View - ResearchGate

More documents

Recommendations

Info

DNA Vector-Based shRNA-Expression Systems 237Fig. 6. Experimental procedures for assessing the inhibition efficiency of shRNAexpressionconstructs. (A) Seeding of targeting cell line. The targeting cell line is subcultured24 h before transfection and plated into six-well culture plate at 1 × 10 5 cellsper well. (B) Transfection of shRNA-expression construct. The cultured cells are eithertransfected with 2 µg of shRNA-expression construct or cotransfected 0.5 µg of RNAitarget-gene expression construct and 1.5 µg of trigger shRNA-expression construct byusing Lipofectamine 2000 according to the manufacturer’s instructions. (C)Assessment of inhibition efficiency. After 48 h incubation, the transfected cells are harvestedand lysed for either RNA or protein level analysis of target-gene expression byusing Northern blot, RT-PCR, Western blot, immunostaining, or functional reporterassay (luciferase activity).
Page 2:
Gene Function Analysis
Page 6:
METHODS IN MOLECULAR BIOLOGYGene Fu
Page 12:
PrefaceThis volume of Methods in Mo
Page 16:
Prefaceixcolleagues demonstrate how
Page 20:
xiiContentsPART III EXPERIMENTAL ME
Page 26:
ICOMPUTATIONAL METHODS I
Page 34:
4 BidautTable 1Input File Format Us
Page 38:
6 BidautTable 2Folder Layout to Use
Page 42:
8 Bidaut• alphaA: this is the num
Page 46:
10 Bidautcomputing the maximum corr
Page 50:
12 BidautFig. 3. The complete Clutr
Page 54:
Table 3Some Identified Patterns (5,
Page 58:
16 BidautFig. 4. This is a comparis
Page 62:
18 BidautReferences1. Hughes, T. R.
Page 66:
20 Kirov et al.way to associate gen
Page 70:
22 Kirov et al.based on a study ass
Page 74:
24 Kirov et al.1. Retrieve the gene
Page 78:
26Fig. 1. Functional associations f
Page 82:
28 Kirov et al.Fig. 2. Pathway anal
Page 86:
30 Kirov et al.3. Gene symbols usag
Page 90:
32 Kirov et al.9. OBO_Team, Open Bi
Page 94:
3Estimating Gene Function With Leas
Page 98:
Estimating Gene Function With LS-NM
Page 102:
Page 106:
Page 110:
Page 114:
Page 118:
Page 122:
50 Gonye et al.activity and problem
Page 126:
52 Gonye et al.Currently, PAINT can
Page 130:
54 Gonye et al.dynamic nature of th
Page 136:
Prediction Using PAINT 57represente
Page 140:
Prediction Using PAINT 59In PAINT,
Page 144:
Prediction Using PAINT 6114. On the
Page 148:
Prediction Using PAINT 634.2. Size
Page 152:
65Fig. 4. Localization of enrichmen
Page 156:
Prediction Using PAINT 673. Okubo,
Page 160:
5Prediction of Intrinsic Disorder a
Page 164:
Prediction of ID and Its Use in Fun
Page 168:
Table 1Summary of the Web Servers O
Page 172:
Page 176:
Page 180:
Page 184:
Page 188:
Page 192:
Page 196:
Page 200:
Page 204:
Page 208:
IICOMPUTATIONAL METHODS II
Page 212:
94 Crabtree et al.genomes, which is
Page 216:
96 Crabtree et al.Fig. 2. Sybil pro
Page 220:
98 Crabtree et al.Fig. 3. Computing
Page 224:
100 Crabtree et al.3.1.5.1. FILTER
Page 228:
102 Crabtree et al.3. For the sake
Page 232:
104 Crabtree et al.Fig. 5. Best bid
Page 236:
106 Crabtree et al.17. Some cluster
Page 240:
108 Crabtree et al.19. Chado—The
Page 244:
