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==Regression Analysis of CA12kNov2014 V4 probeset + 100x suppressor== *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 *[[Matt:LabNotes/2015-5-8 | in vitro capture counts]] *HBRR FPKM values from: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE49712 **File: GSE49712_gene_FPKM.txt.gz ***Experiment was sequencing UHRR (Sample A) and HBRR (Sample B) and did 5 replicates of each ***I averaged the FPKM of the 5 Sample B replicates *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=== *Captured cDNA from HBRR *Normalize with gDNA counts *Compare to HBRR FPKM values [[File:CDNA_vs_HBRR.png|450px]] *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|450px]] ===DARTFISH vs BAs and HBRR=== *DARTFISH counts normalized by gDNA counts **Despite DARTFISH being from BA8 it is the worst correlation... [[File:DARTFISHgNorm_vs_BA8.png|450px]] [[File:DARTFISHgNorm_vs_BA10.png|450px]] [[File:DARTFISHgNorm_vs_BA17.png|450px]] [[File:DARTFISHgNorm_vs_BA21.png|450px]] [[File:DARTFISHgNorm_vs_BA22.png|450px]] [[File:DARTFISHgNorm_vs_BA41.png|450px]] *HBRR has best correlation **Is this due to BA sequencing by Smart-Seq bias? [[File:DARTFISHgNorm_vs_HBRR.png|450px]] ===DARTFISH vs BAs and HBRR=== *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|450px]] [[File:DARTFISHcNorm_vs_BA10.png|450px]] [[File:DARTFISHcNorm_vs_BA17.png|450px]] [[File:DARTFISHcNorm_vs_BA21.png|450px]] [[File:DARTFISHcNorm_vs_BA22.png|450px]] [[File:DARTFISHcNorm_vs_BA41.png|450px]] *HBRR [[File:DARTFISHcNorm_vs_HBRR.png|450px]] ===DARTFISH (on BA8) vs BA8 neuronal nuclei Bulk RNA-Seq=== *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|450px]] *cDNA normalized DARTFISH barely improved (R^2=0.283 vs 0.28) [[File:DARTFISHcNorm_vs_BA8n.png|450px]]
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