Elchrom Scientific Direct Sequencing
For Cost Effective Sequencing Analyse
«Half the
costs and
a third of
labour.»
Elchrom Scientific introduces Direct Sequencing, a new analysis
procedure utilizing non-agarose, non-acrylamide hydrogels:
Pure – DNA fragment is ready for sequencing, no cleaning required.
Cost savings – 50% less cost on Big Dye Sequencing chemistry.
Less labor – Simple and less intensive procedures, direct from gel to PCR.
Faster – 3 times faster than alternative procedures.
Mechanically stable – gels are elastic and resistant to tearing.
Temperature stable – do not melt at 95 °C and do not inhibit enzymes.
| Electrophoresis
Elchrom Scientifi c AG
DNA/RNA Analysis and Purifi cation
Gewerbestrasse 8
CH-6330 Cham
Switzerland
www.elchrom.com
+41 41 747 2550
service@elchrom.com
www.elchrom.com
Microsatellite
Microsatellite analy
Analysis with Elc
sis with
hrom High Resolution Hydrogels
Microsatellite amplification by PCR
Elchrom high resolution hydrogels.
Simplified PCR protocol allows for high throughput
microsatellite analysis. Procedure: PCR master mix,
Introduction
i
The
nclud
electrophoresis
ing DNA, is loaded
can
on a
be
P
performed
CR plate. Th
either
e prime
in
rs
regular
are
Introduction
electrophoresis
added in equal volume as 2x primer solution, diluted with
Microsatellites or
Mic
Short
rosate
T
ll
andem
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Repea
ort Tan
ts
de
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m Repea
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sequences
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Elchrom PCR Blue Dye solution. The PCR is started
with short repetitive
regions
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Elchrom

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Elchrom
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high resolution
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Introduction inc
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Introduction
i
Microsatel
icrosatellite
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Microsatellite analysis with Spreadex hydrogels
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ngth
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igh resolving power of Elchrom non-acrylamide
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s
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References
o
n
ig
q
d
h
u
a
ly
a
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l
l
s
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n
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o
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. B
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s
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hydrogels, allows for highly accurate size based separation
Microsatellites applications
Elchrom high resolutions Spreadex hydrogels after PCR
H
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Microsatellites Applications p
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1. Population studies of plants, animals and humans
h
d
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r
dro
a- etc)
gels. The
2. Paternity tests (F
1. Po
ig.
pu
1)
lation studies of plants, animals and humans
h
am
yd
p
r
l
o
if
g
ic
e
a
l m
tio
a
n
t
(
ri
P
x
C
a
R
llo
),
w
s
s
e
d
q
i
u
re
e
c
n
t
c
d
in
o
g
w
o
n
r
s
c
tr
l
e
o
a
n
m
ing
r
,
e
w
ac
it
t
h
io
o
n
u
s
t
like re- d
u
efines the resolution need to be achieved. The unit length
previous purification. d
n
e
i
f
t
i
l
n
e
e
n
s
g
t
t
h
h
e
o
r
f
e
m
so
ic
lu
ro
tio
sa
n
t
n
el
e
li
e
te
d
r
t
epeat
o be a
(di-, tri-, tet
chieved. Th
ra-
e u
etc)
nit length
3. Individual identifi
2. Paterni
cation in forensics
ty tests (Fig. 1.)
a
p
m
re
p
v
l
i
i
o
fi
u
c
s
a
p
tio
u
n
ri
(
fi
P
ca
C
t
R
io
)
n
, s
.
equencing or cloning, without a
d
nd also the length of the PCR fragments define the
a
e
n
f
d
in
a
e
ls
s
o
t
t
h
h
e
e
r
l
e
e
s
n
o
g
lu
t
t
h
io
o
n
f
n
th
e
e
e
P
d t
C
o
R
b
f
e
r

a
a
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v
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s
d
d
. T
ef
h
in
e
e
u
t
n
h
i
e
t l

