
DOI: 10.7554/eLife.94288.2
Resource: (R and D Systems Cat# MAB66861, RRID:AB_10973343)
Curator: @areedewitt04
SciCrunch record: RRID:AB_10973343
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ab64159, Abcam
DOI: 10.7554/eLife.94288.2
Resource: (Abcam Cat# ab64159, RRID:AB_2266875)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2266875
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4H8-2, Sigma
DOI: 10.7554/eLife.94288.2
Resource: (Sigma-Aldrich Cat# L0663, RRID:AB_477153)
Curator: @areedewitt04
SciCrunch record: RRID:AB_477153
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86298, Cell Signaling Technology
DOI: 10.7554/eLife.94288.2
Resource: (Cell Signaling Technology Cat# 86298, RRID:AB_2715541)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2715541
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2118, Cell Signaling Technology
DOI: 10.7554/eLife.94288.2
Resource: (Cell Signaling Technology Cat# 2118, RRID:AB_561053)
Curator: @areedewitt04
SciCrunch record: RRID:AB_561053
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GraphPad Prism 8
DOI: 10.7554/eLife.94288.2
Resource: GraphPad Prism (RRID:SCR_002798)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002798
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elifesciences.org elifesciences.org
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Patchmaster software (HEKA electronics
DOI: 10.7554/eLife.93749.2
Resource: Patchmaster (RRID:SCR_000034)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_000034
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GraphPad Prism 9
DOI: 10.7554/eLife.93749.2
Resource: GraphPad Prism (RRID:SCR_002798)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002798
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elifesciences.org elifesciences.org
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sc-13538, Santa Cruz Biotechnology
DOI: 10.7554/eLife.92796.2
Resource: (Santa Cruz Biotechnology Cat# sc-13538, RRID:AB_626690)
Curator: @areedewitt04
SciCrunch record: RRID:AB_626690
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925-32210, Li-COR Biosciences
DOI: 10.7554/eLife.92796.2
Resource: (LI-COR Biosciences Cat# 925-32210, RRID:AB_2687825)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2687825
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sc-166029 Santa Cruz Biotechnology
DOI: 10.7554/eLife.92796.2
Resource: (Santa Cruz Biotechnology Cat# sc-166029, RRID:AB_2275892)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2275892
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ab22595, Abcam
DOI: 10.7554/eLife.92796.2
Resource: (Abcam Cat# ab22595, RRID:AB_2069006)
Curator: @areedewitt04
SciCrunch record: RRID:AB_2069006
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ab92726, Abcam
DOI: 10.7554/eLife.92796.2
Resource: (Abcam Cat# ab92726, RRID:AB_10561589)
Curator: @areedewitt04
SciCrunch record: RRID:AB_10561589
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ab10241 Abcam
DOI: 10.7554/eLife.92796.2
Resource: (Abcam Cat# ab10241, RRID:AB_296978)
Curator: @areedewitt04
SciCrunch record: RRID:AB_296978
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sc-5275, Santa Cruz Biotechnology
DOI: 10.7554/eLife.92796.2
Resource: (Santa Cruz Biotechnology Cat# sc-5275, RRID:AB_627877)
Curator: @areedewitt04
SciCrunch record: RRID:AB_627877
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elifesciences.org elifesciences.org
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Jellyfish
DOI: 10.7554/eLife.92618.2
Resource: Jellyfish (RRID:SCR_005491)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_005491
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elifesciences.org elifesciences.org
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Jackson Labs, 007914
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_007914,RRID:IMSR_JAX:007914)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:007914
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Jackson Labs, 028364
DOI: 10.7554/eLife.90596.2
Resource: RRID:IMSR_JAX:028364
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:028364
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mouse genomic BAC library
DOI: 10.7554/eLife.90596.2
Resource: Gene Expression Nervous System Atlas (RRID:SCR_002721)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_002721
-
Jackson Labs, 027720
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_027720,RRID:IMSR_JAX:027720)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:027720
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Jackson labs, 021504
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_021504,RRID:IMSR_JAX:021504)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:021504
-
Jackson Labs, 007900
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_007900,RRID:IMSR_JAX:007900)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:007900
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Jackson Labs, 026220
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_026220,RRID:IMSR_JAX:026220)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:026220
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Jackson Labs, 027719
DOI: 10.7554/eLife.90596.2
Resource: (IMSR Cat# JAX_027719,RRID:IMSR_JAX:027719)
Curator: @areedewitt04
SciCrunch record: RRID:IMSR_JAX:027719
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elifesciences.org elifesciences.org
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Stan
DOI: 10.7554/eLife.89892.2
Resource: Stan (RRID:SCR_018459)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_018459
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elifesciences.org elifesciences.org
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BEAST
DOI: 10.7554/eLife.87018.4
Resource: BEAST (RRID:SCR_010228)
Curator: @areedewitt04
SciCrunch record: RRID:SCR_010228
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elifesciences.org elifesciences.org
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Addgene: 74099
DOI: 10.7554/eLife.107067.1
Resource: RRID:Addgene_74099
Curator: @evieth
SciCrunch record: RRID:Addgene_74099
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HEK293S GnTI- (CRL-3022)
DOI: 10.7554/eLife.107067.1
Resource: (RRID:CVCL_A785)
Curator: @evieth
SciCrunch record: RRID:CVCL_A785
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HEK293 (CRL-1573)
DOI: 10.7554/eLife.107067.1
Resource: (DSMZ Cat# ACC-305, RRID:CVCL_0045)
Curator: @evieth
SciCrunch record: RRID:CVCL_0045
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elifesciences.org elifesciences.org
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#36355 GD VDRC
DOI: 10.7554/eLife.106169.1
Resource: RRID:Flybase_FBst0461646
Curator: @evieth
SciCrunch record: RRID:Flybase_FBst0461646
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#26899 Bloomington Drosophila Stock Center
DOI: 10.7554/eLife.106169.1
Resource: RRID:BDSC_26899
Curator: @evieth
SciCrunch record: RRID:BDSC_26899
-