Talk:Jenna Reed

2/8/18

Bio343 HTSeq Results

Male Mutant 25 and 24 = paired reads, Male mouse 2078, C201R 15 and 14 = paired reads, Male mouse 2073, C201R 3 and 2 = paired reads, Male mouse 2079, C201R

Male WT 21 and 20 = paired reads, Male mouse 2076, WT 19 and 18 = paired reads, Male mouse 2075, WT 17 and 16 = paired reads, Male mouse 2074, WT

Female Mutant 13 and 12 = paired reads, Female mouse 2072, C201R 11 and 10 = paired reads, Female mouse 2071, C201R 9 and 8 = paired reads, Female mouse 2070, C201R

Female WT 23 and 22 = paired reads, Female mouse 2077, WT 7 and 6 = paired reads, Female mouse 2081, WT 5 and 4 = paired reads, Female mouse 2080, WT

Gene Cards Gene Weaver GO rilla FNTM String NCBI

2/8/18 Loaded data from "Histories Shared with Me"

NefL >>> deltaCMT 1F 2E NefH >>> deltaALS Sphk2 >>> kinase

    Male v Female
    MaleWT v MaleCMT
    FemaleWT v FemaleCMT

Gm4210 NefM (neurofilament medium) Close with NefL, and Gm2410 Calca >>> calcium regulator

About this data

    Took the spinal cord of the mice and sent it off for RNASeq

2-fold change

    -0.7 = 1.62 fold change
    -0.8 = 1.74 fold change
    -7.56 =  128fold change, p=10^-14

What's our fold-change cutoff?

    JAX had a strict cutoff and got only 20 genes

Lack of signal because of CMT could cause repression of transcription (because usually ligand binding induces transcription) RNASeq data will always have differential expression from natural variation Is it enough differential expression that it could be caused by the disease?