text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

characteristic: NCBI submission model

text: Drosophila melanogaster

characteristic: organism

text: Cl.8 small RNAs BioRep-2 TechRep-1


status: PUBLIC

characteristic: External Id

text: Gingeras, Cold Spring Harbor Labs

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission package

characteristic: SRA accession

tag: attribute

characteristic: biorep

characteristic: cell line

text: Drosophila melanogaster

characteristic: techrep

text: Cl.8 small RNAs BioRep-2 TechRep-2

characteristic: title


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Cl.8 small RNAs BioRep-2 TechRep-3


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Cl.8 small RNAs BioRep-2 TechRep-4


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167 small RNAs BioRep-1 TechRep-1


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167 small RNAs BioRep-1 TechRep-2


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167 small RNAs BioRep-2 TechRep-1


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167 small RNAs BioRep-2 TechRep-2


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-1


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-2


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-3


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-4


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-5


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-6


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-7


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: Kc167_PolyA+ BioRep-1 TechRep-8


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-1 TechRep-1


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-1 TechRep-2


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-1 TechRep-3


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-1 TechRep-4


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-2 TechRep-1


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-2 TechRep-2


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-2 TechRep-3


text: Gingeras, Cold Spring Harbor Labs

text: live

text: Generic

text: Drosophila melanogaster

text: S2-DRSC small RNAs BioRep-2 TechRep-4


text: INRA

text: live

text: Generic

text: Plasmodium falciparum

text: Generic sample from Plasmodium falciparum


text: UT Austin

text: live

text: Generic

text: Strain REL607, the Ara positive clone used to found half of the populations in the long-term E. coli evolution experiment. Note that it differs by two point mutations from strain REL606, which was used to found the Ara-1 population.

characteristic: description

text: Escherichia coli B str. REL606

characteristic: strain

text: Generic sample from Escherichia coli B str. REL606


text: UT Austin

text: live

text: Generic

text: Strain REL1164A, the A clone isolated at 2,000 generations from the Ara-1 population of the long-term E. coli evolution experiment. Genomic DNA was isolated from several milliliters of overnight LB culture using a Qiagen Genomic-tip 100/G kit. Paired-end sequencing was performed using an Illumina 1G Genome Analyzer by Macrogen, Inc.

text: Escherichia coli B str. REL606


text: UT Austin

text: live

text: Generic

text: Strain REL2179A, the A clone isolated at 5,000 generations from the Ara-1 population of the long-term E. coli evolution experiment. Genomic DNA was isolated from several milliliters of overnight LB culture using a Qiagen Genomic-tip 100/G kit. Paired-end sequencing was performed using an Illumina 1G Genome Analyzer by Macrogen, Inc.

text: Escherichia coli B str. REL606


text: UT Austin

text: live

text: Generic

text: Strain REL4536A, the A clone isolated at 10,000 generations from the Ara-1 population of the long-term E. coli evolution experiment. Genomic DNA was isolated from several milliliters of overnight LB culture using a Qiagen Genomic-tip 100/G kit. Paired-end sequencing was performed using an Illumina 1G Genome Analyzer by Macrogen, Inc.

text: Escherichia coli B str. REL606


text: UT Austin

text: live

text: Generic

text: Strain REL7177A, the A clone isolated at 15,000 generations from the Ara-1 population of the long-term E. coli evolution experiment. Genomic DNA was isolated from several milliliters of overnight LB culture using a Qiagen Genomic-tip 100/G kit. Paired-end sequencing was performed using an Illumina 1G Genome Analyzer by Macrogen, Inc.

text: Escherichia coli B str. REL606


text: UT Austin

text: live

text: Generic

text: Strain REL8593A, the A clone isolated at 20,000 generations from the Ara-1 population of the long-term E. coli evolution experiment. Genomic DNA was isolated from several milliliters of overnight LB culture using a Qiagen Genomic-tip 100/G kit. Paired-end sequencing was performed using an Illumina 1G Genome Analyzer by Macrogen, Inc.

text: Escherichia coli B str. REL606


text: UT Austin

text: live

text: Generic

text: Strain REL10938, the A clone isolated at 40,000 generations from the Ara-1 population of the long-term E. coli evolution experiment. Genomic DNA was isolated from several milliliters of overnight LB culture using a Qiagen Genomic-tip 100/G kit. Paired-end sequencing was performed using an Illumina 1G Genome Analyzer by Macrogen, Inc.

