Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Inhibition of Jak2 in SET2 cell line with INC424 (two time points and 3 dose levels in triplicate)

ABSTRACT: SET2 cells were incubated with increasing concentration of INC424/Ruxolitinib for 3-6 h and RNA was purified. Affymetrix Genechip miRNA array 2.0 was used to identify miRNA species showing a differential expression in treated cells compared with control cells. Exponentially growing SET2 cells were cultured in medium supplemented with 10% fetal bovine serum in the presence or the absence (control cells) of 160, 800 e 1,600 nM concentrations of the JAK1 and JAK2 inhibitor INC424/Ruxolitinib for 3 and 6 h. Triplicate cultures were prepared for each drug concentration and culture time. Total cellular RNA, including small RNAs, was extracted using RNeasy Micro kit (Qiagen, Valencia, CA). Disposable RNA chips (Agilent RNA 6000 Nano LabChip kit, Agilent Technologies, Waldbrunn, Germany) were used to determine the purity/integrity of RNA samples using Agilent 2100 Bioanalyzer. NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE) was used to evaluate the RNA sample concentration, and 260/280 and 260/230 nm ratios were considered to verify the purity of total RNA. Total RNA (500ng for samples) was labeled using the FlashTag Biotin HSR kit (Genisphere) and hybridized to the Affymetrix Genechip miRNA array 2.0 using manufacturer's protocols.

ORGANISM(S): Homo sapiens

SUBMITTER: Stefania Bortoluzzi

PROVIDER: E-GEOD-33809 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Characterization and discovery of novel miRNAs and moRNAs in JAK2V617F-mutated SET2 cells.

Bortoluzzi Stefania S Bisognin Andrea A Biasiolo Marta M Guglielmelli Paola P Biamonte Flavia F Norfo Ruggiero R Manfredini Rossella R Vannucchi Alessandro M AM

Blood 20120105 13

To gain insights into a possible role of microRNAs in myeloproliferative neoplasms, we performed short RNA massive sequencing and extensive bioinformatic analysis in the JAK2V617F-mutated SET2 cell line. Overall, 652 known mature miRNAs were detected, of which 21 were highly expressed, thus being responsible of most of miRNA-mediated gene repression. microRNA putative targets were enriched in specific signaling pathways, providing information about cell activities under massive posttranscription ...[more]

PMID: 22223824

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Project description:To address whether hypoxia contributes to muscle patho-physiology, normal, adult C57 mice were exposed to chronic, normobaric and hypobaric hypoxic environments for 2 weeks in order to simulate levels of hypoxaemia reported in DMD patients with advanced respiratory insufficiency. Control mice were maintained under normoxic conditions. Control and experimental mice were studied. Experiment Overall Design: Adult male C57Bl/10 mice were used in experiments. At the beginning of the experiment mice were divided into two groups, control (room condition) and hypoxic (hypoxic condition), over a period of 2 weeks. The hypoxic group was gradually exposed to lower levels of hypoxia in an especially designed and hermetically closed hypoxic chamber. A Pegas 4000 MF(Columbus Instruments) gas blending system was used. The oxygen level was gradually decreased from 21% to 8% over one week and animals were kept at 8% oxygen for another 7 days. Animalâs weights were monitored daily. Food and water were changed daily for the time of the experiment. After two weeks animals were euthanized using CO2, Extensor digitorum longus (EDL) and Soleus muscles were dissected for physiological studies. Prior to physiological analysis each group was divided into two smaller groups (subgroups). In the first subgroup the primary focus on physiological muscle analysis was on (EDL) while in the other subgroup it was on Soleus. This division allowed us that both muscles, EDL and Soleus were analyzed at the same time after euthanization. Experiment Overall Design: RNA isolation Experiment Overall Design: Total RNA was isolated from each QF muscle by Tri-Reagent (Ambion, Austin, TX) as described by manufacturer. Isolated total RNA were cleaned up by RNeasy mini kit (Qiagen, Valencia, CA) as described by manufacturer. The purity and concentration of total RNA were determined by measurement of absorbance at 260 and 280nm using a Nanodrop ND-1000 spectrophotometer (NanoDrop Technologies, Wilmington, DE). To satisfy our purity criteria, we discarded all RNA samples that did not have a 260/280 ratio between 1.8 and 2.1. To satisfy our criteria for integrity, we required that all RNA used in our experiments have single peaks for the 18S and 28S bands as determined by the Agilent 2100 Bioanalyzer (Agilent Technologies Inc., Palo Alto, CA). Experiment Overall Design: Linear amplification and cRNA labeling Experiment Overall Design: Three microliter total RNA was used for each sample to obtain linearly amplified labeled cRNA by using GeneChipÂ® One-Cycle Target Labeling kit (Affymetrix, Santa Clara, CA) as manufacturer described. Briefly; total RNA was used to generate double-stranded cDNA with the T7-oligo (dT) primer. This double-stranded cDNA was used in vitro transcription and biotin labeling steps. Labeled cRNA yield and purity were determined by measuring the absorbance at 260 and 280nm. All the cRNA 260/280 ratios were between 1.9 and 2.1. Quality control (QC) of the labeled cRNA products was assessed by performing 1Âµg labeled cRNA on 2% agarose gel to see similar RNA smear type. Experiment Overall Design: Fragmentation and microarray hybridization Experiment Overall Design: Fifteen micrograms labeled cRNA of hypoxic or normoxic QF muscle was fragmented, and 10Î¼g was hybridized to AffymetrixÂ® Mouse 430 ver 2.0 GeneChip arrays for 18â24h (Affymetrix Inc.). Each microarray was washed and stained with streptavidinâphycoerythrin and scanned at a 6-Î¼m resolution with Agilent model G2500A GeneArray scanner A visual quality control measurement was performed to ensure proper hybridization after each chip was scanned.

Dataset Information

Inhibition of Jak2 in SET2 cell line with INC424 (two time points and 3 dose levels in triplicate)

Publications

Characterization and discovery of novel miRNAs and moRNAs in JAK2V617F-mutated SET2 cells.

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