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177 protocols using lamin a c

1

Western Blot Analysis of GDF15 Protein Expression

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Cell lysates were mixed with Laemmli buffer (BioRad) with β-mercaptoethanol in a 1:1 volume ratio. Samples were then boiled for 10 min before cooling on ice. Samples were then transferred to a 4–20% Mini PTOTEAN TGX gradient gel (BioRad) and subjected to electrophoresis. Semi-dry transfer of protein to nitrocellulose membrane was done using the Trans-Blot Turbo system from BioRad. After transfer, blots were stored in 1 × PBS, 0.1% Tween-20 wash buffer overnight at 4°C Blots were then blocked in 5% milk dissolved in 1 × PBS, 0.1% Tween-20, for 1 h at room temperature. Rabbit polyclonal antibody to human GDF15 (Santa Cruz Biotechnology, Inc., Dallas, Texas) was used at a 1:500 dilution and incubated for 1 h at room temperature. Lamin A/C (Santa Cruz Biotechnology, Inc.) was used as loading control and rabbit polyclonal antibody against Lamin A/C was used at a 1:2,000 dilution. After primary antibody incubation, blots were washed for 5 min using wash buffer five times with agitation. A HRP conjugated goat anti-rabbit secondary antibody was applied to the membrane in a 1:20,000 dilution and incubated for 1 h at room temperature followed by 5 min wash repeated five times. Membranes were incubated with Supersignal West Dura extended duration substrate (Thermo Scientific, Waltham, MA) and the blot was exposed to Amersham Hyperfilm ECL chemiluminescence film (GE, Pittsburgh, PA).
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2

Antibodies in Immunoblotting and Immunofluorescence

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The following antibodies were used at the indicated dilutions: PME‐1, Santa Cruz Biotechnology (Dallas, TX, USA) sc‐20086 (H‐226), Western blotting 1 : 1000; PME‐1, Santa Cruz Biotechnology sc‐25278 (B‐12), Immunohistochemistry 1 : 1000, Immunofluorescence 1 : 100; cleaved PARP‐1, Abcam (Cambridge, UK) ab32064 [E51], Western blotting 1 : 1000; GAPDH, HyTest 5G4‐6C5, Western blotting 1 : 5000; c‐MYC, Abcam ab32072 [Y69], Western blotting 1 : 1000; p‐Myc S62, Abcam ab78318, Western blotting 1 : 1000; AKT1/2/3, Cell Signaling Technology #9272, Western blotting 1 : 2000; p‐AKT S473, Cell Signaling Technology #4060, Western blotting 1 : 1000; Lamin‐A/C, Santa Cruz Biotechnology sc‐7292 (636), Immunofluorescence 1 : 250; Lamin‐A/C, Santa Cruz Biotechnology sc‐6215 (N‐18), Western blotting 1 : 1000; p‐Lamin‐A/C S392, Abcam ab58528, Western blotting 1 : 5000; EEA1, Santa Cruz Biotechnology sc‐137130 [G4], Immunofluorescence 1 : 100; p‐FAK Y397, Cell Signaling Technology #8556, Immunofluorescence 1 : 100; Histone H3K9me3, Cell Signaling Technology #13969 [D4W1U], Immunofluorescence 1 : 500; Histone H3K27me3, Cell Signaling Technology #9733 [C36B11], Immunofluorescence 1 : 500; PPP2R2A, Cell Signaling Technology #5689, Western blotting 1 : 1000.
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3

Quercetin and Chloroquine Modulate TFEB and Lysosomal Function

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Quercetin and chloroquine were obtained from Sigma-Aldrich; Primary antibodies for western boltting are as follows: TFEB (Cell Signaling Technology, Danvers, MA, USA), a-tubulin (Sigma-Aldrich, St. Louis, MO, USA), LAMP-1 (Santa Cruz, Santa Cruz, CA, USA), FTL (Abcam, USA), LaminA/C (Santa Cruz, Santa Cruz, CA, USA), GAPDH (Santa Cruz); TFEB siRNA was purchased from Life Technologies. (Santa Cruz), FTL (Abcam), LaminA/C (Santa Cruz), GAPDH (Santa Cruz, Santa Cruz, CA, USA) were used in this study. TFEB siRNA was purchased from Life Technologies; Fe on assay kit, MDA assay kit, and carbonylated protein ELISA kit were purchased from Nanjing Jiancheng Biological Engineering (Nanjing, China). The cytoplasmic cytosolic protein extraction and isolation kits were purchased from Beyotime (Beijing, China). Breast cancer cell lines were sourced from the National Collection of Authenticated Cell Cultures.
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4

