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45 protocols using buffer el

1

Isolation of White Blood Cells

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WBCs were prepared by lysing the red blood cells with Buffer EL (Qiagen). Briefly, 0.5 ml of whole blood was combined with 2.5 ml of Buffer EL (Qiagen). The tube was inverted several times and incubated for 10–15 min at room temperature. After centrifugation at 228 g for 5 min at room temperature, the supernatant was discarded. The pellet was re-suspended with 2.5 ml of Buffer EL and the process repeated. Finally, the WBCs were washed once with 1 ml of Buffer EL, pelleted and re-suspended in 0.5 ml PBS.
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2

Humanized Mouse Model for Hematopoietic Studies

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NBSGW mice from Jackson laboratory were used for the in vivo studies under the protocol approved by the office of laboratory animal care (OLAC) in UC Berkeley. Electroporated hCD34+ cells were injected to 6‐ to 12‐week‐old gender‐matched mice via tail vein. To monitor human chimerism, mice blood was collected from submandibular vein into EDTA‐coated collection tubes after transplantation. Red blood cells were lysed using EL buffer (QIAGEN) and washed twice with phosphate‐buffered saline (PBS). Recipient mice were euthanized at weeks 16–20 post‐transplantation. Bone marrow cells were collected from femur and tibia. In these isolations, we did not observe any overt indications for hematopoietic neoplasia. For ex vivo culture, hCD34+ cells from bone marrow were sorted using FACS Aria Fusion (BD Biosciences) and cultured using limited dilution culture method in methylcellulose‐based medium on 96‐well plate for 3 weeks.
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3

Isolation and Characterization of Immune Cells

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100–200 µl of homogenized spleen or peripheral blood was treated with 2 ml of EL buffer (QIAGEN) for 1 min to lyse red blood cells. The reaction was quenched by adding 5–6 volume of chilled PBS. After centrifugation and removing supernatant, cells were stained with specific surface marker antibodies. The following antibodies (BD Biosciences) were used: V450 mouse anti‐human CD19 (BD 560353), PE rat‐anti‐mouse CD45 (BD 553081), PE‐Cy7 mouse anti‐human CD34 (BD 348791), and FITC mouse anti‐human CD45 (BD 555482). The cells were sorted using FACS Aria Fusion instrument. FACS data were analyzed using FlowJo software.
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4

Multiparametric Flow Cytometry of Human and Murine Cells

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For flow cytometry, red blood cells were lysed with EL Buffer on ice (Qiagen), with remaining cells washed and resupsended in 1x PBS with 1% BSA and stained for 15 minutes with the following antibodies: human CD45-APC (Clone 2D1) (Biolegend), human CD33-PE-Cy7 (Clone P67.6) (Biolegend), murine CD45-PE (Clone 30-F11) (Biolegend) and DAPI (Biolegend). For detection of human stem and progenitor cells, additional human CD34 (Clone 561; Biolegend) and CD38 (Clone HIT2; Biolegend) antibodies were used. Cells were washed and submitted for flow cytometric analysis using a 3-laser LSRII (Becton Dickinson).
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5

Collecting Immune Cells from Hematologic Malignancies

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Peripheral mononuclear cells (PBMC) from AML, CLL and CML patients and bone marrow mononuclear cells (BMNC) from MM patients (provided by the Departments of Hematology and Oncology in Tübingen, Leipzig and Aachen, Germany) at the time of initial diagnosis or relapse prior to therapy were isolated by density gradient centrifugation (Biocoll, Biochrom GmbH, Berlin, Germany) and erythrocyte lysis (EL buffer, Qiagen, Venlo, Netherlands). For all AML and CLL samples the frequency of malignant cells within the PBMC isolate was > 80%. For MM samples the percentage of malignant plasma cells within the BMNC fraction was > 60%. For CML we analyzed whole blood samples of 12 CML patients in the chronic phase (no blasts), two in the accelerated phase (18-20% myeloid blasts) and two in a blast crisis (50-60% myeloid blasts). Informed consent was obtained in accordance with the Declaration of Helsinki protocol. The study was performed according to the guidelines of the local ethics committee (373/2011BO2, 142/2013BO2). HLA typing was carried out by the Department of Hematology and Oncology, Tübingen, Germany. Samples were stored at −80 °C until further use.
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6

