Project page for author first pass form

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Instructions

[Sample Author Firstpass form]

Instructions for authors

Congratulations on the publication of your paper!
"title" journal, date
Please click the box next to the type of data your publication includes.
If this is not a primary research article (e.g., this is a review, book chapter, etc.), please click here.

If your paper contains experiments on C. elegans and related nematodes, please continue with the form below.
Click the "?" to find out more about the data type.

Author First-pass form postgres table details

Species Data type Section Data type PGdb name Instructions for author Curator Flagged
SPECIES:
C. elegans (default checked) celegans Please uncheck if you are not reporting data for C. elegans.
C. elegans other than Bristol cnonbristol Please indicate if data for C. elegans isolates other than N2 (Bristol) are presented in this paper.
Nematodes other than C. elegans nematode Please indicate if data is presented for any species other than C. elegans, e.g., C. briggsae, Pristionchus pacificus, Brugia malayi, etc.
Non-nematode species nonnematode Please indicate if data is presented for any non-nematode species.
GENE IDENTIFICATION AND MAPPING:
nematode Genes studied in this paper genestudied Please use text box below to list any genes that were a focus of analysis in this research article.
nematode Newly cloned gene genesymbol Please indicate if your paper reports a new symbol for a known locus or the name of a newly defined locus, if it doesn't exist in WormBase already. genenames@wormbase.org, vanauken@its.caltech.edu
elegans Genetic mapping data mappingdata Please indicate if your paper contains 3-factor interval mapping data, i.e., genetic data only. Include Df or Dp data, but no SNP interval mapping. genenames@wormbase.org
GENE FUNCTION:
Mutant, overexpression, or chemical-based phenotypes
nematode? Phenotype analysis newmutant Please indicate if your paper reports any nonRNAi-based phenotype for a mutant. emsch@its.caltech.edu, garys@its.caltech.edu, jolenef@its.caltech.edu
elegans Overexpression phenotype overexpr Please indicate if your paper reports an abnormal phenotype based on the overexpression of a gene or gene construct. E.g., "...constitutively activated SCD-2(neu*) receptor caused 100% of animals to arrest in the first larval stage (L1)..." emsch@its.caltech.edu, garys@its.caltech.edu
nematode Chemicals chemicals Please indicate if the effects of small molecules, chemicals, or drugs were studied on worms. E.g., paraquat, butanone, benzaldehyde, aldicarb, etc. The use of mutagens for the generation of mutants in genetic screens do not need to be indicated.
elegans Small-scale RNAi (less than 100 experiments reported) rnai Please tell us the sequences or source of sequences used for RNAi experiments so we can map these experiments in relation to the genome. garys@its.caltech.edu
elegans Large-scale RNAi (more than 100 experiments reported) lsrnai Please indicate if your paper reports gene knockdown phenotypes for more than 100 individual RNAi experiments. raymond@its.caltech.edu
elegans Mosaic analysis mosaic ->Please indicate if your paper reports cell specific gene function based on mosaic analysis, e.g., extra-chromosomal transgene loss in a particular cell lineage leads to loss of mutant rescue, etc. raymond@its.caltech.edu
elegans Tissue or cell site of action siteaction Please indicate if your paper reports anatomy-specific function for a gene. raymond@its.caltech.edu
elegans Time of action timeaction Please indicate if your paper reports a temporal requirement for gene function. raymond@its.caltech.edu
elegans Molecular function of a gene product genefunc Please indicate if your paper discusses a new function for a known or newly defined gene. emsch@its.caltech.edu
elegans Homolog of a human disease-associated gene. humdis Please indicate if any gene reported in your paper is a homolog/ortholog of a human disease-related gene or if your study models some aspect of a human disease. ranjana@its.caltech.edu
INTERACTIONS:
elegans Genetic interactions geneint Please indicate if your paper reports the analysis of more than one gene at a time, e.g., double, triple, etc. mutants, including experiments where RNAi was used concurrent with other RNAi-treatments or mutations. emsch@its.caltech.edu
any gene expressed in elegans or elegans gene in anything else? Functional complementation funccomp Please indicate if your paper reports functional redundancy between separate genes, e.g., the rescue of gen-A by overexpression of gen-B, or any other extragenic sequence.
elegans Gene product interactions geneprod Please indicate if your paper reports data on protein-protein, RNA-protein, DNA-protein, or Y2H interactions, etc. emsch@its.caltech.edu
REGULATION OF GENE EXPRESSION:
