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6 protocols using imdm media

1

Mammalian Cell Culture Protocols

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All mammalian cells were grown in a standard water-jacketed incubator with 5% CO2. MDA-MB-231, U2OS, HEK293T, MDA-MB-453 all grown in DMEM media (45000–304, Corning) with 10% FBS (26140079, Gibco) and 1X penicillin/streptomycin (15140122, Thermo Scientific). K562 cells were grown in IMDM media (45000–366, Corning) with 10% FBS and 1X penicillin/streptomycin. All mammalian cells were acquired from American Type Culture Collection (ATCC). Plasmocin prophylaxis (1:500) was used when generating of new stable cell line. All cells were maintained below an 85% confluency and passaged less than 25 times. For passaging, cells are trypsinized with 0.25% Trypsin-EDTA (25200114, Thermo Scientific). For hypoxia incubation, cells were incubated in a humidified Baker Ruskinn InvivO2 (I400) hypoxia chamber at 1% O2 and 5% CO2 for the indicated times. Puromycin (2µg/mL), blasticidin (5µg/mL), and zeocin (50µg/mL) were added when necessary for selection. 1X Hanks’ Balanced Salt Solution (HBSS) (45000–456, Corning) was used to wash cells when passaged.
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2

Engineered Cell Lines for Autophagy Study

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K562 cells expressing tf‐NBR1, tf‐TAX1BP1, tf‐NDP52, tf‐SQSTM1, and tf‐LC3 were generated previously (Shoemaker et al, 2019). All cells were grown in a standard water‐jacketed incubator with 5% CO2. K562 cells were grown in IMDM media (10‐016‐CV, Corning) with 10% FBS (26140079, Thermo Fisher) and 1× penicillin/strep (15140122, Thermo Fisher). Cells were maintained below 1 million cells per milliliter. HEK293T cells were grown in DMEM media (10‐013‐CV, Corning) with 10% FBS and 1× pen/strep. Normocin (1:500) was used as a common additive. All cells were passaged < 25 times. For passaging, cells were trypsinized with Trypsin‐EDTA (25300‐054, Gibco). Puromycin (2 µg/ml), blasticidin (5 µg/ml), and zeocin (50 µg/ml) were added when necessary for selection. HBSS was used to wash cells (14025092, Thermo Fisher).
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Culturing Human Cancer Cell Lines

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The human cancer cell lines MV4-11, SKM-1, SU-DHL-2, U2932, JVM-2, Namalwa were purchased from the American Type Culture Collection (ATCC) (Manassas, VA, USA). The human AML cell lines MOLM-13, MOLM14, HEL and the human ALL cell line PF382 were provided by Dr. Scott Armstrong, Dana Farber Cancer Institute (DFCI), Boston, MA. The AML line, NB4 (KRAS A18D), was obtained from Dr. Gary Gilliland. ALL the rest cell lines were purchased from Cobioer Biosciences CO. LTD (NanJing, China). MV4-11 and MEC-1 was cultured in IMDM media (Corning, USA) with 10% FBS and supplemented with 2% L-glutamine and 1% pen/strep. OCI-AML-3 was cultured in α-MEM media (Cornig, USA) with 10% FBS and supplemented with 2% L-glutamine and 1% pen/strep. OCI-AML-2 was cultured in α-MEM media (Cornig, USA) with 20% FBS and supplemented with 2% L-glutamine and 1% pen/strep. ALL the rest cell lines were cultured in RPMI 1640 media (Corning, USA) with 10% fetal bovine serum (FBS) and and supplemented with 2% L-glutamine 1% penicillin/streptomycin. All cell lines were maintained in culture media at 37°C with 5% CO2.
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4

Erythroid Maturation of G1E Cell Lines

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G1E, G1E-ER4 and G1E-GATA1(V205M)-ER cells were grown in IMDM media (Corning, 10–016-CV) with 15% fetal calf serum (Gemini, lot A08H00K), 2% penicillin/streptomycin (Gibco, 15140–122), 140 μm 1-thioglycerol (Sigma, M6145), 2 units/ml epoetin (Amgen) and conditioned medium from a kit ligand-producing CHO cell line. Cells were grown at a density of 100,000 to 1,000,000 cells/ml. Erythroid maturation experiments were performed by plating cells at a cell density of ~200,000 cells/ml in fresh G1E medium containing 100 nm estradiol (Sigma, E2758) for durations indicated for each experiment.
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5

Mammalian Cell Culture Protocols

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All mammalian cells were grown in a standard water-jacketed incubator with 5% CO2. MDA-MB-231, U2OS, HEK293T, MDA-MB-453 all grown in DMEM media (45000-304, Corning) with 10% FBS (26140079, Gibco) and 1× penicillin/streptomycin (15140122, Thermo Scientific). K562 cells were grown in IMDM media (45000-366, Corning) with 10% FBS and 1× penicillin/streptomycin. Mammalian cells (HTB-26, MDA-MB-231; CCL-243, K562; CRL-3216, HEK293T) were acquired from the American Type Culture Collection (ATCC) where cell authentication is performed. Cell authentication was not performed on U2OS and MDA-MB-453 cells. Plasmocin prophylaxis (1:500) was used when generating of new stable cell line. All cells were maintained below an 85% confluency and passaged less than 25 times. For passaging, cells are trypsinized with 0.25% Trypsin-EDTA (25200114, Thermo Scientific). For hypoxia incubation, cells were incubated in a humidified Baker Ruskinn InvivO2 (I400) hypoxia chamber at 1% O2 and 5% CO2 for the indicated times. Puromycin (2 µg/mL), blasticidin (5 µg/mL), and zeocin (50 µg/mL) were added when necessary for selection. In all, 1× Hanks’ Balanced Salt Solution (HBSS) (45000-456, Corning) was used to wash cells when passaged.
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6

Isolation of LSK Hematopoietic Stem Cells

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Bone marrow lineage negative (Lin), Sca-1+, c-kit+ (LSK) hematopoietic stem/progenitor cells were obtained from Csf2raKO mice30 (link) according to SOPs (Table S5). In brief, bone marrow cells were obtained from 7 to 10-week-old Csf2raKO donor mice (n = 24, 12 males/12 females, body weight = 17.6–27.5 g) by removing and crushing the pelvic iliac crests, tibias, and femurs in IMDM media (Corning) containing 2% heat-inactivated fetal bovine serum (FBS), and 1% penicillin/streptomycin solution (Gibco). Mononuclear cells were hematopoietic lineage depleted with biotin-conjugated mouse lineage antibodies: mouse monoclonal CD5 (clone 53-7.3; BD Pharmingen), CD8a (clone 53-6.7; BD Pharmingen), CD45R/B220 (clone RA3-6B2; BD Pharmingen), CD11b (clone M1/70; BD Pharmingen), Gr-1 (clone RB6-8C5; BD Pharmingen), and TER-119 (BD Pharmingen) followed by magnetic bead separation (Dynabeads Sheep anti-Rat IgG, Invitrogen). After removing lineage-positive cells, the remaining cells were stained with 7-aminoactinomycin D (7-AAD) (Invitrogen), Streptavidin-FITC (fluorescein isothiocyanate), Sca-1 (clone D7)-PE (R-Phycoerythrin), and CD117/c-kit (clone 2B8)-APC (allophycocyanin) antibodies (BD Biosciences) and Lin c-Kit+ Sca-1+ cells were sorted using a FACS Aria II (BD Biosciences) gated on live cells (7-AAD negative).
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