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Nucleotide Sequence Databases


Ictalurus punctatus (Catfish)
  • Database of Expressed Sequence Tags (dbEST): 3577040
  • Database of Genome Survey Sequences (dbGSS: 63402
  • GenBank Nucleotide: 405336
  • Sequence Read Archive: (SRA)
    1. RNAseq analysis of catfish gill in response to heat stress 3 ILLUMINA (Illumina HiSeq 2000) runs: 88.5M spots, 17.7G bases, 11Gb downloads Accession:SRX313501
    2. RNAseq of liver in response to heat 3 ILLUMINA (Illumina HiSeq 2000) runs: 90.7M spots, 18.1G bases, 11.2Gb downloads Accession:SRX313500
    3. Channel catfish Testis RNA-Seq 1 ILLUMINA (Illumina HiSeq 2000) run: 147.3M spots, 29.5G bases, 18.4Gb downloads Accession:SRX220256
    4. Transcriptomic Signatures of Attachment, NF-?B Suppression and IFN Stimulation in the Catfish Gill Following Columnaris Bacterial Infection 1 ILLUMINA (Illumina HiSeq 2000) run: 24.5M spots, 4.9G bases, 3.1Gb downloads Accession:SRX145401
    5. Transcriptomic Signatures of Attachment, NF-?B Suppression and IFN Stimulation in the Catfish Gill Following Columnaris Bacterial Infection 1 ILLUMINA (Illumina HiSeq 2000) run: 25.1M spots, 5.1G bases, 3.2Gb downloads Accession:SRX145398
    6. Transcriptomic Signatures of Attachment, NF-?B Suppression and IFN Stimulation in the Catfish Gill Following Columnaris Bacterial Infection 1 ILLUMINA (Illumina HiSeq 2000) run: 27.2M spots, 5.5G bases, 3.4Gb downloads Accession:SRX145397
    7. Transcriptomic Signatures of Attachment, NF-?B Suppression and IFN Stimulation in the Catfish Gill Following Columnaris Bacterial Infection 1 ILLUMINA (Illumina HiSeq 2000) run: 24.9M spots, 5G bases, 3.2Gb downloads Accession:SRX145402
    8. Catfish RNA-Seq using Illumina HiSeq 2000 1 ILLUMINA (Illumina HiSeq 2000) run: 24.5M spots, 5G bases, 3.1Gb downloads Accession:SRX100881
    9. RNA-Seq for gynogen catfish transcriptome using Hiseq 2000 1 ILLUMINA (Illumina HiSeq 2000) run: 133.3M spots, 26.7G bases, 17.3Gb downloads Accession:SRX113171
    10. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus 1 ILLUMINA (Illumina HiSeq 2000) run: 22.4M spots, 4.5G bases, 3Gb downloads Accession:SRX101980
    11. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus 1 ILLUMINA (Illumina HiSeq 2000) run: 27.1M spots, 5.5G bases, 3.7Gb downloads Accession:SRX101979
    12. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus 1 ILLUMINA (Illumina HiSeq 2000) run: 22.9M spots, 4.6G bases, 3.1Gb downloads Accession:SRX101978
    13. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus 1 ILLUMINA (Illumina HiSeq 2000) run: 26.4M spots, 5.3G bases, 3.6Gb downloads Accession:SRX101949
    14. BAC clones using 454 sequencing 1 LS454 (454 GS FLX) run: 200,901 spots, 109.6M bases, 237Mb downloads Accession:SRX099697
    15. Pooled BAC clones sequencing 1 ILLUMINA (Illumina Genome Analyzer II) run: 14.5M spots, 1.9G bases, 1.1Gb downloads Accession:SRX099696
    16. channel catfish RNAseq 1 ILLUMINA (Illumina Genome Analyzer II) run: 86.9M spots, 17.4G bases, 11.1Gb downloads Accession:SRX029323
    17. Channel catfish RNA-seq 1 ILLUMINA (Illumina Genome Analyzer II) run: 24.3M spots, 1.7G bases, 1.7Gb downloads Accession:SRX029322
    • Citations 
    1. Xu Z, Qin Q, Ge J, Pan J, Xu X. Bioinformatic identification and validation of conservative microRNAs in Ictalurus punctatus. Mol Biol Rep. 2012 Dec;39(12):10395-405. doi: 10.1007/s11033-012-1918-z. Epub 2012 Oct 9. PubMed PMID: 23053943.
    2. Li C, Zhang Y, Wang R, Lu J, Nandi S, Mohanty S, Terhune J, Liu Z, Peatman E. RNA-seq analysis of mucosal immune responses reveals signatures of intestinal barrier disruption and pathogen entry following Edwardsiella ictaluri infection in channel catfish, Ictalurus punctatus. Fish Shellfish Immunol. 2012 May;32(5):816-27. doi: 10.1016/j.fsi.2012.02.004. Epub 2012 Feb 17. PubMed PMID: 22366064.
    3. Chen F, Lee Y, Jiang Y, Wang S, Peatman E, Abernathy J, Liu H, Liu S, Kucuktas H, Ke C, Liu Z. Identification and characterization of full-length cDNAs in channel catfish (Ictalurus punctatus) and blue catfish (Ictalurus furcatus). PLoS One. 2010 Jul 12;5(7):e11546. doi: 10.1371/journal.pone.0011546. PubMed PMID: 20634964; PubMed Central PMCID: PMC2902525.
    4. Wang S, Peatman E, Abernathy J, Waldbieser G, Lindquist E, Richardson P, Lucas S, Wang M, Li P, Thimmapuram J, Liu L, Vullaganti D, Kucuktas H, Murdock C, Small BC, Wilson M, Liu H, Jiang Y, Lee Y, Chen F, Lu J, Wang W, Xu P, Somridhivej B, Baoprasertkul P, Quilang J, Sha Z, Bao B, Wang Y, Wang Q, Takano T, Nandi S, Liu S, Wong L, Kaltenboeck L, Quiniou S, Bengten E, Miller N, Trant J, Rokhsar D, Liu Z; Catfish Genome Consortium. Assembly of 500,000 inter-specific catfish expressed sequence tags and large scale gene-associated marker development for whole genome association studies. Genome Biol. 2010 Jan 22;11(1):R8. doi: 10.1186/gb-2010-11-1-r8. PubMed PMID: 20096101; PubMed Central PMCID: PMC2847720.
    5. Kocabas AM, Li P, Cao D, Karsi A, He C, Patterson A, Ju Z, Dunham RA, Liu Z. Expression profile of the channel catfish spleen: analysis of genes involved in immune functions. Mar Biotechnol (NY). 2002 Dec;4(6):526-36. PubMed PMID: 14961227.
    6. Karsi A, Cao D, Li P, Patterson A, Kocabas A, Feng J, Ju Z, Mickett KD, Liu Z. Transcriptome analysis of channel catfish (Ictalurus punctatus): initial analysis of gene expression and microsatellite-containing cDNAs in the skin. Gene. 2002 Feb 20;285(1-2):157-68. PubMed PMID: 12039042.
    7. Cao D, Kocabas A, Ju Z, Karsi A, Li P, Patterson A, Liu Z. Transcriptome of channel catfish (Ictalurus punctatus): initial analysis of genes and expression profiles of the head kidney. Anim Genet. 2001 Aug;32(4):169-88. PubMed PMID: 11531695.
    8. Ju Z, Karsi A, Kocabas A, Patterson A, Li P, Cao D, Dunham R, Liu Z. Transcriptome analysis of channel catfish (Ictalurus punctatus): genes and expression profile from the brain. Gene. 2000 Dec 31;261(2):373-82. PubMed PMID: 11167026.

