- WBPaper00065623:53
CellRanger, DecontX, Monocle3, Louvain algorithm.
Single-cell RNA-Seq cell group 53 expressed in: Body wall muscle posterior.
- WBPaper00048980:aging_upregulated
Proteins that significantly changed across replicates were identified using the rank product algorithm. The false discovery rate corresponding to each rank product was calculated by 10,000 random permutations of the ranks for each of the three replicates. At a 10% false discovery rate, 53 proteins significantly changed in abundance with age.
Proteins that showed signicantly increased expression in day 13 animals comparing to in day 4 animals.
- WBPaper00048980:aging_downregulated
Proteins that significantly changed across replicates were identified using the rank product algorithm. The false discovery rate corresponding to each rank product was calculated by 10,000 random permutations of the ranks for each of the three replicates. At a 10% false discovery rate, 53 proteins significantly changed in abundance with age.
Proteins that showed signicantly decreased expression in day 13 animals comparing to in day 4 animals.
- WBPaper00028802:intestine_unique
To select a set of genes that are candidates to be expressed strongly and exclusively in the intestine, authors consider only genes for which the I/S tag ratio >= 3 and for which the tag number in the intestine library is >= 50. One hundred genes meet these two criteria. Twenty of these 100 genes encode ribosomal proteins or are involved in ribosome assembly, suggesting that the intestine persists as the major site of ribosome synthesis in the adult worm. However, because most ribosomal protein genes are unique in the genome and therefore must be widely expressed at other developmental stages, these genes were removed from the list to leave the set of 80 highly-expressed intestine-specific or intestine-enriched (non-ribosomal) genes.
Genes with unique expression in intestine, according to SAGE analysis on dissected intestine.
- WBPaper00062056:lin-37(n758)_upregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly increased expression in lin-37(n758) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:dpl-1(n2994)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in dpl-1(n2994) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:efl-1(se1)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in efl-1(se1) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-35(n745)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-35(n745) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-36(we31)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-36(we31) comparing to in N2 animals at starved L1 larva stage.
- WBPaper00062056:lin-37(n758)_downregulated
A gene model was built based on the WS260 annotation. Tag counts for each gene were extracted from STAR aligned BAM files, anddifferential gene expression between N2 and mutant backgrounds was tested using DESeq2. A false discovery rate(FDR) < 0.01 and LFC > 0.5849 was used to define genes as upregulated, and FDR < 0.01 and LFC < -1 was used to define genes asdownregulated.
Transcripts that showed significantly decreased expression in lin-37(n758) comparing to in N2 animals at starved L1 larva stage.