Isolation of Immune Cells from Healthy and Disease Samples

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PBMC and bone marrow mononuclear cells (BMNC) from healthy volunteers were isolated by density gradient centrifugation (Biocoll, Biochrom GmbH, Berlin, Germany) and erythrocyte lysis (EL buffer, Qiagen, Venlo, Netherlands). Normal tissue samples from patients and autopsy material were provided by the University Hospital Tübingen, Germany and the University Hospital Zürich, Switzerland (Supplementary Table 1). Specimens were frozen in liquid nitrogen immediately after resection. Informed consent was obtained in accordance with the Declaration of Helsinki protocol
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7

Lymphocytes Isolation from Whole Blood

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Lymphocytes extraction was carried out not later than 1-hour after blood collection; Every 10 ml whole blood sample was divided into 2 tubes containing 25ml EL buffer (Qiagen), gently mixed and incubated on ice for 20 min. Tubes were centrifuges for 8-min in 2000rpm at 4°C. Supernatant was removed and 10 milliliters of EL buffer was added. Tubes were mixed, incubated on ice for 15-min and centrifuges for 8-min in 2000rpm at 4°C. Supernatant was removed and 1 milliliter of EL buffer was added. Tubes were mixed and centrifuges for 5-min in 5500rpm at 4°C. Supernatant was removed and 200 microliters of EL buffer was added. Tubes were mixed and centrifuges for 5-min in 2000 rpm at 4°C. Supernatant was removed and pellets were kept in -80°C for later use.
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8

Plasma Analysis of Liver Enzymes

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Whole blood was collected from animals [males displaying macroscopic adenomas (A, n=7 ), VEH controls (V, n=7 ), and TBT-treated males without any macroscopic adenomas (T, n=5 )] at the time of euthanasia (45 weeks of age) via cardiac puncture, and plasma was isolated by centrifugation at 4°C for 10 min at 500×g after red blood cell lysis with EL Buffer (Qiagen, Catalog No. 79217) and stored at 80°C until analysis. Alanine and aspartate transaminase (ALT/AST) activity levels were analyzed in the plasma of 45-week-old animals using an alanine transaminase activity assay (ab105134; Abcam) or an aspartate transaminase activity assay (MAK055; Sigma) as per the manufacturer’s instructions. Briefly, plasma was diluted (1:5 for ALT and 1:10 for AST) and mixed with Reaction Mix, then read on the BioTek EL808 plater reader (BioTek, Instruments) in a kinetic fashion every 3 min for 60 min while incubating at 37°C. For analysis two time points (T) were chosen where all samples fell within the standard curve. Pyruvate/glutamate levels were calculated from a standard curve and activity (in nanomoles per minute per milliliter or in milliunits per milliliter) was calculated as (B/DT×V)×D for ALT or (B×D)/(DT×V) for AST, where B=pyruvate/glutamate  (nmol) , ΔT=T2T1 , V=volume of original sample , and D=dilution factor . From this data, the ALT/AST ratio was calculated.
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9

Isolation of Human and Murine PMNs

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To isolate human PMNs anticoagulated blood from healthy human donors was layered on a polysaccharide gradient (Polymorphprep, Axis Shield). After 30 min of centrifugation (500g), the PMN interphase was harvested and pelleted for 5 min at 300g. Remaining erythrocytes were lysed with EL buffer (Qiagen). Isolation of murine PMNs, which were obtained from bone marrow of C57BL/6NCrl mice, was performed using the EasySep™ Mouse Neutrophil Enrichment Kit (Stem Cell Technologies) according to the manufacturer’s protocol. Both murine and human PMNs were cultured in RPMI 1640 Medium with 5% FCS.
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10

Purification of PDX-Derived Cells

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For ex vivo analysis from PDX-derived cells, bone marrow was flushed from treated mice and subjected to a red blood cell lysis (EL Buffer, Qiagen) for 15min. on ice before undergoing enrichment of human cells using a mouse cell depletion kit (Miltenyi). After depletion, cells were tested for purity staining for human CD45-APC (Clone 2D1; Biolegend) and murine CD45-PE (Clone 30-F11; Biolegend) and subjected to flow cytometric analysis using a 3-laser LSRII (Becton Dickinson). All MNC cells used in ex vivo assays were >96% purity for hCD45.
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