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7 protocols using mms 101p

1

Co-IP with Benzonase Treatment for Protein Complex Analysis

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Co-IP was performed as described above except using Dynabeads (Life Technologies). For co-IP with Benzonase treatment, lysate was treated with 250 Unit of Benzonase per mouse brain for 1hr at 4°C before incubating with beads. Proteins were eluted by adding 1X LDS sample buffer (Life Technologies) and heated at 95°C for 10min.
Proteins were resolved in a 10% SDS-PAGE gel and transferred into a nitrocellulose membrane. Membrane was blocked with 5% non-fat milk in PBS for 1 hour followed by incubating with primary antibody overnight at 4°C. Membrane was washed 3 times with PBST and incubated with DyLight Fluor Secondary Antibodies (Pierce) for one hour at room temperature. Membrane was imaged on a LI-COR Odyssey Imager. Western blot quantification was done using ImageJ. Primary antibodies used in this study were: anti-DHX9 (Abcam ab26271, 1:2000), anti-FLAG (Sigma M2, 1:1000), anti-FUS (Bethyl A300-293A, 1:10000), anti-HA (Covance MMS-101P, 1:5000), anti-hnRNP F+H (Abcam ab10689, 1:3000), anti-LEDGF (Bethyl A300-847A, 1:1500), anti-MeCP2 (Abcam ab50005, 1:2000), anti-Myc (Cell signaling 71D10, 1:1000), and anti-TDP-43 (ProteinTech 10782-2-AP, 1:1000).
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2

Quantitative Subcellular Protein Localization

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Cell lines were plated on glass coverslips into 24-well plates and cultured for 3 days up to 70% confluence in 500 ng ml−1 doxycycline–containing medium. Growth medium was refreshed (1 ml) prior to a 15 min fixation with 1 ml 8% paraformaldehyde (PFA) added dropwise. Cells were washed three times with PBS, permeabilized with 0.1% saponin PBS for 20 min, and blocked with 1% BSA 0.1% saponin PBS for 30 min before incubation with anti-HA (bioLegend, Covance catalog #MMS-101P, 1:1,000) and anti-lamin-B1 (abcam ab16048, 1:1,000) antibodies in 1% BSA 0.1% saponin PBS 2 h at room temperature (RT) under agitation. Samples were washed three times with PBS and incubated with Alexa 647-conjugated (A647) anti-mouse antibody (1:1,000) and A568 anti-rabbit antibody (1:1,000) in 1% BSA 0.1% saponin PBS for 40 min at RT. Three final washes were performed before mounting the slides in Vectashield with DAPI (Vector Laboratories). Images were acquired on a ZEISS LSM 700 confocal microscopy and analyzed with Fiji software.
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3

Generating Drosophila Neuroblast MARCM Clones

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To generate Drosophila neuroblast MARCM clones, FRT-G13, aPKCK06403/CyO Virgin flies were crossed to ;;3xHA-aPKC V606A male flies. The resulting non-Cyo male progeny were crossed to elav-Gal4, UAS-mCD8:GFP, hs:flp; FRT-G13, tubPGal80 Virgins and allowed to lay for 24 hours at room temperature. The vials were then allowed to stay at room temperature for an additional 24 hours at which time they were heat-shocked @37°C for 90 minutes. This was followed by a possible second 90 minute heat-shock within 18 hours. Vials were raised at 18°C or room temperature until wandering third instar stage when they were dissected and stained as described above with the following antibodies: Primary antibodies: Rat α-Mira (1:500; Abcam, ab197788), Rabbit α-HA C29F4(1:1,000; Cell Signaling Technologies, 3724) or Mouse α-HA (1:500; Covance, MMS-101P), and Chicken α-GFP (1:500; Abcam, ab13970). Secondary antibodies: Dk α-Rt Cy3 (712-165-153; 1:500), Dk α-Rb 647 (711-605-152; 1:500) or Dk α-Ms 647 (715-605-151; 1:500), and Dk α-Ck 488 (703-545-155). Brains were imaged using a Leica TCS SPE upright confocal microscope using an ACS APO 40× 1.15 NA Oil CS objective or an Olympus Fluoview FV1000 upright confocal microscope using a PlanApo N 60× 1.42 NA Oil objective.
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4

