biostudies-arrayexpressMetabolomicsUnknownTranscriptomicsGenomicsProteomicsAzadeh Fahim Golestanehtranscription profiling by arrayMus musculusMus musculushttps://www.ebi.ac.uk/biostudies/studies/E-MTAB-6747LLC cells transduced with shCsf1 and shKdm5c were injected in right flank of C57BL/6 mice. Tumors reaching 100 mm3 were treated with Sunitinib (SU-11248, Pfizer, Inc., New Yourk) at dose of 50mg/kg/day SIDbiostudies-arrayexpressSample Collection - LLC cells (mouse Lewis Lung Carcinoma-ATCC® CRL-1642 ™) were cultured in DMEM media (ATCC) complemented with 10% fetal calf serum (FCS) (GIBCO). Stable knock down of Kdm5c and Csf1 was achieved by transducing cells with lentiviral particles, using Polybrene as tranduction reagent. cells were injected in right flank of C57BL/6 mice and tumors were either treated with 50mg/kg/day SID sunitinib or with no treatment. Tumors were recovered afterwards and were snap frozen in liquid nitrogen.Nucleic Acid Extraction - Total RNA, from the transduced LLC cells were isolated in phase lock tubes using the procedure of total RNA isolation with Trizol (Ambion) and the RNeasy Kit (QIAGEN). RNA 6000 Nano Lab on Chip kits and Agilent 2100 Bioanalyzer (Agilent-CA) were utilized to check RNA quality and quantity, respectively.Labeling - Biotin-labeled cRNA samples for hybridization on Illumina Human/Mouse/Rat Sentrix-6/8/12 BeadChip arrays (Illumina, Inc.) were prepared according to Illumina's recommended sample labeling procedure based on the modified Eberwine protocol (Eberwine et al., 1992). In brief, 250 – 500 ng total RNA was used for complementary DNA (cDNA) synthesis, followed by an amplification/labeling step (in vitro transcription) to synthesize biotin-labeled cRNA according to the MessageAmp II aRNA Amplification kit (Ambion, Inc., Austin, TX). Biotin-16-UTP was purchased from Roche Applied Science, Penzberg, Germany. The cRNA was column purified according to TotalPrep RNA Amplification Kit, and eluted in 60-80 µl of water. Quality of cRNA was controlled using the RNA Nano Chip Assay on an Agilent 2100 Bioanalyzer and spectrophotometrically quantified (NanoDrop).Sample Treatment - 50mg/kg/day SID sunitinib with oral gavageScaning - Scaning and feature extraction werer performed with Illumina BeadChip scanner (IsScan+) and Illumna feature extracton software.Hybridization - Hybridization is performed at 58°C, in GEX-HCB buffer (Illumina Inc.) at a concentration of 100 ng cRNA/µl, unsealed in a wet chamber for 20h. Spike-in controls for low, medium and highly abundant RNAs were added, as well as mismatch control and biotinylation control oligonucleotides. Microarrays were washed once in High Temp Wash buffer (Illumina Inc.) at 55°C and then twice in E1BC buffer (Illumina Inc.) at room temperature for 5 minutes (in between washed with ethanol at room temperature). After blocking for 5 min in 4 ml of 1% (wt/vol) Blocker Casein in phosphate buffered saline Hammarsten grade (Pierce Biotechnology, Inc., Rockford, IL), array signals are developed by a 10-min incubation in 2 ml of 1 µg/ml Cy3-streptavidin (Amersham Biosciences, Buckinghamshire, UK) solution and 1% blocking solution. After a final wash in E1BC, the arrays are dried and scanned.MIAME ScoreRaw DataAssays and DataMAGE-TAB FilesArray DesignsChrisitan SchwagerAzadeh Fahim GolestanehfalseDeciphering the molecular regulators of tumor resistance to VEGF-receptor tyrosine kinase inhibitor SunitinibLLC cells transduced with shCsf1 and shKdm5c were injected in right flank of C57BL/6 mice. Tumors reaching 100 mm3 were treated with Sunitinib (SU-11248, Pfizer, Inc., New Yourk) at dose of 50mg/kg/day SID2026-09-15T00:00:00Z2026-09-17T10:39:12.979Z2022-03-04T18:55:29.013ZE-MTAB-6747E-MTAB-6745E-MTAB-6746E-MTAB-6749E-MTAB-6748EFO_0002768EFO_0003814EFO_0002944EFO_0003813EFO_0005518EFO_0003969EFO_0003815