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Protocols

SAGEmap specifications

Information


Unique identifier OMICS_26829
Name SAGEmap
Restrictions to use None
Community driven No
Data access File download
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline Alex Lash

Publication for SAGEmap

SAGEmap citations

 (4)
library_books

Accelerated Recruitment of New Brain Development Genes into the Human Genome

2011
PLoS Biol
PMCID: 3196496
PMID: 22028629
DOI: 10.1371/journal.pbio.1001179

[…] atively longer mappable region, duplicated genes with too short a mappable region (<30 bp) were excluded (124 or 0.6% of all genes).In the case of SAGE data, we downloaded the tag annotation from the SAGEmap database , “SAGEmap_Mm_NlaIII_17_best.gz”, and mapped tags to Ensembl genes with unique NCBI Entrez gene symbols. We checked these mappings by searching tag sequences against Ensembl transcrip […]

call_split

Poly A Transcripts Expressed in HeLa Cells

2008
PLoS One
PMCID: 2481391
PMID: 18665230
DOI: 10.1371/journal.pone.0002803
call_split See protocol

[…] sapiens/mRNA_Prot/), mRNA (http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/), EST (ftp://ftp.ncbi.nih.gov/repository/dbEST/). Two types of SAGE tag reference databases were used, including the SAGEmap full database that contains annotated SAGE tags based on the known human transcript sequences (http://www.ncbi.nlm.nih.gov/projects/SAGE/) and the GEO SAGE database that contains experimentall […]

library_books

iCartiGD: the Integrated Cartilage Gene Database

2007
BMC Genet
PMCID: 1808061
PMID: 17316453
DOI: 10.1186/1471-2156-8-4

[…] d to create iCartiGD. These databases include several of the National Center for Biotechnology Information (NCBI) databases such as Genbank, Entrez Gene, UniGene, MapViewer, dbEST, dbSNP, HomoloGene, SAGEmap, PubMed, Gene Expression Omnibus (GEO), RefSeq and OMIM. Other resources and databases used are Ensembl, UniProt, the UCSC genome browser, the Protein Data Bank (PDB), InterPro, Sage Genie, Ha […]

library_books

Comparative genomic analysis of prion genes

2007
BMC Genomics
PMCID: 1781936
PMID: 17199895
DOI: 10.1186/1471-2164-8-1

[…] LAST queries, we searched the available tetrapode genomes in Ensembl.The Human_EST, Mouse_EST and EST_others EST libraries in NCBI were searched using available SPRNs as queries and BLASTN. The human SAGEmap dataset included 327 libraries with 1296360 unique tags and 19300584 total tag counts, and the mouse SAGEmap dataset included 213 libraries with 1552119 unique tags and 16549657 total tag coun […]

Citations

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SAGEmap institution(s)
National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD, USA; National Cancer Institute, National Institutes of Health, Bethesda, MD, USA; Department of Pathology, Duke University Medical Center, Durham, NC, USA

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