ength
3. Individual identification in forensic
previous purification. optimal type of Spreadex hydrogel and running conditions
4. Monitoring tool during Speed Congenics for animals (Fig. 2.
a
o
n
p
d
tim
a
a
ls
l
o
t
t
yp
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e
e
o
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tions
4. Monitoring tool during Speed Congenics for animals
Microsatellites Applications
optimal type of Spreadex hydrogel and running conditions
GenoMouse)
(Fig. 2. GenoMouse) M
Microsatel
icrosatellit
lites
e ana
A
l
p
ys
p
is
lic
c
atio
an b
ns
e used for:
5. Quality control
5. Qua
in
lity c
breeding
ontrol in bree
facilities
ding facilities
(plant
(plant an
and
d anim
animal
Microsatel
al 1
M
. P
icr
o
o
p
s
u
a
l
t
a
e
t
l
i
l
o
i
lites
t
n
e
s
a
t
n
A
u
a
d
l
p
i
y
e
s
p
s
i
lic
o
s c
atio
f
a
p
n
la
b
ns
n
e
ts
u
, a
se
n
d
im
f
a
o
l
r
s
:
M
and humans
production) 2. Paterni
1.
i
P
cr
o
o
p
s
u
a
l
t
a
e
t
t
l
y
i
l
o
it
t
n
e
es
s
a
ts
t
n
u
a
(Fi
d
l
i
y
e
s
s
is
g. 1.)
o
c
f
a
p
n
la
b
n
e
ts
u
, a
se
n
d
im
fo
a
r
ls
:
production)
and humans
1
6. Diagnostics (Fig. 3.) 3
2. Paterni
. Populat
. Individu
t
i
a
y
o
l
t
n
i
es
st
de
ts
ud
nt
(Fi
ies
ific
g. 1.)
of plants, animals and humans
6. Diagnostics (Fig. 3)
2. Paterni
ation in forensic
4
3
.
.
M
In
o
d
n
iv
it
id
o
u
t
ri
a
y t
n
l
g
i
es
t
d
o
e
ts
o
n
(Fi
l
t
d
ifi
u
c
g. 1.)
r
a
in
tio
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n
S
i
p
n
e
f
e
o
d
re
C
ns
o
i
n
c
g

3
enics for animals
4
.
.
I
M
n
o
d
n
iv
i
i
t
d
o
u
ri
a
n
l
g
i
t
d
o
e
o
n
l
t
d
ific
u
a
ri
t
n
io
g
n
S
in
p
f
e
o
e
r
d
e
C
ns
o
i
n
c
genics for animals
M C F
(
4
Fig. 2. GenoMouse)
5
(F
. M
. Q
ig.
o
u
2
n
a
.
i
l

t
it
G
or
y c
e
in
n
g
o
o
t
n
M
o
tro
o
o
l
us
l d
in
e
u
b
)
ring Speed Congenics for animals
Microsatellite amplifi cation by PCR
reeding facilities (plant and animal
production)
5
(F
. Q
ig.
u
2
a
.
l

i
G
ty
e
c
n
o
o
n
M
tr
o
o
us
l in
e
b
)
reeding facilities (plant and animal
Simplifi ed PCR protocol allows for high throughput microsatellite
5
6
production)
. Quality control in breeding facilities (plant and animal
Ta
. D
bble
i
l
a
e 1
g
. 1R
n
. e
o
c
s
Ro
t
me
ic
cm
s
o
(
enm
F
d
i
e
g
md
. 3
eSnp
.)
rdeeadd exS gpelr etyaped aenx d gruenl nitnygp ce onadintiod nsr fuonnr seilnecg tecd onditions for
analysis: PCR master mix, including DNA, is loaded on a PCR plate.
production)
6. Diagnostics (Fig. 3.)
m6
s
.
e
ic D
l
r
e
oisa
c
a
t
gt
e
enl
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loites
m
taicn
ic
asl
r
(y
o
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s
sig.
a
.
t
3
el
.
l
)
ite analysis.
The primers (2x), diluted with Elchrom PCR Blue Dye solution,
M C F
Fig. 1. Paternity test. Tetranucleotide repeats at 6 loci. M C F
are added. PCR is started without additional mixing (http://www.
M C F
Fig. 1. Paternity test. Tetranucleotide
elchrom.com/public/index.php?article=144).
“Find the Best Gel” program will give the orepptiemaatls Sapt re6 aldoecxi.
Table 1. Recommended Spreadex gel type and running conditions for selected
6
hydrogel type for analysis of the samples defined by size.
Table 1. Recommended Spreadex gel type and running conditions for selected
B 1
2
9
“ELQuant” program will show detailed running conditions
microsatellite analysis.
T
m
a
ic
b
r
l
o
e
sa
1.
t

