ABSTRACT: Mouse liver RNA was extracted using Trizol (Invitrogen) and Qiagen RNeasy kits. RNA was checked with an Agilent Bioanalyzer for evidence of sub-genomic DNA and degradation. Targets were produced using standard Affymetrix protocols. Each sample represents data from a single mouse liver. Keywords: other
Project description:Mouse liver RNA was extracted using Trizol (Invitrogen) and Qiagen RNeasy kits. RNA was checked with an Agilent Bioanalyzer for evidence of sub-genomic DNA and degradation. Targets were produced using standard Affymetrix protocols. Each sample represents data from a single mouse liver.
Project description:Analysis of gene expression in the liver of insulin-deficient mice regulated by icv leptin administration. Control group received icv PBS administration. Icv leptin administration ameliorates hyperglycemia in insulin-deficient mice. Our transcriptome data provides important aspects of the leptin’s anti-type 1 diabetes action. Mice were harvested 10 days after icv leptin administration (25ng/0.11uL/hour). Liver samples were quickly removed, frozen in liquid nitrogen and subsequently stored at –80ºC. RNAs were extracted by Qiagen mRNA extract kits (RNeasy plus). gDNA was eliminated in this procedure by gDNA eliminator column, which is included in Qiagen mRNA extract kits. Genomics and Microarray Core Facility at UT-Southwestern (http://microarray.swmed.edu/) checked RNA quality with Bioanalyzer Chip and processed the samples for hybridization with Illumina Mouse-6 V2 BeadChip (Illumina Inc., San Diego, CA).
Project description:Microarray was conducted on Illumina Human Ref-6 Version 2 Expression Chip (Illumina, San Diego, CA). Three independent cultures were used for RNA isolation with RNeasy plus mini kit (Qiagen, Valencia, CA). RNA quality was checked by Agilent Bioanalyzer (Agilent, Santa Clara, CA). An Ambion labeling kit was used for labeling cDNA followed by hybridization to Illumina chips. ChIP scan data was extracted by Illumina Beadstudio and subsequently analyzed using Bioconductor lumi package.
Project description:RNA was isolated from Vehicle/Entacapone(ENT) treated mouse inguinal White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen). For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 5 µg of mRNA was used for m6A-IP. The immunoprecipitated m6A modified mRNAs were then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500(Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
Project description:Fto conditional knockout mutation was generated using phage-based Escherichia coli homologous recombination systems. Construct targeting the third exon of mouse Fto gene was introduced into ES cell by homologous recombination. The mice with homozygous targeted allele were crossed to Albumin-Cre for deletion the third exon of mouse Fto gene in liver. Total RNA was isolated from Liver Tissue using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
Project description:RNA was isolated from 4 weeks old Prrc2a flox/flox whole brain using the TRIzol (Invitrogen) reagent by following the company manual. mRNA was isolated by using Dynabeads mRNA Purification Kit (Invitrogen) For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq3000 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
Project description:To further development of our gene expression approach to microRNA-26a over-expression, we have employed whole mRNA microarray expression profiling as a discovery platform. Hela cells at 70–80% confluence in 6-well plates were transfected using Lipofectamine 2000 (Invitrogen). Negative control mimics or miR-26a mimics (100nM) were transfected in each well. Cell extracts were prepared 48 h after transfection, total RNA was checked for a RIN number to inspect RNA integration by an Agilent Bioanalyzer 2100 (Agilent technologies, Santa Clara, CA, US).
Project description:RNA was isolated from widetype C57BL/6J using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. All samples showed a RIN (RNA integrity number) of higher than 9. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq2500 or 3000 (Illumina) in paired-read mode, creating reads with a length of 125 or 101 bp. Sequencing chemistry v2 (Illumina) was used.
Project description:The DIO mouse were treated with Vehicle/Entacapone for 3 weeks. Total RNA was isolated from White Adipose Tissue using the TRIzol (Invitrogen) reagent by following the company manual. For all samples the RNA integrity was checked using an Agilent Bioanalyzer 2100. Approximately 2.5 µg of total RNA was then used for library preparation using a TruSeq™ RNA Sample Prep Kit v2 (Illumina, San Diego, CA, USA) according to the manufacturer’s protocol.The libraries were sequenced using HiSeq 2500 (Illumina) in paired-read mode, creating reads with a length of 101 bp. Sequencing chemistry v2 (Illumina) was used.
Project description:RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries), EWS-FLI1 (4 libraries), or lnc277 (7 libraries) was isolated with TRIzol (Invitrogen). Each sample was DNase treated and further purified on an RNeasy Mini column (Qiagen) before quality analysis on an Agilent 2100 Bioanalyzer. For each sample, 100-150ng of RNA was synthesized into cDNA, sheared on a Covaris ultrasonicator, and amplified using the NuGen Encore Complete kit (NuGen) to produce strand-specific and rRNA-depleted libraries. Samples were multiplexed (4/lane) for 2x100bp paired-end sequencing on an Illumina HiSeq 2000