Defining the Oocyte Epigenome

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The oocyte epigenome was defined by immunofluorescence staining of adult ovaries using a panel of 21 primary antibodies (Supplementary Table 2). In addition, the following primary antibodies were used: rabbit anti-H3K4me3 (1:1000 dilution, Active Motif 39160); rabbit anti-H3K27me3 (1:250 dilution, Active Motif 39158); rabbit anti-H3K9me2 (1:200 dilution, Upstate 07–441); rabbit anti-pSer2 RNAPII (1:500 dilution, Abcam ab5095); rabbit anti-pSer5 RNAPII (1:1000 dilution, Abcam ab5131); mouse anti-HA (1:100 dilution, Covance MMS-101P); rabbit anti-HA (1:500 dilution, Abcam ab9110) and mouse anti-Orb (clones 4H8 and 6H4, 1:30 dilution each, Developmental Studies Hybridoma Bank). The following primary antibodies were used for ovary and embryo immunoblotting: rat anti-dKDM5 (1:5,000 dilution, from F. Azorín, Institute of Molecular Biology of Barcelona, Spain); rabbit anti-H3K4me3 (1:500 dilution, Active Motif 39160); rat anti-HA (1:500 dilution, Roche 11867423001); rabbit anti-H3 (1:8,000 dilution, Cell Signalling Technology #9715) and mouse anti-α-Tubulin (1:50,000 dilution, Sigma T6199).
Secondary detection was performed with Cy3, Cy5 and HRP-conjugated antibodies at 1:1,000 (immunofluorescence) and 1:4,000 (immunoblotting) dilutions (Jackson ImmunoResearch).
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5

Western Blot Analysis of Yeast Proteins

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Yeast proteins were extracted either by NaOH or TCA protocol as previously described59 (link) and resolved on polyacrylamide gels, transferred to nitrocellulose membranes blots, and probed with primary rabbit/mouse antibody against Pma1 (Abcam, ab4645), HA (Covance, MMS-101P) or GFP (Abcam, ab290). The membranes were then probed with a secondary goat-anti-rabbit/mouse antibody conjugated to IRDye800 or to IRDye680 (LI-COR Biosciences). Membranes were scanned for infrared signal using the Odyssey Imaging System.
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6

Western Blot Analysis of Yeast Proteins

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Yeast proteins were extracted either by NaOH or trichloroacetic acid (TCA) protocol as previously described59 and resolved on polyacrylamide gels, transferred to nitrocellulose membranes blots, and probed with primary rabbit/mouse antibody against Pma1 (Abcam, UK, ab4645), HA (Covance, NJ, USA, MMS‐101P) or GFP (Abcam, UK ab290). The membranes were then probed with a secondary goat‐anti‐rabbit/mouse antibody conjugated to IRDye800 or to IRDye680 (LI‐COR Biosciences, NE, USA). Membranes were scanned for infrared signal using the Odyssey Imaging System.
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7

Western Blotting of Embryonic Proteins

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For western blotting, animal caps were homogenised in (20 mM Tris-HCl pH 7.5, 50 mM NaCl, 1 mM EGTA, 2 mM MgCl2) using an end-over-end invertor (Rotamix RM1) at 4°C for 10 min and centrifuged at 1000 g for 10 min at 4°C. The supernatant was boiled in Llamelli buffer prior to SDS-PAGE and transfer onto a PDVF membrane.
Western blots were performed according to standard protocols. Primary antibodies used were mouse anti-HA.11 (Clone 16B12, Covance MMS-101P), rabbit anti-Myc (Abcam, AB9106), and mouse anti-β-catenin antibodies. Secondary antibodies used were sheep anti-mouse-IgG antibody conjugated to horseradish preoxidase (HRP; Amersham, NA931) and mouse anti-rabbit-light-chain antibody conjugated to HRP (Jackson, 211-032-171).
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