elegans New expression pattern for a C. elegans gene otherexpr Please indicate if your paper reports new temporal or spatial (e.g., tissue, subcellular, etc.) data on the pattern of expression of any C. elegans gene in a wild-type background. You can include: reporter gene analysis, antibody staining, In situ hybridization, RT-PCR, Western or Northern blot data. wchen@its.caltech.edu, vanauken@its.caltech.edu
elegans Alterations in C. elegans gene expression by genetic or other treatment genereg Please indicate if your paper reports changes or lack of changes in gene expression levels or patterns due to genetic, chemical, temperature, or any other experimental treatment. xdwang@its.caltech.edu
elegans Regulatory sequence features seqfeat Please indicate if your paper reports any gene expression regulatory elements, e.g., DNA/RNA elements required for gene expression, promoters, introns, UTR's, DNA binding sites, etc. xdwang@its.caltech.edu, worm-bug@sanger.ac.uk, stlouis@wormbase.org
elegans Position frequency matrix (PFM) or Position weight matrix (PWM) matrices Please indicate if your paper reports PFMs or PWMs, which are typically used to define regulatory sites in genomic DNA (e.g., bound by transcription factors) or mRNA (e.g., bound by translational factors or miRNA). PFMs define simple nucleotide frequencies, while PWMs are scaled logarithmically against a background frequency. xdwang@its.caltech.edu, emsch@its.caltech.edu
elegans Microarray microarray Please indicate if your paper reports any microarray data. wchen@its.caltech.edu
PROTEIN FUNCTION AND STRUCTURE:
elegans Protein analysis in vitro(flagged) invitro Please indicate if your paper reports any in vitro protein analysis such as kinase assays, agonist pharmacological studies, reconstitution studies, etc.
elegans Domain analysis domanal Please indicate if your paper reports on a function of a particular domain within a protein.
elegans Covalent modification (flagged) covalent Please indicate if your paper reports on post-translational modifications as assayed by mutagenesis or in vitro analysis
elegans Structural information(flagged) structinfo Please indicate if your paper reports NMR or X-ray crystallographic information.
elegans Mass spectrometry (flagged-done) massspec Please indicate if your paper reports data from any mass spec analysis e.g., LCMS, COSY, HRMS, etc. gw3@ebi.ac.uk, worm-bug@sanger.ac.uk
REAGENTS:
elegans C. elegans antibodies antibody Please list any new or known C. elegans antibody created by your lab or another researcher's lab, that is used in this paper; do not check this box if antibodies were commercially bought. wchen@its.caltech.edu
elegans Integrated transgenes expressed in C.elegans transgene ->Please list any integrated transgene used in this paper that doesn't exist in WormBase already, especially if the transgene does not have a canonical name. wchen@its.caltech.edu
elegans Transgenes used as tissue markers marker Please indicate if reporters (integrated transgenes) were used to mark certain tissues, subcellular structures, or life stages, etc. as a reference point to assay gene function or location. wchen@its.caltech.edu, vanauken@its.caltech.edu
GENOME SEQUENCE DATA:
nematode? Gene structure correction structcorr (this use to be two different fields) Please indicate if your paper reports a gene structure that is different from the one in WormBase, e.g., different splice-site, SL1 instead of SL2, etc. worm-bug@sanger.ac.uk, wormticket@watson.wustl.edu
nematode? Sequencing mutant alleles seqchange Please indicate if your paper reports new sequence data for any mutation. genenames@wormbase.org
nematode? New SNPs newsnp Please list any SNP reported in your paper that doesn't exist in WormBase already. dblasiar@watson.wustl.edu, tbieri@watson.wustl.edu
CELL DATA:
elegans Ablation data ablationdata Please indicate if your paper reports data from an assay involving any cell or anatomical unit being ablated by laser or by other means (e.g., by expressing a cell-toxic protein). raymond@its.caltech.edu
elegans Cell function cellfunc Please indicate if your paper reports a function for any anatomical part (e.g., cell, tissue, etc.), which has not been indicated elsewhere on this form. raymond@its.caltech.edu
IN SILICO DATA:
elegans Phylogenetic data phylogenetic Please indicate if your paper reports any phylogenetic analysis.
elegans Other bioinformatics analysis othersilico Please indicate if your paper reports any bioinformatic data not indicated anywhere else on this form.
OTHER:
nematode Supplemental materials supplemental Please attach supplemental material. qwang@its.caltech.edu
nematode NONE of the aforementioned data types are in this research article nocuratable Please indicate if none of the above pertains to your paper. Feel free to list the data type most pertinent to your research paper in the "Add information" text area.
all Feedback comment Please give us feedback on this form or on any topic pertinent to how we can better extract data from your paper. kyook@caltech.edu, vanauken@caltech.edu