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TranscriptomicsEvaluating bias-reducing protocols for RNA sequencing library preparation
The ligation step in RNA sequencing library generation is a known source of bias. We present the first comparison of the standard duplex adaptor protocol supplied by Life Technologies for use on the Ion Torrent PGM with an alternate single adaptor approach involving CircLigase (CircLig). We also...
ORGANISM(S): synthetic construct 
2014-06-24 | E-MTAB-2566 | biostudies-arrayexpress
GenomicsEffect of a KRAS peptide nucleic acid clamp on the Ion Torrent sequencing protocol
To test whether the addition of a peptide nucleic acid (PNA) clamp, which binds WT KRAS at codon 12, can increase the efficacy of mutation detection for KRASG12D within a targeted NGS setting. We tested the effect of clamping the wild-type KRAS sequence in a reference standard (Tru-Q 7, 1.3% Tier fr...
ORGANISM(S): Homo sapiens 
2017-07-29 | E-MTAB-5718 | biostudies-arrayexpress
UnknownTargeting MerTK decreases efferocytosis and increases anti-tumor immune infiltrate in prostate cancer.
Not available
S-EPMC10465384 | biostudies-literature
TranscriptomicsTranscriptomic (RNA-seq) analysis of wild-type and Nolz1-/- (Zfp503) mutant striatal tissue reveals altered expression of several genes involved in striatal projection neuron specification.
Midbrain dopaminergic (DA) axons make long longitudinal projections towards target areas in the forebrain, including the striatum. After demonstrating a striatal specific requirement of transcriptional regulator Nolz1 (Zfp503) in regulating DA axon guidance and innervation, we performed RNA-seq anal...
ORGANISM(S): Mus musculus 
2020-05-12 | E-MTAB-8240 | biostudies-arrayexpress
UnknownDevelopment of a SNP-based assay for measuring genetic diversity in the Tasmanian devil insurance population.
Not available
S-EPMC4607143 | biostudies-literature
GenomicsThe Genomic Landscape of Response to EGFR Blockade in Colorectal Cancer
Colorectal cancer (CRC) is the third most common cancer world-wide with 1.2 million patients diagnosed yearly. In late stage CRC, the most commonly used targeted therapies are monoclonal antibodies cetuximab and panitumumab, which inactivate EGFR. Recent studies have identified alterations in KRAS...
EGAS00001001305 | EGA
GenomicsDAC for the study of response to EGFR Blockade in Colorectal Cancer
Data Access Committee EGAC00001000360
EGAC00001000360 | EGA
GenomicsDirect Detection of Early-stage Cancers Using Circulating Tumor DNA
Early detection and intervention are likely to be the most effective means for reducing morbidity and mortality of human cancer. However, development of methods for noninvasive detection of early-stage tumors has remained a challenge. We have developed an approach called targeted error correction se...
EGAS00001002577 | EGA
Genomicsena-DATASET-JHU-SOM-01-09-2017-17:11:13:045-143 - samples
The dataset for Direct Detection of Early-Stage Cancers using Circulating Tumor DNA includes 602 bam files from next-generation sequencing on the Illumina HiSeq2500 or MiSeq. The samples analyzed include cancer cell lines as well as plasma and tissue specimens from healthy individuals and patients ...
EGAD00001003601 | EGA
Genomicsena-DATASET-JHU-29-06-2015-20:17:30:536-212 - samples
Clinical Implications of Genomic Alterations in the Tumour and Circulation of Pancreatic Cancer Patients
EGAD00001001421 | EGA
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