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Protocols

GRC specifications

Information


Unique identifier OMICS_27151
Name GRC
Alternative name Genome Reference Consortium
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Taxon


  • Primates
    • Homo sapiens
  • Rodents
    • Mus musculus
  • Vertebrates
    • Danio rerio
    • Gallus gallus

Documentation


GRC citations

 (154)
library_books

Identification of usual interstitial pneumonia pattern using RNA Seq and machine learning: challenges and solutions

2018
BMC Genomics
PMCID: 5954282
PMID: 29764379
DOI: 10.1186/s12864-018-4467-6

[…] re sequenced on NextSeq 500 instruments (2 × 75 bp paired-end reads) using the High Output kit (Illumina, San Diego, CA). Raw sequencing (FASTQ) files were aligned to the Human Reference assembly 37 (Genome Reference Consortium) using the STAR RNA-seq aligner software []. Raw read counts for 63,677 Ensembl-annotated gene-level features were summarized using HTSeq []. Data quality metrics were gene […]

library_books

Reconstruction of a replication competent ancestral murine endogenous retrovirus L

2018
Retrovirology
PMCID: 5930517
PMID: 29716624
DOI: 10.1186/s12977-018-0416-3

[…] plication-competent MuERV-L sequence we first catalogued the diversity of MuERV-L related sequences in the mouse genome. Currently, there are two available complete mouse genome assemblies: the Mouse Genome Reference Consortium build 38 (GRCm38 also known as mm10) corresponding to the C57BL/6J strain [], and the whole genome shotgun (WGS) assembly (Celera) that corresponds to a mixture of 5 strain […]

library_books

Mitochondrial nicotinamide adenine dinucleotide reduced (NADH) oxidation links the tricarboxylic acid (TCA) cycle with methionine metabolism and nuclear DNA methylation

2018
PLoS Biol
PMCID: 5927466
PMID: 29668680
DOI: 10.1371/journal.pbio.2005707

[…] filtering (phred score > 20), we obtained approximately 100 million 126-nt paired-end reads per individual sample (7–8 flow cell lanes/sample), which were aligned to the hg19 human reference genome (Genome Reference Consortium GRCh37 from February 2009) [] with TopHat-Fusion function []. Composite RPKM counts within genomic coordinates of 20,304 nonhaplotype HGNC-annotated genes were used to calc […]

call_split

A Reappraisal on the Potential Ability of Human Neutrophils to Express and Produce IL 17 Family Members In Vitro: Failure to Reproducibly Detect It

2018
Front Immunol
PMCID: 5913333
PMID: 29719541
DOI: 10.3389/fimmu.2018.00795
call_split See protocol

[…] dge, UK) using TruSeq DNA Library Prep Kit (Illumina). After sequencing, reads were quality-filtered according to the Illumina pipeline. Single end (51 bp) reads were then mapped to the human genome (Genome Reference Consortium GRCh37, Feb/2009) using BOWTIE v1.0.0 (). Only reads with no more than two mismatches (when compared to the reference genome) were converted to tag directories using HOMER’ […]

library_books

Adar3 Is Involved in Learning and Memory in Mice

2018
Front Neurosci
PMCID: 5914295
PMID: 29719497
DOI: 10.3389/fnins.2018.00243

[…] 1 and Data Sheet 2. Briefly, trimmed paired-end RNA-seq reads were aligned with bowtie v1.1.0 (http://bowtie-bio.sourceforge.net/index.shtml) (Langmead et al., ) to the mouse reference genome (mm10, Genome Reference Consortium GRCm38). A-to-G mismatches were called with Samtools v1.12 (http://www.htslib.org/doc/samtools.html) (Li et al., ). The positions of common SNPs from dbSNPs138 were removed […]

library_books

Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex pro inflammatory, pro repair, angiogenic activation pattern, likely associated with macrophage iron accumulation

2018
PLoS One
PMCID: 5896901
PMID: 29649237
DOI: 10.1371/journal.pone.0194803

[…] ed average score = 33, ribosomal RNA content < 2%) (Cofactor Genomics, Saint Louis, MO, USA).Raw read counts were mapped on UCSC mRNA transcript human database based on the GRCh37/hg19 version of the Genome Reference Consortium consensus representation of the human genome using the NovoAlign tool. Raw counts per transcript were then aggregated onto unique UCSC gene symbols (26,605 unique gene symb […]

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