Báo cáo y học: "Improving RNA-Seq expression estimates by correcting for fragment bias" doc

... expression estimates by correcting for fragment bias Adam Roberts 1 , Cole Trapnell 2,3 , Julie Donaghey 2 , John L Rinn 2,3 and Lior Pachter 1,4* Abstract The biochemistry of RNA-Seq library preparation ... Most protocols also include a fragmentation step, typically RNA hydrolysis or nebulization, or alter- natively cDNA fragmentation by DNase I treatment or sonication. Many...

Ngày tải lên: 09/08/2014, 22:24

... hipermodified base Y3 7 (wybutine) (Figs 6 and 7). Also other amino- glycosides, as kanamycin A, neomycin B and a synthetic neomycin-neomycin dimer have been shown to induce fragmentation of tRNA Phe at Y3 7 ... tRNA Phe induced by the Cu(II)-Ami-H 2 O 2 system Figure 6 shows the results of the strand-break assay of yeast tRNA Phe in the presence of Ami, Cu(II)-Ami and the Cu(II)-Ami-H 2 O...

Ngày tải lên: 21/02/2014, 01:21

... analyzed by dot blot hybridization with [ 32 P]-labeled cDNA populations from SIV-associated monkey lymphomas and monkey B-lymphocytes. Those cDNAs whose hybridization signals were markedly stronger ... stronger with lymphoma cDNA than with cDNA of B- lymphocytes were further analyzed by Northern blot hybridization. Some genes (a-myb, set, SMG-1, ND4) involved in HIV-associated lym...

Ngày tải lên: 02/11/2012, 11:08

... of DNase. Finally RNA was released from cup and stored in –70° C for use. Micro-array analysis For gene array analysis, 100 µg RNA was reversely transcripted in to cDNA. cDNA fragments from ... removed by centrifugation at 14,000 rpm 5 minutes. The lysate was collected and the radioactivity was determined by Trichloroacetic acid (TCA) precipitation. For protein analysis, 100µl cel...

Ngày tải lên: 02/11/2012, 11:17

... mg protein), were assayed for sterol D14-reductase activity by incubation for 30 min with C27D 8,14 in the conditions described i n Materials and methods. Enzymatic activity was evaluated on the ... Biophys. Acta 1437, 80±92. 26. C leveland, D.W., Fischer, S.G., Kirschner, M.W. & Laemmli, U.K. (1977) Peptide mapping by limited proteolysis in sodium dodecylsulfate and a nalysis by...

Ngày tải lên: 08/03/2014, 16:20

... first report for such steroid activity from a plant AKR enzyme. Expression of DpAR genes The size of the DpAR transcripts and their expression profile were determined by Northern hybridization analysis of ... reaction, are catalysed by enzymes of the aldo-keto reductase (AKR) superfamily [8]. The members of the AKR superfamily are cytosolic, monomeric proteins that catalyse mainly the...

Ngày tải lên: 18/03/2014, 01:20

... RPMI- . Lymphocytes were counted using a hemocy- tometer chamber (Superior, Germany), and viability was de- termined by trypan blue exclusion. Antibodies and Flow Cytometric Analysis Antibodies ... host im- munity, possibly by upregulating the expression of CD on vaginal and peripheral T cells. Furthermore, resolution of the infection may depend on the ability of T lymphocytes...

Ngày tải lên: 08/08/2014, 21:20

... restricted to activated T lympho- cytes [5,22,23] and could be observed in resting T lym- phocytes, B lymphocytes, monocytes or granulocytes [20,24]. In contrast, Th2 lymphocytes were reported to produce ... separated by 12% sodium dodecyl sulfate–polyacrylamide gel electrophoresis and subsequently transferred to Hybond-N nitrocellulose mem- branes (Amersham Biosciences, Piscataway, NJ, USA...

Ngày tải lên: 09/08/2014, 01:23

... analyzed individually. Flow cytometry analysis The cell type composition and level of protein expression for some genes in the inguinal lymph nodes were analyzed by flow cytometry. Single cell suspensions ... lymph nodes were detected by Affymetrix and validated by custom-made oligomer glass arrays. Some of the detected genes were also analyzed by real- time PCR for confirmation...

Ngày tải lên: 09/08/2014, 01:23

... members of the TNF family were represented on the cDNA arrays, the expression of genes for only these two cytokines was modulated by protein I/II. IL-6 and leukemia inhibitory factor, which both ... 2.0 Software (Clontech), developed specifically for analysis of the Atlas cDNA expression arrays. All spots were individu- ally checked by hand to ensure accuracy of the detection meth...

Ngày tải lên: 09/08/2014, 06:22