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10 protocols using hpa001893

1

Comprehensive Histological Analysis of Inner Ear

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Histological examination, whole-mount and section immunostaining and ISH were carried out according to standard procedures. Briefly, inner ears were fixed in 4% paraformaldehyde (PFA) for 1 hr at 4°C, dehydrated, and embedded in wax. Paraffin sections were generated at 6 μm. For ISH, tissues were fixed overnight. We used five embryos for each genotype at each stage for each probe and the result was consistent in each embryo.
Primary antibodies: anti-Sox2 (PA1-094, Thermo Fisher), -Myo7A (25–6790, Proteus and 138-1-s, DSHB), -Six1 (HPA001893, Sigma), -Atoh1 (Math1-s, DSHB), -p27kip1 (554069, BD Pharmingen), -Calretinin (MA5-14540, Thermo Fisher), -p75NTR (#07–476, EMD Millipore), -N-cadherin (610921, BD Bioscience), -E-cadherin (U3254, Sigma), -S100A (ab11428, Abcam), -GLAST (ab416, Abcam), -Pou4f3 (sc-81980, Santa Cruz), -Prox1 (AB5475, Millipore), -Acetylated tubulin (T7451, Sigma), -Cy3-, Cy2-, Cy5- and FITC-conjugated secondary antibodies were used. Alexa Fluor 488 or 350-conjugated phalloidin (A12379 and A22281, Life technologies) were used for actin staining. Hoechst 3342 was used for nuclear staining.
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2

Quantifying Six1 Protein Levels

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Western blots were performed with protein extracts of GP and soleus muscles from cSix1KO mice and control mice as previously described [9] (link). 1∶1000 dilutions of anti-Six1 antibodies (HPA001893, Sigma) or anti-β−tubulin antibodies (2128, Cell Signaling) were used.
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3

Whole Mount Embryo Immunostaining Protocol

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For whole mount immunostaining we used the protocol described by Ezin and colleagues(Ezin et al., 2009 (link)). Briefly, after fixation embryos were dissected and washed in PBS with 0.3% Triton supplemented with 0.1% DMSO. Embryos were blocked for 2 hours in the same solution supplemented with 10% donkey serum. The following antibodies were used: Anti-CSRNP1 (Axud1) antibody produced in rabbit (Sigma, HPA045207, 1:300), anti-WNT1 rabbit polyclonal (Abcam, b15251, 1:200) and anti-HNK1 (DSHB, 1:10), anti-cleaved Caspase-3 antibody (Cell Signaling, 9661, 1:200), anti-Sox2 (R&D Systems, AF2018, 1:200) and anti-Six1 (Sigma, HPA001893, 1:200). Secondary antibodies used included donkey anti-rabbit IGG, or goat anti-mouse IGM, conjugated with Alexa Fluor 488/555/594/647 (1:2000, Molecular probes). For anti-WNT1(Serralbo and Marcelle, 2014 (link)), signal was amplified with the Tyramide TSA system from Perkin Elmer according to the manufacturer’s instruction.
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4

Muscle Protein Extraction and Western Blot

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Muscle proteins were extracted from the TRIzol organic phase following the procedure recommended by the manufacturer. Protein pellets were resolubilized in Urea-SDS Sample Buffer (6 M Urea, 1% SDS, 20 mM Tris pH 6.8) at a ratio of about 3 μL buffer per 1 mg of tissue and were allowed to solubilize with gentle rocking overnight at 4 °C. Sample protein concentrations were determined using the BCA Protein Assay Kit (Thermo Scientific). Primary antibodies were anti-Six1 (rabbit polyclonal HPA001893, Sigma) and anti-beta-Tubulin (mouse monoclonal hybridoma clone E7, DSHB). Secondary antibodies conjugated with HRP were used. Signal was acquired on X-ray films, which were subsequently digitized and analyzed in the FIJI software for densitometric quantitation.
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5

