Matt:LabNotes/2015-5-14

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Regression Analysis of CA12kNov2014 V4 probeset + 100x suppressor[edit]

  • Files in Dropbox/GradZhangLab/CA12k_Nov2014/V4_CaptureAnalysis/20150514/
  • DARTFISH counts from Summary2_S1_V4_Supp_2015-05-06_Try1.txt
    • 18 Positions of V4 in BA8 using first generation of 100x suppressor oligos for CA12kNov2014 probeset
  • Brain Tissue RNA-Seq FPKM Data:
 /media/LTS_33T/RL_LTS33T/201404_201405_7Samples_BulkNucleiBatch1-20140623_Expt146/STAR/
  • Files moved to Dropbox/GradZhangLab/CA12k_Nov2014/V4_CaptureAnalysis/
    • eg. RL-BA8-sec9-t-N701-15May14_S1_mapped_genes.fpkm_tracking.txt
    • BA8, BA10, BA17, BA21, BA22, BA41

Normalize in vitro Capture and check with RNA-Seq[edit]

  • Captured cDNA from HBRR
  • Normalize with gDNA counts
  • Compare to HBRR FPKM values

File:CDNA vs HBRR.png

  • Better than comparing with BA8 (as expected)
    • Some correlation also expected since HBRR is from all areas of brain and many samples

File:CDNA vs BA8.png

DARTFISH vs BAs and HBRR[edit]

  • DARTFISH counts normalized by gDNA counts
    • Despite DARTFISH being from BA8 it is the worst correlation...

File:DARTFISHgNorm vs BA8.png File:DARTFISHgNorm vs BA10.png File:DARTFISHgNorm vs BA17.png File:DARTFISHgNorm vs BA21.png File:DARTFISHgNorm vs BA22.png File:DARTFISHgNorm vs BA41.png

  • HBRR has best correlation
    • Is this due to BA sequencing by Smart-Seq bias?

File:DARTFISHgNorm vs HBRR.png

DARTFISH vs BAs and HBRR[edit]

  • DARTFISH counts normalized by cDNA counts
    • cDNA counts normalized by HBRR RNA-Seq FPKM (divided)
    • All correlations improved equally approximately

File:DARTFISHcNorm vs BA8.png File:DARTFISHcNorm vs BA10.png File:DARTFISHcNorm vs BA17.png File:DARTFISHcNorm vs BA21.png File:DARTFISHcNorm vs BA22.png File:DARTFISHcNorm vs BA41.png

  • HBRR

File:DARTFISHcNorm vs HBRR.png

DARTFISH (on BA8) vs BA8 neuronal nuclei Bulk RNA-Seq[edit]

  • Dr. Zhang suggested comparing to sorted neuronal nuclei RNA-Seq data
    • Previous comparisons are with whole tissue since DARTFISH data is gathered indiscriminately
  • gDNA normalized DARTFISH improved a lot (R^2=0.289 vs 0.208)

File:DARTFISHgNorm vs BA8n.png

  • cDNA normalized DARTFISH barely improved (R^2=0.283 vs 0.28)

File:DARTFISHcNorm vs BA8n.png