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!"A %&'()*((*+ !*,* An*.+/&/ ')0(/1 - 3%B"35 - 6*0/*nn1
!ntro&uction*to*+icro,rr,-s
78&// 9n/,&,0,1 ):B&)&n:)(;*,&'/ - <= 4.200B
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
<()D.1;E
! Fn').)G+ H1I*(,;1n,
! 7);1 I*,&1n,/ (1/I)nH ,) &ru/*0 D0, n), &ru/*1
! 50;)( ,+I1 B &/ ;)(1 /0/'1I,&D.1 ,) (1/I)nH ,) H(0G ,(1*,;1n,
! JK*, &/ ,K1 I()Gn)/&/ ): ,K1 I*,&1n,
! 2uestion E How can we predict the pharmacological response prior to treatment?
! !art%a&'(ns+er : By understanding and identifying the tumor.
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
L)8 '*n 81 (1')Gn&z1 ,0;)0(/ N
!"#$%&'(o*'+$,-./.0o(1$!'l'.0o(1$#*3l0405/.0o(
6"#$$%78/(95803.o*'+
:8o.'0($%:8o.'o*'+
;<-(5.0o(=
%&'(o.>3'+
%:?'(o.>3'+
!"#$,058o/88/>9
78/(95803.0o(1$@3l050(g1BBB
78/(9l/.0o(
:o9.C.8/(9l/.0o(
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
O1n);&'/ =0nH*;1n,*./ - P);I.1Q&,+
!&::&'0.,&1/E
"P)n,*;&n*,&)n/
"A.,1(n*,&R1 7I.&'&nG
"A.,1(n*,&R1 <).+AH1n+.*,&)n
;S"A I0(&:&'*,&)n
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
3QI(1//&)n *n*.+/&/
! 6)8 ,K()0GKI0,# ")(,K1(n D.),# !&::1(1n,&*. H&/I.*+# T0*n,&,*,&R1 <PS
! L&GK ,K()0GKI0,# !"A *((*+/ / ;&'()*((*+/
! 7I),,1H *((*+/ (7,*n:)(H *((*+/)! A::+;1,(&Q (IK),).&,K)G(*IK+ &n/I&(1H)! F.&G)-*((*+/ (AG&.1n,X "&;D.1O1n)
# 71(&*. An*.+/&/ ): O1n1 3QI(1//&)n (7AO3)
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
Tr,nsition
! !ntro&uction*to*5icro,rr,- techno7o/-
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
JK*, *(1 !"A %&'()*((*+/ N
%&'()*((*+ *n*.+/&/ &/ * ,1'Kn).)G+ ,K*, *..)8/ /'&1n,&/,/ ,) /&;0.,*n1)0/.+ H1,1', ,K)0/*nH/ ): G1n1/ &n * /;*.. /*;I.1 *nH ,) *n*.+z1 ,K1 1QI(1//&)n ): ,K)/1 G1n1/.
%&'()*((*+/ *(1 /&;I.+ )(H1(1H /1,/ ): !"A ;).1'0.1/ ): Yn)8n /1Z01n'1. [/0*..+ (1',*nG0.*( /K*I1HX ,K1+ '*n ')n/&/, ): * :18 K0nH(1H ,) K0nH(1H/ ): ,K)0/*nH/ ): /1,/. 3*'K &nH&R&H0*. /1Z01n'1 G)1/ )n ,K1 *((*+ *, I(1'&/1.+ H1:&n1H .)'*,&)n.
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
T01/,&)n *HH(1//1H D+ ;&'()*((*+/
! JK*, *(1 ,K1 H&::1(1n'1/ (&n G1n1 1QI(1//&)n) D1,811n ,8) '1.. .&n1/ N
! JK*, &/ ,K1 H&::1(1n'1 D1,811n Yn)'Y-)0, *nH 8&.H-,+I1 ;&'1N! JK*, &/ ,K1 H&::1(1n'1 D1,811n * ,0;)( *nH * K1*.,K+ ,&//01 N! A(1 ,K1(1 H&::1(1n, ,0;)( ,+I1/ N
! \1+ ')n'1I,E Compare G1n1 1QI(1//&)n &n ,8) ()( ;)(1) '1../,&//01 ,+I1/ N# O1n1 1QI(1//&)n *//1//1H D+ ;1*/0(&nG ,K1 n0;D1( ): S"A
,(*n/'(&I,/.# ") *D/).0,1 ;1*/0(1;1n,.
