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4 protocols using rnaqueous midi kit

1

VHH Library Construction and Validation

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Total RNA was extracted from the peripheral blood lymphocytes with RNAqueous midi kit (Ambion) and the cDNA was prepared using MMLV reverse
transcriptase (Invitrogen) with the CALL002 primer (5’-GGT ACG TGC TGT TGA ACT GTT CC-3’). VHH coding sequences were amplified by PCR with primers
FR1For (5’-GAT GTG CAG CTG CAG GAG TCT GGG GGA GG-3’) and FR4Rev (5’-GGA CTA GTG CGG CCG CTG GAG ACG GTG ACC TGG GT-3’) annealing at the framework-1
and framework-4 regions flanking the CDRs of heavy chain antibodies, respectively. The PCR fragments were ligated into the phagemid vector pHEN4 ( 14 (link)
) after cutting with the restriction enzymes PstI and NotI. Ligated materials were transformed by electroporation in freshly prepared E.
coli TG1 cells, plated on 24×24 cm plates containing 2YT medium (16g tryptone, 10g yeast extract and 5g NaCl) supplemented with ampicillin and
glucose(2YT–AMP–GLU ) and incubated overnight at 37°C. The electroporation was performed with the Eporator (Eppendorf, Germany) in 1mm gap cuvettes
(Sigma) at 1700Kv. Colonies were scraped from the plates and stored at −80°C in 2YTmedium supplemented with 50% glycerol.
To establish the library size, dilution series (10-3, 10-4, 10-5, and 10-6)
were prepared from electroporated cells in a liquid medium and 100 µL
were plated onto 9 cm diameter 2YT–AMP–GLU plates and incubate overnight at 37°C.
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2

Quantitative Analysis of RNA Expression

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Example 15

Total RNA was extracted from tissues using the “RNAqueous-Midi kit” (Ambion Inc., Austin, Tex.). Ten μg of RNA were hybridized with a mix of 32P-labeled RNA probes. The 32P-labeled RNA probe mix was prepared by in vitro transcription using the “In vitro transcription kit”, CK-3, and custom template sets were provided by BD Biosciences/Pharmingen (San Diego, Calif.). The hybridized RNAs were treated with RNAse, using the “RNAse protection Assay kit” (BD Biosciences), precipitated and the protected fragments were resolved on vertical sequencing (10% acrylamide) gels. Following electrophoresis, the gels were dried and exposed to X-ray film (Kodak-X-Omat) and Phosphorlmager screen (Molecular Dynamics, Sunnyvale, Calif.). The signals on the screen were analyzed by Phosphorlmager Image-Quant software. The RNAse protection assay was performed using RNA samples of at least 3 to 5 individual mice per each virus. At least two independently prepared virus stocks were used for RNA levels analysis.

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3

Quantitative Analysis of Gene Expression

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RNA from human tissue was prepared using using TRIzol® (Invitrogen) along with sonication on ice and then extracted using a Phenol (Ambion): Chloroform (Boehringer Mannheim Inc.) mix prior to purification using the RNAqueous Midi Kit (Ambion). cDNA was prepared from purified RNA samples using using High Capacity cDNA Reverse Transcriptase Kit (Applied Biosystems) per manufacturer's instruction. TaqMan® Fast Universal PCR Master Mix (Applied Biosystems) and TaqMan® FAM™ dye-labeled probes including POLR2A (Hs00172187_m1), CAMK1 (Hs00220668_m1), CDH13 (Hs01004530_m1), KISS1R (Hs00261399_m1), KSR1 (Hs01075790_m1), and SSPN (Hs01025520_m1) were combined with prepared cDNA samples to analyze relative mRNA expression via quantitative real time PCR (QPCR). POLR2A expression was used as normalization control. Fold change values were compared between normal and tumor as well as non-target scrambled lentiviral and target lentiviral infected using the ΔΔCt method [63 (link)].
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4

RNA Expression Analysis via RNAse Protection Assay

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Example 15

Total RNA was extracted from tissues using the “RNAqueous-Midi kit” (Ambion Inc., Austin, Tex.). Ten μg of RNA were hybridized with a mix of 32P-labeled RNA probes. The 32P-labeled RNA probe mix was prepared by in vitro transcription using the “In vitro transcription kit”, CK-3, and custom template sets were provided by BD Biosciences/Pharmingen (San Diego, Calif.). The hybridized RNAs were treated with RNAse, using the “RNAse protection Assay kit” (BD Biosciences), precipitated and the protected fragments were resolved on vertical sequencing (10% acrylamide) gels. Following electrophoresis, the gels were dried and exposed to X-ray film (Kodak-X-Omat) and PhosphorImager screen (Molecular Dynamics, Sunnyvale, Calif.). The signals on the screen were analyzed by PhosphorImager Image-Quant software. The RNAse protection assay was performed using RNA samples of at least 3 to 5 individual mice per each virus. At least two independently prepared virus stocks were used for RNA levels analysis.

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