    Databases: Catfish Genome Database - cBARBEL


    Dicentrarchus labrax (European sea bass)
  • Database of Expressed Sequence Tags (dbEST): 86081
  • Database of Genome Survey Sequences (dbGSS: 102806
  • GenBank Nucleotide: 1852
  • Sequence Read Archive: (SRA): 268043
    SRA accession number: SRP010836: RNA seq were performed using 454GSFLX sequnecing technology in two different tissues; gut and head-kidney. For each tissue one control sample (where a sample presents a pool of 4-5 individuals) and one sample after oral vaccine against V. anguillarum were submitted to 454 next generation sequencing. Synthesis of first strand cDNA was performed using oligo nucleotide primer 5’- TTTTTTCTTGTTTTCTTTTCTTV-3’ and cDNA library protocol of GSFLX454 was adapted accordingly
    • Citations 
    1. Sarropoulou E, Galindo-Villegas J, García-Alcázar A, Kasapidis P, Mulero V. Characterization of European sea bass transcripts by RNA SEQ after oral vaccine against V. anguillarum. Mar Biotechnol (NY). 2012 Oct;14(5):634-42. doi:10.1007/s10126-012-9466-z. Epub 2012 Jul 13. PubMed PMID: 22790793.
    2. Sarropoulou E, Sepulcre P, Poisa-Beiro L, Mulero V, Meseguer J, Figueras A, Novoa B, Terzoglou V, Reinhardt R, Magoulas A, Kotoulas G. Profiling of infection specific mRNA transcripts of the European seabass Dicentrarchus labrax. BMC Genomics. 2009 Apr 10;10:157. doi: 10.1186/1471-2164-10-157. PubMed PMID: 19361338; PubMed Central PMCID: PMC2674461.

    Databases: Dicentrarchus labrax transcriptomic database


    Gadus morhua (Atlantic halibut)
  • Database of Expressed Sequence Tags (dbEST): 257453
  • Database of Genome Survey Sequences (dbGSS: 0
  • GenBank Nucleotide: 53879
  • Sequence Read Archive: (SRA): 24
    • Citations 
    1. Star B, Nederbragt AJ, Jentoft S, Grimholt U, Malmstrøm M, Gregers TF, Rounge TB, Paulsen J, Solbakken MH, Sharma A, Wetten OF, Lanzén A, Winer R, Knight J, Vogel JH, Aken B, Andersen O, Lagesen K, Tooming-Klunderud A, Edvardsen RB, Tina KG, Espelund M, Nepal C, Previti C, Karlsen BO, Moum T, Skage M, Berg PR, Gjøen T, Kuhl H, Thorsen J, Malde K, Reinhardt R, Du L, Johansen SD, Searle S, Lien S, Nilsen F, Jonassen I, Omholt SW, Stenseth NC, Jakobsen KS. The genome sequence of Atlantic cod reveals a unique immune system.(2011). Nature Aug 10;477(7363):207-10. doi: 10.1038/nature10342.

