Gan_yeast_tomo_log_shared
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EMPIAR-10227SpeciesStrainGenotypeTreatmentPhenotypeSampleInstrument(s)KeV(s)Camera(s)Other EMPIARDetails are in these papers
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US1363_G1S. cerevisiaeUS1363MATa bar1(unmarked) his3 leu2 trp1 ura3α-factor arrestarrest in G1cryosectionsTitan Krios300Falcon II10062Chen, 2016Liang, 2012
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US1363_nocodazoleS. cerevisiaeUS1363MATa bar1Δ ade2-1 can1-100 leu2-3 his3-11 ura3 trp1-1 (Wild type)nocodazole treatmentarrest in prometaphasecryosectionsTitan Krios300Falcon II10159Ng, 2018Liang, 2012
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US8133_nocodazoleS. cerevisiaeUS8133MATa bar1-1, ura3-1, leu2-3,112, his3-11, can1-100, ade2-1 Dam1-GFP:TRP1nocodazole treatmentarrest in prometaphase; Dam1p-GFPcryosectionsTitan Krios300Falcon II10159Ng, 2018Ng, 2018
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US1375_metaphaseS. cerevisiaeUS1375MATa ura3 his3 cdc20Δ:LEU2 GAL-CDC20::TRP11. α-factor arrest
2. α-factor washout
3. wait 3 hours 40 minutes
arrest @ metaphasecryosectionsTitan Krios300Falcon II10062, 10159Chen, 2016Ng, 2018
Krishnan, 2004
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US4780_TEV-cohesinS. cerevisiaeUS4780MATa, MET3-HA-CDC20: URA3, scc1D:HIS3, SCC1TEV268-HA3-LEU2, GAL-NLS-myc9-TEV protease-NLS2::TRP1, tetR-GFP: HIS3galactosemetaphase, no cohesioncryosectionsTitan Krios300Falcon II10159Ng, 2018Ng, 2018
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Graphical summaries
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Datasets indicated in red text
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Feedback form
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Useful commands
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unzip all data in directory "US1363_G1"
lbunzip2 US1363_G1_tilt/*.bz2
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load tilt series numbered 010 to 019 in slicer
3dmod -S US1363_G1_tomo/14oct31a__01*.rec
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load many many tilt series w/o hitting max memory
3dmod -bin 3 14oct31_*.mrc
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Tutorials & tools
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Cryo-EM basics
Caltech cryo-EM course
An online introductory course taught by Grant Jensen
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Cryo-EM advancedEM-University
Includes the above videos and more; taught by Matthijn Vos and Grant Jensen
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SoftwareIMOD
The IMOD package contains both Etomo (reconstruction) and 3dmod (tutorial), along with many other command-line tools
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ReconstructionEtomo text tutorial
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Reconstruction
Etomo video tutorial
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Visualization3dmod tutorial
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Reconstruction & subtomogram analysis
IMOD RML workshop
Additional tutorial data
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Tools & info from our lab
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Our lab
https://www.anaphase.org/
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Useful scripts
https://github.com/anaphaze/ot-tools
Note: these scripts have depencies on cryo-EM software dependencies
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"Noise" files
https://www.ebi.ac.uk/pdbe/emdb/empiar/entry/10179/
Used for CTF fitting and phase flipping
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