Table 3

Location of the target sequences relative to the NM according to the sample-specific kinetics

TOPOLOGICAL ZONES RELATIVE TO NM


AMPLICON

CONTROL G0

PHX-24

PHX-7D


C

D

P

VC

E

C

D

P

VC

E

C

D

P

VC

E


a

+

+

+

-

-

+

+

+

-*

-*

+

+

-*

-

-

b

+

+

-

-

-

+

+

+*

-

-

+

+

-

-

-

c

+

+

-

-

-

+

+

-*

-

-

+

+

-

-

-

d

+

+

+

-

-

+

+

+

+*

-

+

+

+*

-

-

e

+

+

-

-

-

+

+

+*

-

-

+

-*

-

-

-

f

+

+

-

-

-

+

+

+

-*

-

+

+

-

-

-

g

+

+

-

-

-

+

+

-*

-

-

+

+

-*

-

-

h

+

+

+

-

-

+

+

+

+

-

+

+

-*

-

-

i

+

+

-

-

-

+

+

+

-

-

+

+

-

-

-

j

+

+

-

-

-

+

+

+

-

-

+

+

-*

-

-

k

+

+

+

-

-

+

+

+

+

-*

+

+

-*

-

-

l

+

+

-

-

-

+

+

+*

-

-

+

+

-

-

-

m

+

+

+

-

-

+

+

+

-*

-

+

+

+*

-

-

n

+

+

-

-

-

+

+

+*

-

-

+

+

-

-

-

o

+

+

+

-

-

+

+

+

+

-*

+

+

+*

-

-


Location of the fifteen target sequences from the 162 kbp genomic region studied within the specific topological zones relative to the NM. Such topological zones were defined according to the specific kinetics of nucleoid-DNA digestion for each kind of nucleoid sample (Figure 2A for G0; Figure 2B for PHx-24; Figure 2C for PHx-7D samples). The amplicons were scored either as positive or negative as a function of endonuclease digestion time and for each topological zone relative to the NM, depending on whether or not they were detected by a digital image-analysis system (Kodak 1D Image Analysis Software 3.5) using the default settings. G0, samples from normal rat liver hepatocytes. PHx-24, samples obtained from hepatocytes 24 h after partial hepatectomy. PHx-7 D, samples obtained from hepatocytes 7 days after partial hepatectomy. C, 0' digestion-time control. D, distal to the NM. P, proximal to the NM. VC, very close to the NM. E, embedded within the NM. All target sequences were mapped in repeated experiments with samples from separate animals (n ≥3). *Indicates that one of the repetitions gave a different result: -* in one experiment was positive; +* in one experiment was negative.

Rivera-Mulia et al. BMC Cell Biology 2011 12:3   doi:10.1186/1471-2121-12-3

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