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==Cell Type with Most Expression of Agi26k0gap Probe Genes== *Strategy *#Get gene expression (microarray) data from GEO for each cell type *#Rank genes from high expression to low *#Sum the ranks of genes included in Agi26k0gap probeset *#The cell type with lowest sum has most expression for genes of interest *Agi26k0gap Genes: [[Media:Dec2012_0bp_gap_probes.txt|Dec2012_0bp_gap_probes.txt]] and [[Media:Dec2012_0bp_gap_probes_stemCellGenes.txt|Dec2012_0bp_gap_probes_stemCellGenes.txt]] ===PGP1f=== *Sample: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM313643 *Platform: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL7182 *Used Excel VLOOKUP() to match gene name to intensity values and rank: [[Media:Agi26k0gap_PGP1f_GeneExpressionRank.xlsx|Gene Expression Rank]] ====Result==== *ACTB Rank: 49 *RAB7A Rank: N/A *MALAT1 Rank: 20,709 '''Agi26k0gap''' {| {{table}} | align="center" style="background:#f0f0f0;"|'''Gene''' | align="center" style="background:#f0f0f0;"|'''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''' {| {{table}} | align="center" style="background:#f0f0f0;"|'''Gene''' | align="center" style="background:#f0f0f0;"|'''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=== *Sample: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSM887393 *Plastform: http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL15308 '''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=== *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 *[[Media:Agi26k0gapProbes_PGP1f_top13Genes.txt|Here]] are the Agi26k0gap padlock probe sequences for genes in the top 13 of PGP1f {| {{table}} | align="center" style="background:#f0f0f0;"|'''Dye-Probe''' | align="center" style="background:#f0f0f0;"|'''Sequence''' | align="center" style="background:#f0f0f0;"|'''Probes in brain''' | align="center" style="background:#f0f0f0;"|'''Probes in stem''' | align="center" style="background:#f0f0f0;"|'''Probes in top13 Genes''' | align="center" style="background:#f0f0f0;"|'''Gene''' | align="center" style="background:#f0f0f0;"|'''''' |- | 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|| |}
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