text: Escherichia coli B str. REL606


text: Institute for Genomics and Systems Biology, University of Chicago

text: live

text: Generic

characteristic: development stage

text: Drosophila melanogaster

text: E12-16_combined_RNAseq_1, 2


text: live

text: Generic

characteristic: NCBI submission model

text: AdultMale

text: Drosophila melanogaster

text: AdultMale

text: AdultMale_combined_RNAseq_1, 2


text: live

text: Generic

text: AdultFemale

text: Drosophila melanogaster

characteristic: organism

text: AdultFemale

text: AdultFemale_combined_RNAseq_1, 2


characteristic: External Id

text: live

text: Generic

text: Drosophila melanogaster


characteristic: INSDC center name

text: live

text: Generic

text: Drosophila melanogaster

text: E20-24_combined_RNAseq_1, 2


characteristic: INSDC first public

text: live

text: Generic

text: Pupae

text: Drosophila melanogaster

text: Pupae


characteristic: INSDC last update

text: live

text: Generic

text: Drosophila melanogaster

text: L2_combined_RNAseq_1, 2


Clostridium botulinum 4411 Sample

text: J. Craig Venter Institute

characteristic: INSDC secondary accession

text: live

text: Generic

text: Whole genome sequencing of C. botulinum 4411 using 454 technology; whole genome shotgun library

text: Clostridium botulinum 4411

text: Generic sample from Clostridium botulinum 4411


text: Naval Medical Research Center, Biological Defense Research Directorate

text: live

characteristic: INSDC status

text: Generic

characteristic: culture-collection

text: Yersinia aldovae ATCC 35236

text: ATCC 35236

text: Generic sample from Yersinia aldovae ATCC 35236

text: type strain of Yersinia aldovae

characteristic: type material


text: Scripps Translational Science Institute

text: live

text: Generic

characteristic: NCBI submission package

characteristic: SRA accession

text: NIGMS Human Genetic Cell Repository sample NA15510

text: Homo sapiens

text: Generic sample from Homo sapiens


text: University of Calgary - Department of Biological Sciences

text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. 40

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. mar

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. nat

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. ps6

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. p

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. rox

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. t

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from stems of Opium poppy var. ver

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

text: ESTs derived from cell culture of Opium poppy var. mar

text: Papaver somniferum

text: Generic sample from Papaver somniferum


text: live

text: Generic

characteristic: antibody

characteristic: antibody catalog number

characteristic: antibody lot number

text: Abcam

characteristic: antibody manufacturer

text: Drosophila melanogaster

characteristic: time point

text: Embryos

characteristic: tissue


text: live

text: Generic

characteristic: NCBI submission model

text: Drosophila melanogaster

characteristic: organism

text: input

characteristic: reference

text: Embryos

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: live

text: Generic

text: Abcam

text: Drosophila melanogaster


characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: Drosophila melanogaster