    Databases: Gadus morhua in Ensembl


    Sparus aurata (Gilthead sea bream)
  • Database of Expressed Sequence Tags (dbEST): 114151
  • Database of Genome Survey Sequences (dbGSS): 92468
  • GenBank Nucleotide: 2477
  • Sequence Read Archive (SRA) : 11(all Roche-454 Titanium)
    ERR126118, ERR126117, ERR126116, ERR126115, ERR126114, ERR044008, ERR044009, ERR044011, ERR044012, ERR044013, ERR044014, ERR044010, ERR043990, ERR043992, ERR043993, ERR043995, ERR043996, ERR043997, ERR044004, ERR044005, ERR044007, ERR043991, ERR043994, ERR043998, ERR044006, ERR043999, ERR044000, ERR044001, ERR044003, ERR044002, ERR043989, ERR043987, ERR043988, SRR278741
  • SeaBream NGS data: Shotgun Sequencing of BAC clones and Transcriptome sequencing with GSFLX [HCMR, unpublished data]
    • Citations 
    1. Florbela A. Vieira, M.A.S. Thorne, K. Stueber, M. Darias, R. Reinhardt, M.S. Clark, E. Gisbert, D.M. Power. Comparative analysis of a teleost skeleton transcriptome provides insight into its regulation (2013). General and Comparative Endocrinology 191 (2013) 45–58
    2. Calduch-Giner, J.A., Bermejo-Nogales, A., Benedito-Palos, L., Estensoro, I., Ballester-Lozano, G., Sitjà-Bobadilla, A., Pérez-Sánchez, J. Deep sequencing for de novo construction of a marine fish (Sparus aurata) transcriptome database with a large coverage of protein-coding transcripts (2013) BMC Genomics, 14 (1), art. no. 178.
    3. Teles, M., Boltaña, S., Reyes-López, F., Santos, M.A., Mackenzie, S., Tort, L. Effects of Chronic Cortisol Administration on Global Expression of GR and the Liver Transcriptome in Sparus aurata (2013) Marine Biotechnology, 15 (1), pp. 104-114.
    4. Yúfera, M., Halm, S., Beltran, S., Fusté, B., Planas, J.V., Martínez-Rodríguez, G. Transcriptomic Characterization of the Larval Stage in Gilthead Seabream (Sparus aurata) by 454 Pyrosequencing (2012) Marine Biotechnology, 14 (4), pp. 423-435.
    5. 5. Garcia de la serrana, D., Estévez, A., Andree, K., Johnston, I.A. Fast skeletal muscle transcriptome of the Gilthead sea bream (Sparus aurata) determined by next generation sequencing (2012) BMC Genomics, 13 (1), art. no. 181,.

    Databases: Sparus aurata transcriptomic database


    Acipenser naccarii (Sturgeon)
  • Database of Expressed Sequence Tags (dbEST): 13841
  • Database of Genome Survey Sequences (dbGSS): 19
  • GenBank Nucleotide: 4127
  • Sequence Read Archive (SRA): 13 (12 Population Genomics Iluumina and 1 GS454): Those sequences are not included as they represent mainly genomic DNA.
  • From Sturgeon database downloaded contigs (Sequences belong to eight libraries produced in four different labs):
    1. Libraries AtSk and AtSp: Parco Tecnologico Padano Livestock I Unit, Lodi, Italy (manuscript in preparation)
    2. Library IpSk and IpSp: Auburn University, Auburn, USA (Gene 285 (1-2): 157-168 2002; Mar. Biotechnol. 4 (6): 526-536 2002 and unpublished)
    3. Libraries SsSk and SsSp: Norwegian School of Veterinary Science, Oslo, Norway (unpublished)
    4. Libraries TrSk and TrSp: MRC Human Genome Mapping Project Resource Centre, Cambridge, UK (Genome Res. 13 (12): 2747-2753 2003) Library names reflect the species name and tissue-of-origin.
    • Citations 
    1. 1. Vidotto, M., Grapputo, A., Boscari, E., Barbisan, F., Coppe, A., Grandi, G., Kumar, A., Congiu, L. Transcriptome sequencing and de novo annotation of the critically endangered Adriatic sturgeon (2013) BMC Genomics, 14 (1), art. no. 407.
    2. 2. Hale, M.C., McCormick, C.R., Jackson, J.R., DeWoody, J.A. Next-generation pyrosequencing of gonad transcriptomes in the polyploid lake sturgeon (Acipenser fulvescens): The relative merits of normalization and rarefaction in gene discovery (2009) BMC Genomics, 10, art. no. 203

    Databases: Sturgeon DB, Anaccariibase


    Protein Sequence Databases


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