Immunofluorescence Analysis of SIX1, EYA1, and Cell Markers

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Frozen sections were fixed with 100% ethanol for 15 minutes and permeabilized using 0.05% Tween20 twice (2 minutes per treatment). Blocking was performed using 3% bovine serum albumin for 30 minutes at RT. After washing with phosphate belanced solution (PBS), sections were incubated with rabbit anti-human SIX1 primary antibody (1:100 dilution) (HPA001893, Sigma, St. Louis, MO, USA), rabbit anti-human EYA1 primary antibody (1:100 dilution) (ab85009, Abcam, Cambridge, MA, USA), and mouse anti-human HSA primary antibody (1:1,000 dilution) (MAB1455, R&D Systems, Minneapolis MN, USA) or mouse anti-human GFAP primary antibody (1:100 dilution) (MA5-12023, ThermoFisher, Waltham, MA, USA) at 4 °C overnight. Sections were then incubated with Alexa Fluor®488 donkey anti-mouse immunoglobulin G (IgG) and Alexa Fluor®568 donkey anti-rabbit IgG (1:1,000 dilution) (A21202, A10042, ThermoFisher, Waltham, MA, USA) for one hour at RT. After washing with PBS, sections were counterstained with 4',6-diamidino-2-phenylindole (DAPI). Finally, coverslips were mounted with anti-fade mounting medium, and immunofluorescent signals were visualized and recorded using an Olympus DP72 microscope and the cellSens Standard 1.5 software. (Olympus Corporation, Tokyo, Japan)
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6

Western Blot Protein Detection

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Whole-cell extracts and nuclear extracts were isolated as previously described16 (link). Proteins were electrophoresed and then transferred to polyvinylidene difluoride membranes. After blocking in 5% milk in Tris-buffered saline with 0.1% tween 20, membranes were incubated in specific antibodies overnight at 4 °C (see Supplementary Table 5 for specific antibodies). For Six1 protein detection, antibodies from Sigma (HPA001893) and antibodies generated in our laboratory as previously described66 (link) were used interchangeably. Image lab software was used to quantify western blot analysis. Uncropped images are shown in Supplementary Fig. 18.
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7

SIX1 Transcription Factor Binding and Chromatin Regulation

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Chromatin immunoprecipitation was performed essentially as described 64 (link), using 293T cells transiently transfected with pLPC-SIX1 or IMR90 fibroblasts expressing shSIX1, except that the crosslinking step with DMA was omitted for H3K27Me3 immunoprecipitation. The antibodies used were: anti-SIX1 (HPA001893, Sigma) and anti-H3K27Me3 (07-449, Millipore). The primers used for PCR were CTCAAAGCGGATAATTCAAGAGC, AAGCCTTAAGAACAGTGCCACAC (1050 nt upstream of p16INK4A transcription start site).
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8

Investigating SIX1, EYA1, and TGF-β in CRC

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CRC cancerous tissues and their adjacent non-cancerous tissues and cultured CRC cells were lysed in radioimmunoprecipitation assay (RIPA) buffer (ThermoFisher Scientific, #89901) mixed with protease inhibitor (ThermoFisher Scientific, #78425). Equal amounts of total cell extracts were resolved in 10% sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) gels. After transforming onto polyvinylidene fluoride membranes and blocking with 5% milk for 1 h, proteins were incubated with primary antibodies including anti-SIX1 (Sigma-Aldrich, #HPA001893), anti-EYA1 (Sigma-Aldrich, #HPA028917), anti-CCNA1 (Sigma-Aldrich, #SAB1409961), anti-TGF-β (Abcam, Cambridge, MA, USA, #ab92486), and anti-glyceraldehyde 3-phosphate dehydrogenase (Abcam, #ab8245) overnight at 4°C, respectively. The membranes were further incubated with secondary antibodies at room temperature for 1 h and then protein bands were visualized using an enhanced chemiluminescence kit (ThermoFisher Scientific, #32106).
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9

ChIP-seq Assay for SIX1 and H3K4me3

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Chromatin immunoprecipitation was performed essentially as described in45 (link). The antibodies used were: SIX1 (HPA001893, Sigma), and H3K4me3 (Ab8580, Abcam). The primers used for PCR were: GGTGGTCGTCAAACTCTGCTAATT, AGAGTCTCGGAGAATGCCCT (SRR1) and ATTTATTCAGTTCCCAGTCCAAGC, CCCTCTCCCCCCACGC (SRR2).
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10

Profiling Transcriptional Regulation by SIX1

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Chromatin was immunoprecipitated from tumors with comparable expression of wild-type or mutant SIX1 (anti-SIX1, HPA001893, Sigma) by Active Motif. Sequencing was performed on the HiSeq 2500 platform using the Rapid Run settings. 100-bp paired-end reads were mapped to the 1,000 genomes phase 2 reference assembly (hs37d5) using BWA-MEM, and alignments were merged using SAMtools.
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