Matt:LabNotes/2014-3-7

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Cell Type with Most Expression of Agi26k0gap Probe Genes[edit]

  • Strategy
    1. Get gene expression (microarray) data from GEO for each cell type
    2. Rank genes from high expression to low
    3. Sum the ranks of genes included in Agi26k0gap probeset
    4. The cell type with lowest sum has most expression for genes of interest

PGP1f[edit]

Result[edit]

  • ACTB Rank: 49
  • RAB7A Rank: N/A
  • MALAT1 Rank: 20,709

Agi26k0gap

Gene PGP1f Rank
ADM 3
LGALS1 4
ANXA2 8
VIM 10
TIMP1 36
S100A10 38
ACTB 49
CXCL12 57
IFITM2 78
GNAS 83
ATF4 114
CST3 134
SRPX 159
ENO1 164
ANXA1 167
RTN4 176
COLEC12 195
KIAA1199 200
CCND1 204
RHOA 207
SNX3 209
ACTA2 211
IGFBP4 212
SOD1 217
NPC2 223
KIAA0101 232
CCR6 250
FHL2 252
CTSK 254
PDGFRA 260
LOX 264
CLIC1 265
ANXA5 267
PRRX1 273
GJA1 326
CLIC4 328
EFEMP1 337
THY1 346
FST 349
COL3A1 356
GNG11 357
LMO4 359
FXYD5 360
APOD 371
MOXD1 391
TAGLN 403
GREM1 425
SCARB2 430
MMP3 434
COX8A 435
NT5E 436
COL6A1 440
STC1 441
KCNK2 452
IFITM1 453
LAMP1 469
HOXC6 471
CAMK2N1 489
SPARC 491
LAMC1 527
GLO1 544
PTRF 558
BTG1 572
GLTP 577
LMNA 597
CYR61 609
NNMT 618
SERPINH1 623
TMEM47 625
COL5A2 641
STOM 650
RND3 651
XBP1 655
CNN2 660
CA12 667
PCDH18 675
COMMD3 681
MMP1 695
SCD 713
S100A11 733
SERPINE1 734
HEBP2 756
PPAP2B 759
FAP 780
ZDHHC9 783
MFAP5 792
COMT 793
ATP2A2 795
LAMP2 798
ACTN1 800
RRBP1 818
SNAI2 852
LIPA 868
KLF6 870
DDT 883
PTGS2 890
CRABP2 901
AHNAK 902
AEBP1 909
SH3PXD2A 912
LDB2 916
TFPI2 918
PHGDH 924
OAF 932
MFGE8 936
TNFRSF11B 946
OLFML3 951
THBS2 955
TMEM87A 958
CLNS1A 965
SRGN 968
CCL2 977
GOLGA7 988

Agi26k0gap_Stem

Gene PGP1f Rank
DCN 13
ITGB1 43
CD44 93
COL1A2 138
MME 221
RAC1 353
COL1A1 418
ANPEP 530
ILK 551
DPP4 864
HDAC2 910
HDAC1 922
PDGFRB 1000

NCI-H1975 Cells[edit]

MATLAB

 Celstruct = affyread(GSM887393.CEL)
  • Intensities only matched to probe (X,Y) coordinates
    • Athurva recommended using R to read affymetrix CEL files

R

 biocLite()
 library(affy)
  • R couldn't find the affymetrix library even after reinstalling R and Bioconductor

Conclusion[edit]

  • Will use Agi26k0gap probe set in PGP1f cells
    • Microarray data shows the probe set contains 4 genes in the top 10 and many more in the top 100
    • ACTB was ranked 49 and MALAT1 20,000+, which is near the lowest rank possible and we could still detect these
    • We know good culturing conditions for PGP1f to express mRNA > rRNA
  • Here are the Agi26k0gap padlock probe sequences for genes in the top 13 of PGP1f
Dye-Probe Sequence Probes in brain Probes in stem Probes in top13 Genes Gene '
dcProbe0-Cy3 ACGTATCGGTAGTCGCAACGCA 3641 0 1 VIM
dcProbe1-Cy3 GTCTTGCGTGCGATACGGAGTA 2894 0 1 LGALS1
dcProbe2-Cy3 TCTACTTCGTCGCGTCAGACCA 2950 491 1 VIM
dcProbe3-Cy3 CCGTTTGATCGTTCGACCGAGA 2910 45 0
dcProbe4-Cy3 CTACCATTCGCGTGCGATTCCA 3014 196 2 VIM DCN
dcProbe0-FAM ATGTATCGCGCTCGATTGGCAG 4097 0 1 LGALS1
dcProbe1-FAM CAACGGTATTCGGTCGTCATCC 2849 0 0
dcProbe2-FAM TAGAACTTGCGCGGATACACGG 2925 293 2 DCN ADM
dcProbe3-FAM CGAATTGTCCGCGCTCTACGAT 3190 220 1 ANXA2
dcProbe4-FAM TCGGAATACGTCGTTGACTGCG 2927 207 1 ANXA2