e
R
ll
e
it
c
e
o
a
m
n
m
al
e
y
n
si
d
s
e
.
d Spreadex gel type and running conditions for selected
Microsatellite analysis with Spreadex hydrogels
F
a
i
n
g.
d
1
o
. P
p
at
t
e
im
rnit
a
y
l
t
g
es
e
t.
l
T
f
e
o
tra
rm
nuc
a
le
t.
o

tide repeats at 6 loci. microsatellite analysis.
(Fhigt.t 1p.: P//awtewrniwty .teslct. hTreomtranu.cleoomtid/ep ruepbelaicts/ iant d6 eloxci..p hp?page=6)
High resolving power of Elchrom non-acrylamide hydrogels, allows
.
Fig. 1. Paternity test. Tetranucleotide repeats at 6 loci. “Find the Best Gel” program will give the optimal Spreadex
The electropho
“Find the Best Gel” program will give the optimal Spreadex
for highly accurate size based separation and reproducible analysis
6
9
resis can be performed either in regular
hydrogel type fo
h
“F
y
i
dr
nd
ogel
the B
typ
e
e
st
f
G
o
e
r analysis of the samples defined by size.
r
e
a
l”
n
p
a
r
l
o
y
g
si
r
s
a
o
m
f

t
w
h
i
e
ll g
sa
iv
m
e t
p
h
le
e
s
o
d
p
e
t
f
im
ine
a
d
l S
b
p
y
r
s
ea
iz
d
e
e
.
x
elec
B
6
tr
1
2 Fig. 2. GenoMouse analysis. Pair wis
ophoresis units or in Elchrom specia
“ELQuant” program will show detailed running conditions
B 1
2
9
6 c
l
o
ly
m
d
p
e
a
s
r
i
i
g
s
n
o
e
n
d
o

“
h
E
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pe
ro
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r
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a
w
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i
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ll
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s
is
h
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f t
d
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ta
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n
d
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e
n
f
g
in
c
e
o
d
n
b
di
y
t
s
io
i
n
ze
s
.
of microsatellites. After PCR, Microsatellite samples are loaded
elecB tr1
2
9
ophoresis apparatuses: SEA 2000
®
and ORIGINS
f
b
tw
y
o mou
a
s
n
e
d o
st
p
r
tim
in
a
s
l gel format.
a
“E
n
L
d
Q
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p
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ti
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m
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a
p
l g
ro
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ra
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w
a
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show detailed running conditions
directly by multichannel pipet and resolved on Elchrom’s Spreadex
Elchrom
TM
. After the electrophoresis gels
(
a
B
r
6
e
,
s
12
ta
9
in
)
e
a
d
t
w
24
ith
l

oci.
(http://www.elchrom.com/public/index.php?page=6)
a
(h
n
t
d
tp
o
:/
p
/w
tim
ww
al
.
g
el
e
c
l
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f
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.
a
c
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o
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m/public/index.php?page=6)
standard DNA dyes such as Ethidium Bromide, SYBR
.
The electropho
(
.
http://www.elch
re
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sis can be perfor
.com/public/in
m
de
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x
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her in reg
?page=6
ular
)
hydrogels. The unit length of microsatellite repeat (di-, tri-, tetra-,
Gold, SYBR Green or others. .
The electrophoresis can be performed either in regular
Fig. 2. GenoMouse analysis. Pair wise comparison of
electrophoresis units or in Elchrom specially designed
etc.) defi nes the
two
resolution
mouse strains (
needed
B6,129) at 24
to
loc
be
i.
achieved. The unit length
e
The electropho
e
l
l
e
e
c
c
t
t
r
r
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o
p
p
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h
o
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and also the length of the PCR fragments defi ne the optimal type of
Microsatellite Direct Sequencing
s
E
e
t
l
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c
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S
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For direct sequencing, the bands of interest are picked out
Gold, S
s
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s
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B
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r
s
o
a
m
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d
s
e,
t
S
ain
Y
e
B
d
R
w