110 Dateproducts prevents the under
Page 248:
112 DateDetails of these tasks are
Page 252:
114 DateThis step creates additiona
Page 256:
116 Date>hsapiens|gi|20093443 >hsap
Page 260:
118 DateBLAST score from the match
Page 264:
Table 1A Sample of Results From Pro
Page 268:
122 DateFig. 1. A network of functi
Page 272:
124 Datedescribed by Verjovsky Marc
Page 276:
126 Dateor contracts put forth by t
Page 280:
8Bioinformatics Tools for Modeling
Page 284:
Modeling Transcription Factor Targe
Page 288:
VISTA Program to search for TFBSs H
Page 292:
Page 296:
Page 300:
Page 304:
Page 308:
Ac 0 0 0 1 0 1 0 1 0 1 1 0 0 0 0 0
Page 312:
Page 316:
Page 320:
Page 324:
Page 328:
154 Osborne et al.are included in t
Page 332:
156 Osborne et al.Fig. 2. Flowchart
Page 336:
158 Osborne et al.UMLS source abbre
Page 340:
160 Osborne et al.Fig. 3. Querying
Page 344:
162 Osborne et al.3.4.2. Installati
Page 348:
164 Osborne et al.amount of filteri
Page 352:
166 Osborne et al.public class MMTx
Page 356:
168 Osborne et al.Fig. 4. Input tes
Page 360:
10Statistical Methods for Identifyi
Page 364:
Identifying Differentially Expresse
Page 368:
Page 372:
Page 376:
Page 380:
Page 384:
Page 388:
Page 392:
Page 396:
Page 400:
Page 404:
11Gene Function Analysis Using the
Page 408:
Gene Function Analysis Using the Ch
Page 412:
Page 416:
Page 420:
Page 424:
Page 428:
Page 432:
Page 436:
Page 440: 12Design and Application of a shRNA
Page 444: Design and Application of a shRNA 2
Page 464: 224 Cheng and Chang1. IntroductionR
Page 468: 226 Cheng and ChangFig. 1. Structur
Page 472: 228 Cheng and ChangFig. 2. Sequence
Page 476: 230 Cheng and Chang3. Handheld ultr
Page 480: 232 Cheng and ChangFig. 4. Sequence
Page 484: 234 Cheng and ChangFig. 5. Experime
Page 488: 236 Cheng and Chang3.4. Functional
Page 494: DNA Vector-Based shRNA-Expression S
Page 498: DNA Vector-Based shRNA-Expression S
Page 502: 244 Hust et al.overcome by two appr
Page 506: 246 Hust et al.Fig. 1. Schematic de
Page 510: 248 Hust et al.interaction during p
Page 514: 250 Hust et al.3.4. Titering1. Inoc
Page 518: 252 Hust et al.10. Shortly before u
Page 522: 254 Hust et al.activity by preservi
Page 526: 15A Bacterial/Yeast Merged Two-Hybr
Page 530: Screening in Yeast With a Bacterial
Page 542:
Screening in Yeast With a Bacterial
Page 546:
Page 550:
Page 554:
Page 558:
Page 562:
Page 566:
Page 570:
Page 574:
Page 578:
Page 582:
Page 586:
Page 590:
Page 594:
16A Bacterial/Yeast Merged Two-Hybr
Page 598:
Dual Bait-Compatible Bacterial Two-
Page 602:
Page 606:
Page 610:
Page 614:
Page 618:
Page 622:
Page 626:
Page 630:
Page 634:
Page 638:
Page 642:
Page 646:
318 Thibodeau-Beganny and Joungbeen
Page 650:
320 Thibodeau-Beganny and JoungFig.
Page 654:
Page 658:
324 Thibodeau-Beganny and JoungTypi
Page 662:
Page 666:
328 Thibodeau-Beganny and JoungPCR
Page 670:
330 Thibodeau-Beganny and Joung16-1
Page 674:
332 Thibodeau-Beganny and Joung2. P
Page 678:
334 Thibodeau-Beganny and Joung11.
Page 682:
336 IndexKknockin (gene knockin) 19
show all

View - ResearchGate

Create successful ePaper yourself

Delete template?

Save as template?