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
8otenti,7*,997ic,tion*&o5,ins
! !(0G H&/')R1(+ *nH ,)Q&').)G+ /,0H&1/
! %0,*,&)n/I).+;)(IK&/; H1,1',&)n (7"<]/)
! <*,K)G1n *n*.+/&/
! !&::1(&nG 1QI(1//&)n ): G1n1/ )R1( ,&;1X D1,811n ,&//01/X *nH H&/1*/1
/,*,1/
! <(1R1n,&R1 ;1H&'&n1
! %)(1 ,*(G1,1H H(0G ,(1*,;1n,/
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
5K1 'K*..1nG1
5K1 D&G (1R).0,&)n K1(1 &/ &n ,K1 ^;&'()^ ,1(;. "18 /.&H1/ 8&.. ')n,*&n * /0(R1+ ): ,K1 K0;*n G1n);1 )n * 2 ';2 'K&I_ 5K1 0/1 ): ,K&/ .*(G1-/'*.1 ;1,K)H ,1nH/ ,) '(1*,1 IK1n);1n*. *;)0n,/ ): H*,*X ,K*, K*R1 ,K1n ,) D1 *n*.+z1HX I()'1//1H *nH /,)(1H.
5K&/ &/ * `)D :)(a B&)&n:)(;*,&'/ _
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
1io7o/ic,7*:uestion(e.g. !&::1(1n,&*..+ 1QI(1//1H G1n1/X
7*;I.1 '.*// I(1H&',&)nX etc.)
51/,&nG
B&).)G&'*. R1(&:&'*,&)n *nH &n,1(I(1,*,&)n
%&'()*((*+ 1QI1(&;1n,
3/,&;*,&)n
3QI1(&;1n,*. H1/&Gn
!5,/e*,n,7-sis/T0*.&,+ *//1//;1n,
")(;*.&z*,&)n
P.0/,1(&nG !&/'(&;&n*,&)n
(failed)
Pre-processing steps
Data Analysis
S"#$%&#'#"(P*o"$,,
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
PK)&'1 ): 51'Kn).)G&1/
! 58) !+1 51'Kn).)G&1/ (1QI1(&;1n, / (1:1(1n'1)
# F.&G)*((*+/ (B0 ;1(/)
# '!"A '0/,); *((*R/
! 7&nG.1 !+1 51'Kn).)G&1/
! F.&G)*((*+/ (25 ;1(/)
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
T;<*<=8<>!+<?T*@*5,Ain/*the*chi9
! Desi/nin/*the*chi9*@*# choosin/*/enes*oC*interest*Cor*the*eD9eri5ent
! 8roEe*se7ection*str,te/-*shou7&*ensure@
# 1io7o/ic,77-*5e,nin/Cu7*resu7ts*FThe*truthGGGH# IoJer,/eK*LensitiJit-*FGGG*The*Mho7e*truthGGGH# L9eciCicit-*FGGG*0n&*nothin/*Eut*the*truthH# 0nnot,tion# >e9ro&uc,Ei7it-
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
71.1',&)n ): G1n1 (1G&)n/
! Co.#%/(*$/#o%(012F4(! A%%o&6&#o%(*$l6$l9(,6'$! :o(;*o<l$=,(>#&?(6l&$*%6$(;ol9A(,#&$,! :o(*$;$&#$($l$=$%&,(o*(o&?$*('u%%9(,$Au$%"$,! .6%/$*(o'("lo,$(#,o'o*=,! .6%/$*(o'(6l&$*%6$(,;l#"#%/
BC(u%&*6%,l6&$.(*$/#o%! A%%o&6&#o%(l$,,(,6'$! .6%/$*(o'(6l&$*%6$(;ol9A(,#&$,! .6%/$*(o'(*$;$&#$($l$=$%&,! l$,,(l#D$l9(&o("*o,,E?9<*#.#F$(>#&?(#,o'o*=,! l#&&l$(.6%/$*(o'(6l&$*%6$(,;l#"#%/
! GC(u%&*6%,l6&$.(*$/#o%! "lo,$(l#%D6/$(&o(;*o=o&$*! '*$Au$%&l9(%o&(686#l6<l$
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
+icro,rr,-s@*the*5,Ain/*oC
%&'()/I),,&nG *nH &nY-`1,,&nG
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A((*+ <()H0',&)nE 7I),,&nG
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
1- 7*;I.1/
2- 3Q,(*',&nG ;S"A
d- 6*D1.&nG
4- L+D(&H&z&nG
5- 7'*nn&nG
B- e&/0*.&z&nG
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
7I),,1H *nH ).&G) *((*+ 0/*G1
Hybridizationwashing
Relative mRNAlevels
Scanning
cy5 labeledcDNA
cy3 labeledcDNA
Mix
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A((*+ <()H0',&)nE fIK),).&,K)G(*IK+^
! 3*'K I()D1 25 DI .)nG! 22-40 I()D1/ I1( G1n1! <1(:1', %*,'K (<%) */ 81.. */
%&/%*,'K (%%) I()D1/
A::+;1,(&Q =1D&,/"&;D.1O1n
! <()D1 .1nG,KE 24;1( -70;1(! O1n1/A((*+E [I ,) dhX000! <()D1//O1n1E 10-25! Fn.+ I1(:1', ;*,'K I()D1/
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A::+;1,(&Q 'K&I I(1I*(*,&)n
9n-/&,0 /+n,K1/&/
25 DI /1Z01n'1/
71Z01n'1 H*,*D*/1/
%&..&)n/ ): 1QI1(&;1n,/8)(.H8&H1
<()D1 (/1Z01n'1) H1/&Gn-Yn)8n G1n1/ -I0,*,&R1 G1n1/-*.,1(n*,&R1 /I.&'&nG-OP ')n,1n,/
B&)&n:)(;*,&'/ ,K&nY&nG+&1.H/ G1n1-/I1'&:&' /1Z01n'1/ (d]-1nH)
i100/ ): DI j')n/1n/0/f/1Z01n'1/
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A::+;1,(&Q /+/,1;
!11 to 16'
Usually the most 3 prime area, often UTR
25mer25mer25mer
AAAA..