Immunofluorescence Staining Protocol

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The following antibodies were used: mouse monoclonal antibodies against α-tubulin (Santa Cruz, sc-23948), BAF (Abnova, H00008815-M07), GAPDH (Santa Cruz, sc-32233), PP2A (BD science, 610555), mAb414 (Covance, MMS-120P), Lamin A/C (Santa Cruz, sc-7292), GFP (Santa Cruz, sc-9996), phospho γ-H2A.X (Ser139) (EMD Millipore, 05-636) [all at a 1:500 dilution in phosphate-buffered saline (PBS) supplemented with 3% BSA] and Flag (Sigma-Aldrich, F1804) at a 1:5000 dilution in PBS supplemented with 3% BSA; and a rabbit polyclonal antibody against Lamin B1 (Abcam, ab16048) at a 1:500 dilution in PBS supplemented with 3% BSA. Horseradish peroxidase-conjugated anti-mouse (G21040) and anti-rabbit (G21234) antibodies were obtained from Invitrogen (used at a 1:5000 dilution in TBST). The following fluorochrome-conjugated secondary antibodies were used (at a 1:500 dilution in PBS supplemented with 3% BSA): anti-mouse Alexa Fluor-488 (Invitrogen, A11059), anti-rabbit Alexa Fluor-488 (Invitrogen, A11034), TRITC-conjugated phalloidin (Jackson Immunoresearch, P1951), anti-mouse Cy3 (Jackson Immunoresearch, 715-165-151), and Alexa Fluor-594 (Invitrogen, A11037).
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5

Multiparametric Profiling of Myeloid Cells

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Protein extracts from Gr-1+CD11b+,
CD11b+Ly6C+, and CD11b+Ly6G+cells were analyzed by Western blot. The following primary antibodies were used:
Lamin A/C (SC-6214, Santa Cruz 1:1000), Gfi-1 (ab21061, abcam 1:2000),
C/EBPε (NBP1–85446, Novus 1:1000) Acetyl-H3 (9649S, CST 1:1000),
Histone 3 (14269S, CST 1:1000) and β-actin (SC69879, Santa Cruz 1:2000).
Anti-mouse/rabbit/goat secondary antibodies were purchased from Bio-Rad
(1:3000–5000 dilution). The blotting images were taken by
ChemiDoc™ Touch Imaging System (Bio-Rad), and Image Lab software
(Bio-Rad) was used for analysis.
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6

Chromatin Immunoprecipitation Sequencing Protocol

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ChIP assays were performed as previously described17 (link),18 (link),63 (link),64 (link) for the following histone marks: H3K4me3 (Abcam, #ab8580), H3K4me1 (Active Motif, #39297), H3K36me3 (Abcam, #ab9050), H3K27ac (Active Motif, #39133), H2AZac (Abcam, #ab18262), H3K9ac (Millipore, #06-599) and H3K27me3 (Millipore, #07-449). ChIP of H3K9me3 (Diagenode, #C15500003) was performed as previously described65 (link). We performed lamin ChIP assays in PrEC and LNCaP as previously described66 (link) for both Lamin B1 (Abcam, #ab16048) and Lamin A/C (Santa Cruz, #sc7292). Each ChIP assay was validated by qPCR against an IgG control and enrichment above input. Libraries were prepared with the Illumina TruSeq Chip Library Prep Kit and sequenced on an Illumina HiSeq 2500.
Sequencing data was processed as previously described17 (link),63 (link). Briefly, ChIP-seq reads were aligned to hg19 using bowtie58 (link) (v1.1.0) allowing up to 3 mismatches, discarding ambiguous and clonal reads. All histone ChIP-seq peaks were called using PeakRanger67 (v1.16). Broad domains of lamins (LADs), H3K9me3 and H3K27me3 were called using the enriched domain detector (EDD) for identification of wide genomic enrichment domains68 (link).
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7

