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29 protocols using sirna duplexes

1

Silencing RTVP-1, IL-6, STAT3, and C/EBPβ with siRNA

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Small interfering RNA (siRNA) duplexes were synthesized and purified by Dharmacon (Lafayette, CO). The siRNA sequence for targeting RTVP-1 mRNA was 5′-AAGACTGCGTTCGAATCCATA-3′ (siRNA1). In addition, for some of the experiments we used pools of four siRNA duplexes for RTVP-1 and IL-6 and for the TF STAT3 and C/EBPβ that were also obtained from Dharmacon. Transfection of siRNAs was done using Oligofectamine (Invitrogen) according to the manufacturer's instructions. Experiments were performed 72 h after transfection.
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2

siRNA Knockdown of Key Cytoskeletal Proteins

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siRNA duplexes were purchased from Dharmacon. A siRNA duplex targeting GFP was used as control (Ctrl siRNA 5′-GGCUACGUCCAGGAGCGCACC-3′) (66 (link)). Previously reported siRNA duplexes were used to deplete human 4.1R (h4.1R 5′-CCAGCACAGUUAACAGAAGACAUAA-3′) (28 (link)), mouse 4.1R (m4.1R 5′- GAAGGUCUGUGUGGAGCAU-3′), human LGN (hLGN 5′-GCUGCAGUUCAAGUUGGAACU-3′) (67 (link)), mouse LGN (mLGN 5′- GGUCUAAGCUACAGCACAAAU-3′) (68 (link)), human NuMA (hNuMA 5′-GGCGUGGCAGGAGAAGUUC-3′) (69 (link)), mouse NuMA (mNuMA 5′-GCCAGAUGGAUCGAAAGAUU-3′) (70 (link)), human and mouse dynein-heavy chain (dynein 5′-AGGCUUUAACCAAGCAGAUAA-3′) (71 (link)), mouse Numb (mNumb 5′-GCACCUGCCCAGUGGAUCC-3′) (72 (link)), human p150Glued (hp150Glued 5′-GCCUUGAACAGUUCCAUCAUU-3′) (73 (link)), and human Gαi3 (hGαi3 5′-CCGAAUGCAUGAAAGCAUG-3′) (40 (link)).
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3

Knockdown of Mitotic Regulators

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siRNA duplexes (Dharmacon) against BubR1 (GAUGGUGAAUUGUGGAAUA), Bub1 (CGAAGAGUGAUCACGAUUU), CDC20 (CGGAAGACCUGCCGUUACAUU) and ON-TARGETplus non-targeting siRNA pool (Sigma) were transfected at a final concentration of 50nM with RNAimax (Invitrogen) according to the manufacturer’s protocol. Transfection was carried out 5 hr after release from a thymidine block. For siRNA and plasmid co-transfection Lipofectamine 3000 (Invitrogen) was used.
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4

Reverse Transfection and Drug Treatment

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The siRNA duplexes were purchased from Dharmacon (listed in Table 2). 1.8 million cells were seeded in a 15 cm dish and reverse transfection was performed according to manufacturer’s instructions. 18 hours after the transfection, fresh growth medium was added. 72 hrs after the transfection, the indicated drug treatments were performed and cells were harvested.
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5

Bovine Follicular Cell Signaling

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Highly purified ovine LH (NIADDK oLH-S-16) was obtained from the National Hormone and Pituitary Program (NHPP), Torrance, CA, USA. Recombinant human (rh) BMP2, BMP4, BMP6, BMP7, TNFα, TGFα and EGF were purchased from R&D systems (Abingdon, UK). Highly purified bovine inhibin A and pro-αC were prepared ‘in house’ from pooled bovine follicular fluid (see below). Treatment solutions were sterilized using 0.2 µm membrane filters before dilution in sterile culture medium to required concentrations. For experiments involving knockdown of endogenous INHA and INSL3, siRNA duplexes against bovine INHA (sense strand: GGGAACUUGUCCUGGCCAAUU; antisense strand: UUGGCCAGGACAAGUUCCCUU) and bovine INSL3 (Sense strand: GGCAAGACCUGCUGACCCUUU; antisense strand: AGGGUCAGCAGGUCUUGCCUU) were custom-designed and synthesized by Dharmacon Thermo Scientific (Lafayette, CO, USA). Controls included cells transfected with a non-silencing control RNAi (NSC3; Dharmacon) as well as cells exposed to transfection reagent only (DharmaFECT 2; Dharmacon). All cell culture experiments were repeated using TC prepared from n = 4 independent batches of follicles.
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6

siRNA-mediated Knockdown of PR55α

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siRNA duplexes were purchased from Dharmacon. Non-targeting Control-siRNA were designed by the manufacturer to contain at least 4 mismatches to any human, rat or mouse genes. SMARTpool siRNA targeting PPP2R2A (PR55α) contains four siRNA targeting multiple sites on PR55α. Cells were transfected with 100 nM siRNA using DharmaFECT-1 (Dharmacon). The siRNA sequences are included in Supplementary Materials.
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7

Reverse Transfection siRNA Silencing Assay

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Cells were reverse transfected with Dharmafect1 (Dharmacon, Lafayette, CO, USA) and a pool of the four individual siRNA-silencing reagents (12.5 nmol/l each, 50 nmol/l total). For western blot analysis, FACS analysis and immunoprecipitation assay cells were transfected in 24- and 6-well plates, respectively, for 72 h. For real-time quantitative PCR analysis, cells were transfected in 96-well plates for 72 h. All siRNA duplexes were purchased from Dharmacon.
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8

Gene Silencing of Key Regulators

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All siRNA duplexes were purchased from Dharmacon (Lafayette, CO). siRNA targeting REGγ (catalog #L-012133-00-0010), PKAca (catalog #L-004649-00), FoxO1 (catalog #M-003006-01-05) or control siRNA (catalog #D-001810-10-20) were transfected into cells by 48–72 h using Lipofectamine 2000 (Invitrogen) following the instructions provided by the company.
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9

Knockdown of LKB1 using siRNA

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We followed shRNA methods described in our previous report.46 (link) For siRNA, a pool of four siRNA duplexes targeting human or mouse LKB1 and a nontargeting siRNA pool were purchased from Dharmacon, Inc. (Lafayette, CO, USA). Cells were grown in a six-well plate to 40% confluence and incubated with a mixture of a 60 nmol siRNA duplex and 5 μl of transfection reagent 1 (Dharmacon, Inc.). After 4 h, FBS was added to a final concentration of 10% (v/v). Additional transfection was performed at 48-h intervals later for some MEFs.
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10

Silencing Ferritin and RapGEF2 in Cells

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Small short interfering RNA (siRNA) was used to transiently silence Ferritin heavy chain 1 (FTH1) and RAPGEF2. To decrease the expression of Ferritin, a pool of three siRNA duplexes (cat# SR301663, Origene Technologies, Rockville, MD) against FTH1 and scramble siRNA (cat# SR30004) were used. To reduce the expression of RapGEF2, a pool of four siRNA duplexes (cat# L-009742-00-0005, Dharmacon, Lafayette, CO) was applied. siRNA were delivered to cells by SiTran Transfection reagent (Origene Technologies). After transfection for 72 hr, cells were treated with cAMP for intracellular labile Fe(II) measurement. Cells in a subset of wells were harvested for RNA and protein extraction and subsequent qRT-PCR and immunoblot assays.
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