25mer
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
O1n1 <()D1/1,/ *nH <()D1/
71Z01n'1 ): O1n1 jAAf
<%
%%
<()D1/1, jAA1f <()D1/1, jAA2f
“Probeset redundancy may be a blessing and a curse !”
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A::+;1,(&Q 'K&I 0/*G1
Relative mRNAlevels
Hybridizationwashing
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
P);I*(&/)n ): ,1'Kn&Z01/
0&J,nt,/esk ") n11H ,) &/).*,1 *nH I0(&:+ '!"A/
D1'*0/1 ).&G)n0'.1),&H1/ '*n D1 /+n,K1/&z1H.
k 7K)(, ).&G)n0'.1),&H1/ *(1 .1// .&Y1.+ ,) K*R1 '()//-(1*',&R&,+ 8&,K ),K1( /1Z01n'1/ &n ,K1 ,*(G1, !"A.
k !1n/&,+ ): 'K&I/ &/ K&GK1( ,K*n 8&,K '!"A/.
Ni5it,tionsk 5K1 /1Z01n'1 K*/ ,) D1 Yn)8n.k 7+n,K1/&/ '*n D1 1QI1n/&R1 *nH ,&;1-
')n/0;&nG.k 5K1 /K)(, /1Z01n'1/ *(1 n), */ /I1'&:&' :)(
,*(G1, !"AX /) *II()I(&*,1 ')n,()./ ;0/, D1 *HH1H.
!nOsitu*L-nthesis*P*Q7i/os 8I>*8ro&ucts*P*cD?0*8roEes
0&J,nt,/esk =.1Q&D&.&,+ ,) /,0H+ '!"A/ :(); *n+ /)0('1.k '!"A/ H) n), (1Z0&(1 *n+ * I(&)(&
&n:)(;*,&)n *D)0, ,K1 ')((1/I)nH&nG G1n1/.k 6)nG1( /1Z01n'1/ &n'(1*/1 K+D(&H&z*,&)n
/I1'&:&'&,+X 8K&'K (1H0'1/ :*./1 I)/&,&R1/.
Ni5it,tionsk 9/).*,&)n ): &nH&R&H0*. '!"A/ ,) &;;)D&.&z1
)n 1*'K /I), '*n D1 '0;D1(/);1.k !1n/&,+ &/ .)81( ,K*n /+n,K1/&z&nG
).&G)n0'.1),&H1/ )n ,K1 /0(:*'1 ): ,K1 'K&I.k '!"A/ *(1 .)nG1( /1Z01n'1/ *nH *(1 ;)(1
.&Y1.+ ,) (*nH);.+ ')n,*&n /1Z01n'1/ :)0nH &n ,*(G1, !"AX 8K&'K (1/0.,/ &n '()//-(1*',&R&,+.
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
71.1',&)n ): G1n1 (1G&)n/
dl [5S
FS=
5l [5S
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A.,1(n*,&R1 I).+*H1n+.*,&)n
<*(,&'0.*( I()D.1; 8&,K A::+;1,(&Q
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A.,1(n*,&R1 /I.&'&nG
78&// 9n/,&,0,1 ): B&)&n:)(;*,&'/ - <= 9.200B
A.,1(n*,&R1 I();),1( 0/*G1
