Sentences with phrase «deep sequencing reads»

The ∼ 16.5 kb mitochondrial genomes of 22Rv1 and LNCaP were assembled from 555,977 and 171,418 mtRNA deep sequencing reads, respectively.

Importantly, while the RNA from sample VP62 extracted in 2006 was positive for XMRV, RNA extracted from the same prostate tissue in 2012 was found to be negative not only by ViroChip and PCR (Fig. 2; Table 1) but also by deep sequencing, with no XMRV sequences detected out of 4 million deep sequencing reads (Fig. 5).

Unlike profiling strategies involving whole or partial genome sequencing of mitochondrial DNA [55], [56], here the ∼ 16.5 kb mitochondrial genome is assembled from only RNA - derived deep sequencing reads.

A consensus sequence based on mapped deep sequencing reads was generated for each of the prostate cancer XMRV genomes and used to correct errors in the previously published sequences, with the requirement of no ambiguity at each discrepant nucleotide position.

SNP analysis of deep sequencing reads corresponding to the XMRV genomes of 22Rv1 (A) and LNCaP (B), as well as the mitochondrial genomes of these two cell lines (C) was performed.

From a total of 10,896,742 raw deep sequencing reads, 40,844 reads were mapped to the 22Rv1 - associated XMRV genome (Fig. 5, «LNCaP (from 2003)»), and the resulting consensus assembly was found to be identical to 22Rv1 - associated XMRV (Fig. 6, «LNCaP (from 2003, consensus)»).

The poor apparent coverage was the result of high sequence divergence of the TMAdV genome from SAdV - 18, which hindered the identification of most of the 16,524 actual deep sequencing reads derived from TMAdV (Fig. 2B, red).

In light of these findings and since tRNAs are repeat sequences themselves, the team had to devise a complex and stringent scheme with which they mapped the deep sequencing reads.

Not exact matches

A study of this scope is possible thanks to innovative techniques for in vitro selection (such as mRNA display), as well as a revolutionary technology permitting massively parallel RNA sequencing (known as deep sequencing), which provides unprecedented speed and read accuracy.

To assess low frequency disruption events, we conducted 454 deep sequencing on all 15 sites in both control CD4 + T cells and those treated with X4 - ZFNs, yielding approximately 7,500 — 26,000 reads per site in the ZFN - treated samples (Table S2).

No reads corresponding to mouse mitochondrial or intracisternal A-particle (IAP) sequences were detected in these 3 samples by deep sequencing and specific RT - PCR (data not shown).

Small subunit (SSU) rRNA gene sequencing on second generation platforms leverages their deep sequencing and multiplexing capacity, but is limited in genetic resolution due to short read lengths.

MyAML combines long read chemistry and deep sequencing with an optimized and validated custom bioinformatics pipeline, MyInformatics ™, to specifically examine genomic variants in AML patients.

Raw single reads (and their mate pairs) from deep sequencing libraries corresponding to 3 XMRV - positive samples [VP35, 14,589,296 reads; VP42, 14,573,990 reads; and VP62 (2006), 18,308,352 reads] and 3 XMRV - negative samples [VP10, 5,270,536 reads; VP30, 4,378,204 reads; and VP62 (2012), 3,985,692 reads] were then stripped of adapter and primer sequences and aligned to the CRS mitochondrial genome using BLASTn (word size = 11, E-value = 1 × 10 − 10).

Harvard Graduate School of Education will work with the Strategic Education Research Partnership and other partners to complete a program of work designed to a) investigate the predictors of reading comprehension in 4th - 8th grade students, in particular the role of skills at perspective - taking, complex reasoning, and academic language in predicting deep comprehension outcomes, b) track developmental trajectories across the middle grades in perspective - taking, complex reasoning, academic language skill, and deep comprehension, c) develop and evaluate curricular and pedagogical approaches designed to promote deep comprehension in the content areas in 4th - 8th grades, and d) develop and evaluate an intervention program designed for 6th - 8th grade students reading at 3rd - 4th grade level.The HGSE team will take responsibility, in collaboration with colleagues at other institutions, for the following components of the proposed work: Instrument development: Pilot data collection using interviews and candidate assessment items, collaboration with DiscoTest colleagues to develop coding of the pilot data so as to produce well - justified learning sequences for perspective - taking, complex reasoning, academic language skill, and deep comprehension.Curricular development: HGSE investigators Fischer, Selman, Snow, and Uccelli will contribute to the development of a discussion - based curriculum for 4th - 5th graders, and to the expansion of an existing discussion - based curriculum for 6th - 8th graders, with a particular focus on science content (Fischer), social studies content (Selman), and academic language skills (Snow & Uccelli).

Students learn more than surface - level phonemic awareness and phonics — they dive deep and master these foundational reading skills through Smarty Ant's complete scope and sequence.