ith
Spreadex hydrogel and running conditions.
F
of the h
ig. 2. Gen
y
o
drogel
Mouse an
with
alysis.
B
Pa
a
ir
n
w
d
ise
P
c
ic
om
k
p
and mixed
arison of
with the
s
Gold, S
tandard
Y
D
BR
NA
Gre
dy
en or othe
es such a
rs.
s Ethidium Bromide, SYBR
t
s
Fwi
e
go.
q
m2
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Gus
n
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c
os
i
Mt
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e
( Ba
a
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comparison of
Gold, SYBR Green or others.
Ftwigo. m2.o Guseen osMtraoiunse ( Ba6na,1ly2s9i)s .a Pt 2a4ir lwocisei. comparison of
“Find the Best Gel” program will give the optimal Spreadex hydrogel
twoo c moonuset astnrati vnso (Blu6m,12e9) a atn 2d4 i loncei. rt matrix, the gel piec
F
e
i

g. 3. LOH on
Microsatellite Direct Sequencing
c
Microsatellite Direct Sequencing
N
o
C
n

taining PCR fragment of interest, can be use
type. “ELQuant” program will show detailed running conditions
c
d
hr
d
o
ir
m
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o
tl
s
y
o

For direct sequencing, the bands of interest are picked out
Microsatel
w
N
i
C
thout

further purification.
me 17.
of the h
For direct seque
ydrogel
lite Di
with
ncing, the bands
rect Seq
Band P
u
i
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n
of intere
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st are pic
with the
ked out
N C
Tetranucleotide
s
For direct seque
of the h
equenc
y
i
drogel
ng reag
with
ncing, the bands
ents
B
. D
an
u
d
e
P

ick and mixed
of interest are pic
with the
ked out
and optimal gel
Fig. 3.
forma
LOH on c
t
hrom
(http://www
osome 17. Tetran
.elchrom.com/public/index.
ucleotide
t
s
of the h
o
e
c
q
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s
n
t
c
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n
n
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with
m
e
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n
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ts
B
n
. D
a
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P
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rt
ic
m
k
a
and mixed
trix, the ge
w
l p
ith the
iece
repeats at 12 loci. repeats at 12 loc
c
s
t
i
o
o
.e
c
quencing reagents. Due
php?page=6). References
nt
o
a
n
in
s
i
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a
g P
t v
C
o
R
lu
f
m
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n
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nte
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ri
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g
b
e
e
l p
u
i
s
e
e
c
d
e
d

irectly
to constant volume and inert matrix, the gel piece
Elchrom Scientific AG - Publications
w
co
ithout
ntaini
furthe
ng PC
r p
R f
urification.
ragment of interest, can be used directly
c
w
o
ithout
ntaini
furthe
ng PC
r p
R f
urification.
ragment of interest, can be used directly
Fig. 3. LOH on chromosome 17. Tetranucleotide
without further purification.
rFeipge. a3t.s L aOt H1 2o nlo chi. romosome 17. Tetranucleotide
Freigp.e 3a.t sL aOtH 1 2o nlo chi.r omosome 17. Tetranucleotide References
Protocol Guide ı 2008 View entire protocol repeats at online 12 loci. at www.biotechniques.com/protocol ı BioTechniques
E
Referen
lchrom S
ces ı
c
21
ientific AG - Publications
Referen
Elchrom S
ces
cientific AG - Publications
Elchrom Scientific AG - Publications
Elchrom Protocol.indd 21 10/25/07 6:54:55 PM
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