UV-Induced Keratinocyte Lamin and Actin

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Primary human keratinocytes were seeded on glass cover slips in 6 cm dishes and incubated for 24 hours prior to UV irradiation. At 3 days post UV irradiation, cover slips were fixed with 2% paraformaldehyde for 15 mins, followed by incubation with primary antibodies lamin B1 (YenZym), lamin A/C (Santa Cruz, SC-6215), actin (Sigma, A5441) for 1 hour and secondary antibodies and DAPI for 30 mins. Slides were mounted in Prolong-Gold Anti-fade reagent (Invitrogen) and immunofluorescence images acquired on a Olympus FV1000 inverted confocal laser scanning microscope.
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8

Immunoblotting of key cellular proteins

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Nuclear and cytosolic extracts or total cell lysates were prepared as described before [49 (link)]. After electrophoresis and semi-dry electroblotting onto PVDF membranes, the following primary antibodies were used for immunodetection at 1:1000-fold dilution in 5% (w/v) non-fat milk powder, 0.05% Tween20 in TBS (Tris-buffered saline; 50 mM Tris/HCl, pH 7.6, and 150 mM NaCl): Nrf2, Slug, lamin-A/C, Smad2/3, vimentin and Hsp90 (all from Santa Cruz Biotechnology, Heidelberg, Germany), E-cadherin and JNK (both from Cell Signaling, Frankfurt/a.M., Germany) or L1 (clone L1-9.3, provided by Gerd Moldenhauer, DKFZ Heidelberg). In addition, the following antibodies diluted at 1:500 in in 5% (w/v) bovine serum albumin, 0.05% Tween20 in TBS were used: phospho-JNK, phospho Smad2 (Ser465/467) and phospho Smad3 (Ser423/425) (all from Cell Signaling). After incubation overnight at 4°C, blots were exposed to the appropriate horse-radish peroxidase-conjugated secondary antibody (Santa Cruz) diluted (1:1000) in blocking buffer and developed using the Dura detection kit (Perbio Sciences, Bonn, Germany). Data acquisition was done with the Chemidoc-XRS gel documentation system (BioRad, Munich, Germany) using the Quantity One software (Bio-Rad). Hsp90 and lamin-A/C served as loading control for total cell lysates and nuclear extracts, respectively.
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9

Comprehensive Antibody Characterization for Western Blotting, IPs, and Immunostaining

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Primary antibodies against the following proteins were utilized for western blotting, IPs, or immunostaining [listed in the format ‘protein name (catalog number, supplier)’]: DDX19A (ARP36455_T100, Aviva System Biology); DDX19B (ab70305, Abcam); lamin A/C (sc-376248, Santa Cruz Biotechnology); eIF4E (2067, Cell Signaling Technology); eIF3b (sc-16377, Santa Cruz Biotechnology), β-actin (A5441, Sigma); GAPDH (LF-PA0212, AbFrontier); FLAG (A8592 or F1804, Sigma); HA (11867431001, Roche); Myc (9E10; OP10L, Calbiochem); U1 snRNP 70 (sc-390899, Santa Cruz Biotechnology); CBP80, eIF4G1 and CTIF (6 (link)); and eIF4A3 (32 (link)).
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10

Immunocytochemistry and Western Blot Antibodies

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The following primary antibodies were used for immunocytochemistry and Western blot analysis: rabbit polyclonal antibodies against lamin B1, Tpr, importin α7 (Abcam, Cambridge, MA), pHIST3 (serine 10), MAP-2 (Merck Millipore, Darmstadt, Germany), actin, βIII-tubulin (Sigma-Aldrich, Milano, Italy), pERK, pCREB (Cell Signaling, Beverly, MA), lamin A/C (Santa Cruz Biotechnology, Dallas, TX), synaptophysin (SySy, Gottingen, Germany), and drebrin (Enzo Life Sciences, Farmingdale, NY); and mouse monoclonal antibodies against Nup153, lamin B2, CREB (Abcam), nuclear pore complex (mAb414; Covance, Princeton, NJ), Lap2β (BD Biosciences, East Rutherford, NJ), Tau (Tau-1; Merck Millipore), ERK (Cell Signaling), importin β (Sigma-Aldrich), and Alexa 488–conjugated Tuj1 (Covance). For Western blot analysis, horseradish peroxidase (HRP)–conjugated secondary antibodies (Bio-Rad, Hercules, CA) were used for detection. For immunofluorescence analyses, Alexa fluorophore–conjugated anti-mouse, anti-rabbit, and anti-rat antibodies from Invitrogen (Thermo Fisher Scientific, Waltham, MA) were used. Unless otherwise specified, general reagents and chemicals were from Sigma-Aldrich, and reagents for cell cultures were from Invitrogen.
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