- WBPaper00055334:DLC-1_interacting
DESeq2, fold change > 2,, p-value < 0.01
Transcripts that interact with 3xFLAG-DLC-1 as identified by immunoprecipitation followed by RNA sequencing.
- WBPaper00051311:VGLN-1-interacting
DESeq2
Transcripts that physically bind VGLN-1 protein, according to RNA sequencing on immunoprecipitation using GFP-Trap A proteins, by comparing results on Pvgln-1::vgln-1::gfp (kuIs102) (strain MH4920) with Pvgln-1::gfp (kuIs103) (strain MH4922)
- WBPaper00037777:lipid_raft_proteins
Protein identifications were accepted on the following criteria: (i) a Mascot score of more than 83 (threshold for significance, p < 0.05), (ii) more than 5 matching peptides, and (iii) sequence coverage of more than 10%.
Proteins identified in lipid raft fraction isolated from nematode membrane preparations.
- WBPaper00045809:rsd-2(yp10)_downregulated
R statistical package. Genes that showed more than 16-fold reduction in 22G-RNA reads were considered differentially expressed.
Genes that showed more than 16-fold reduction in 22G-RNA reads in rsd-2(yp10) late-generation (F10) compared to early-generation (F2) rsd-2(yp10), according to small RNA sequencing.
- WBPaper00056165:MINA-1_interacting_mRNA
Expression level cut-off of count per million (cpm) > 1 in all three CLIP replicates and a fold change (FC) > 3 compared with RNA-Seq of MINA-1::GFP animals.
Transcripts that physically interact with MINA-1-GFP, according to high-throughput sequencing with crosslinking immunoprecipitation (HITS-CLIP) experiment of synchronized MINA-1-GFP transgenic animals (opIs408).
- WBPaper00045486:starvation_downregulated
A gene was considered differentially expressed if its fold-changed was greater than 1.5 and it had total reads of more than 10 RPM per comparison.
Genes that showed significantly decreased mRNA expression in starved animals. mRNA samples from N2, rde-4(ne229) and hrde-4(tm1200) animals that were starved or fed for 6 days as L1s were sequenced.
- WBPaper00045486:starvation_upregulated
A gene was considered differentially expressed if its fold-changed was greater than 1.5 and it had total reads of more than 10 RPM per comparison.
Genes that showed significantly increased mRNA expression in starved animals. mRNA samples from N2, rde-4(ne229) and hrde-4(tm1200) animals that were starved or fed for 6 days as L1s were sequenced.
- WBPaper00045974:NSM_enriched_DSN-treated_RNAseq
Gene expression quantification and differential expression was analyzed using cufflinks v2.2.1. Enriched contains only genes significantly enriched (differentially expressed >= 2.4 fold in total RNA or >= 3.2 fold in DSN treated total RNA) in the NSM neurons versus the reference.
Genes significantly enriched in NSM neurons (isolated by FACS) versus the reference, according to RNAseq analysis towards DSN treated(Duplex-Specific Nuclease method to deplete rRNA sequences) total RNA.
- WBPaper00041097:pgl-1_downregulated
The threshold for the detected proteins and matched peptides was set at sequence coverage >= 20% and ProteinPilot unused score >= 1.31 (a confidence threshold of 95%). Theoretical pI and Mw of each identified protein were calculated by using the pI/Mw tool of the ExPASy proteomic server (Swiss Institute of Bioinformatics, Lausanne, Switzerland).
Proteins constantly downregulated in pgl-1(bn101) and pgl-1(ct131) at both 20 C and 25 C, according to 2D-DIGE and LC-MS/MS.
- WBPaper00041097:pgl-1_upregulated
The threshold for the detected proteins and matched peptides was set at sequence coverage >= 20% and ProteinPilot unused score >= 1.31 (a confidence threshold of 95%). Theoretical pI and Mw of each identified protein were calculated by using the pI/Mw tool of the ExPASy proteomic server (Swiss Institute of Bioinformatics, Lausanne, Switzerland).
Proteins constantly downregulated in pgl-1(bn101) and pgl-1(ct131) at both 20 C and 25 C, according to 2D-DIGE and LC-MS/MS.