Internal Datasets

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Descriptions for datasets are indicated below headings. Sources of datastes are indicated in [brackets]. Organisms are noted in heading or in (parentheses).

Proteomics[edit]

Low complexity protein regions[edit]

Calculated amino acid complexities for each protein in the proteome using Shannon's entropy formula. [mafree]

Yeast (S. cerevisiae): File:130329 complexity Scerevisiae 10aa window.pdf

Worm (C. elegans): File:130329 complexity Celegans 10aa window.pdf

Human (H. sapeins): 

Disordered protein regions[edit]

Calculated amino acid disorderedness for each protein in the proteome using IUPred. [mafree]

Yeast (S. cerevisiae): File:130114 Disorder probabilities Scerevisiae.pdf

Worm (C. elegans): File:130223 Disorder probabilities Celegans.pdf

Human (H. sapiens): 

Our mass spectrometry datasets
[edit]

New page


Other mass spectrometry datasets[edit]

C. elegans phosphoproteome [Zielinska D (2009) J Proteome Res]: https://kimlab.johnshopkins.edu/images/1/13/2009_J._Proteome_Res._Zielinska.xls

C. elegans kinase motifs [Zielinska D (2009) J Proteome Res]: https://kimlab.johnshopkins.edu/images/7/71/2009_J._Proteome_Res._Zielinska-4.xls.pdf

Screens[edit]

eri-1;JR screen[edit]

<Description>

File:• EJ F1 FINAL POSITIVES.xls File:• EJ Po FINAL POSITIVES.xls

Integrative genomics screen[edit]

Table of all C. elegans genes with continuous scores for a collection of datasets relevant to small RNAs including: genome-wide screens in C. elegans and D. melanogaster, proteomics coverage, and phylogenetic profile correlation with siRNA or piRNA pathway cofactors. [Tabach Y (2013) Nature]

File:Yuval IntegrativeGenomics.xlsx

Yeast one-hybrid 21UR motif screen[edit]

Yeast one-hybrid screen to identify proteins that bind the 21U RNA upstream sequence to affect 21U RNA biogenesis. "genes to investigate" sheet: summary of positives and information about them from WormBase. Confidence is increased by being sequenced multiple times in the screen and by appearing in more than one screen. "RNAi" sheet: RNA clones for positives that were tested by qPCR. [dayama]

File:110624one hybrid seq results.xlsx

Published screens[edit]

C. elegans cell polarity genes[Fievet BT (2012) Nat Cell Biol]: File:Fievet NatCellBiol 2012 Cell Polarity.xls

C. elegans essential gene network [Green RA (2011) Cell]: File:Green Cell 2011 essential gene network screen.xlsx

C. elegans miRNA pathway components [Parry DH (2007) Curr Biol]: File:Parry CurrBiol 2007 RNAi screen miRNA pathway.xlsx

C. elegans P granule components by RNAi [Updike D and Strome S (2009) Genetics]: File:Updike Genetics 2009 RNAi screen Pgranule.xlsx



Libraries[edit]

SF/JK library
[edit]

RNAi clones hand-curated for genes possessing domains that may be involved in RNAi. [jnkim]

https://kimlab.johnshopkins.edu/images/9/90/SF_JK_RNAi_screen.xlsx


S. cerevisiae YKO MAT a library
[edit]

Collection of deletion strains generated by a PCR-based gene deletion strategy to generate start- to stop-codon deletions. Each deletion was replaced with a KanMX module and uniquely tagged with one or two 20mer sequences (barcodes). An overview of the Saccharomycese Genome Deletion Project can be found here. [kvishal]

File: 130405_YSC1053_Mat_a_obs_v5.0_Final.xls


Source Biosciences RNAi library clones[edit]

Excel database of newly available supplemental clone library from Source Biosciences. SourceBiosci_version_whole_genome_RNAi_2012: RNAi library clones (original and supplemental together) as they exist in Source Biosciences library. Notes sheet contains description of the coding system for clone coordinates. SourceBiosci_supplementals_only_sorted: Supplemental clones only.  Each sheet has all the supplemental clones listed on it (from all chromosomes) but the clones have been sorted in 3 ways: (1) future 96 well coordinates; (2) current 384 well coordinates; (3) genepairs names (alphabetical).

File:130628 SourceBiosci supplementals only sorted.xlsx

File:130628 SourceBiosci version whol genomeRNAi 2012.xlsx

Genomics[edit]

In progress.


Metabolomics[edit]

S. cerevisiae +/- oxygen[edit]

Quantification of metabolic output compounds from yeast under log growth and oxygen depletion conditions. [tinghan]

File:2013-03-27-yeast-gly-tca-report.xlsx

Other[edit]

D. melanogaster RNA-binding proteins [mafree]: File:Drosophila RNA-binding proteins DRSC-UM Final.xlsx

S. cerevisiae and C. elegans homologs [mafree]: File:Scerevisiae Celegans Homologs.xlsx

C. elegans P granule components [Updike D and Strome S (2010) J Androl]: File:2010UpdikeStromPgranuleComponents.xlsx

C. elegans OrthoList [Shaye D and Greenwald I (2011) PLoS One]: File:OrthoList 2011 Shaye PLoSOne.xls

C. elegans germline genes [Reinke V (2004) Dev]: https://kimlab.johnshopkins.edu/images/7/73/Reinke_Dev_2004_germline_genes.xlsx