text: input


text: live

text: Generic

characteristic: NCBI submission package

characteristic: SRA accession

text: Abcam

text: Drosophila melanogaster

text: Pupae

text: Pupae


text: live

text: Generic

text: Drosophila melanogaster

text: input

text: Pupae

text: Pupae


text: live

text: Generic

characteristic: antibody

characteristic: antibody catalog number

text: Abcam

text: Drosophila melanogaster

text: AdultMale

text: AdultMale


text: live

text: Generic

text: Drosophila melanogaster

text: input

text: AdultMale

text: AdultMale


text: live

text: Generic

characteristic: antibody lot number

text: Abcam

characteristic: antibody manufacturer

text: Drosophila melanogaster

text: AdultFemale

text: AdultFemale


text: live

text: Generic

text: Drosophila melanogaster

text: input

text: AdultFemale

text: AdultFemale

characteristic: tissue


text: live

text: Generic

characteristic: NCBI submission model

text: CBP

text: Dr. Mattias Mannervik in Stockholm University

characteristic: antibody provider

text: Drosophila melanogaster

text: AdultFemale

text: AdultFemale

characteristic: tissue/development stage


text: Institute for Genomics and Systems Biology, University of Chicago

text: live

text: Generic

text: Drosophila melanogaster

characteristic: organism

text: INPUT

characteristic: reference

text: AdultFemale

text: AdultFemale

characteristic: title


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Generic

text: CBP

text: Drosophila melanogaster

text: AdultMale

text: AdultMale


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: Drosophila melanogaster

text: INPUT

text: AdultMale

text: AdultMale


text: live

text: Generic

characteristic: NCBI submission package

characteristic: SRA accession

text: CBP

characteristic: antibody

text: Drosophila melanogaster


text: live

text: Generic

text: Drosophila melanogaster

text: INPUT


text: live

text: Generic

text: CBP

text: Drosophila melanogaster

text: Pupae

text: Pupae


text: live

text: Generic

text: Drosophila melanogaster

text: INPUT

text: Pupae

text: Pupae


text: live

text: Generic

text: PolII

characteristic: antibody catalog number

characteristic: antibody lot number

text: Covance

characteristic: antibody manufacturer

characteristic: development point

text: Drosophila melanogaster


text: live

text: Generic

characteristic: NCBI submission model

text: Abcam

text: AdultMale

text: Drosophila melanogaster

text: AdultMale


text: live

text: Generic

text: Abcam

text: Drosophila melanogaster

characteristic: organism


text: live

text: Generic

text: CBP

characteristic: antibody provider

text: Drosophila melanogaster


text: live

text: Generic

text: PolII

text: Covance

text: Pupae

text: Drosophila melanogaster

text: Pupae

characteristic: title


characteristic: External Id

text: live

text: Generic

text: Drosophila melanogaster

text: input

characteristic: reference


characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Generic

text: Pupae

text: Drosophila melanogaster

text: input

text: Pupae


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: Upstate

text: AdultMale

text: Drosophila melanogaster

text: AdultMale


text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission package

text: Upstate

text: Pupae

text: Drosophila melanogaster

text: Pupae


text: live

text: Generic

characteristic: SRA accession

characteristic: antibody

text: Upstate

text: Drosophila melanogaster


text: live

text: Generic

characteristic: antibody catalog number

characteristic: antibody lot number

text: Abcam

text: Pupae

text: Drosophila melanogaster

text: Pupae


text: live

text: Generic

text: Abcam

characteristic: antibody manufacturer

text: AdultFemale

characteristic: development point

text: Drosophila melanogaster

text: AdultFemale


text: live

text: Generic

characteristic: NCBI submission model

text: Abcam

characteristic: development stage

text: Drosophila melanogaster

characteristic: organism


characteristic: External Id

text: live

text: Generic

text: PolII

text: Covance

text: Drosophila melanogaster

characteristic: title


characteristic: INSDC center name

text: live

text: Generic

text: Drosophila melanogaster

text: INPUT

characteristic: reference


characteristic: INSDC first public

characteristic: INSDC last update

text: live

text: Generic

text: CBP

characteristic: antibody provider

text: Drosophila melanogaster


male

text: Center for Genomics and Bioinformatics, Indiana University

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission package

text: neonate, juvenile, and adult male garter snakes

characteristic: description

text: Thamnophis elegans

text: Generic sample from Thamnophis elegans


female

text: live

text: Generic

characteristic: SRA accession

text: neonate, juvenile, and adult female garter snakes

text: Thamnophis elegans

text: Generic sample from Thamnophis elegans


text: Jeffrey I. Gordon, Center for Genome Sciences, Washington University School of Medicine

text: live

text: Generic

text: In vitro

characteristic: defined microbiota

text: Initial plated population

characteristic: environment

text: In vitro

characteristic: mouse genotype

text: Bacteroides thetaiotaomicron

text: INSeq DNA

text: Bacteroides thetaiotaomicron-Input


text: Pennsylvania State University

text: live

text: Generic

characteristic: NCBI submission model

text: G1E ER4

characteristic: cell line

characteristic: chip antibody

text: Mus musculus

text: Chromatin IP against GATA1


characteristic: External Id

text: Pennsylvania State University

text: live

text: Generic

text: G1E ER4

text: Mus musculus

characteristic: organism

text: Chromatin input as control

characteristic: title


text: Hudson Alpha Institute of Biotechnology

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Generic

text: Human pan T cell receptor repertoire a/b cDNA sequences covering CDR3 regions

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Hudson Alpha Institute of Biotechnology

characteristic: INSDC last update

text: live

text: Generic

text: Human pan T cell receptor repertoire a/b cDNA sequences covering CDR3 regions sample 2

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Hudson Alpha Institute of Biotechnology

characteristic: INSDC secondary accession

text: live

text: Generic

text: Human pan T cell receptor a/b repertoire sample 3

text: Homo sapiens

text: Generic sample from Homo sapiens


hTr

text: Hudson Alpha Institute of Biotechnology

text: live

characteristic: INSDC status

text: Generic

text: human regular T cell receptor a/b repertoire

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Hudson Alpha Institute of Biotechnology

text: live

text: Generic

characteristic: NCBI submission package

text: human helper T cell 1 (Th1) receptor a/b repertoire

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Hudson Alpha Institute of Biotechnology

text: live

text: Generic

text: human helper T cell 2 (Th2) receptor a/b repertoire

characteristic: description

text: Homo sapiens

text: Generic sample from Homo sapiens


hTc

text: Hudson Alpha Institute of Biotechnology

text: live

text: Generic

characteristic: SRA accession

text: human Cytotoxic T cell (Tc) receptor a/b repertoire

text: Homo sapiens

text: Generic sample from Homo sapiens


hTn

text: Hudson Alpha Institute of Biotechnology

text: live

text: Generic

text: human naive T cell (Tn) receptor a/b receptor

text: Homo sapiens

text: Generic sample from Homo sapiens


hTa

text: Hudson Alpha Institute of Biotechnology

text: live

text: Generic

text: human activated T cell (Ta) receptor a/b repertoire

text: Homo sapiens

text: Generic sample from Homo sapiens


hTm

text: Hudson Alpha Institute of Biotechnology

text: live

text: Generic

text: human memory T cell (Tm) receptor a/b repertoire

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Naval Medical Research Center, Biological Defense Research Directorate

text: live

text: Generic

characteristic: culture-collection

text: Yersinia bercovieri ATCC 43970

text: ATCC 43970

characteristic: strain

text: Generic sample from Yersinia bercovieri

text: type strain of Yersinia bercovieri

characteristic: type material


pre-bleed

text: University of Calgary

text: live

text: Generic

characteristic: NCBI submission model

text: Pre-inoculation circulating nucleic acids of 24 elk in a Chronic Wasting Disease study.

text: Cervus elaphus

text: Generic sample from Cervus elaphus


text: live

text: Generic

text: Yersinia frederiksenii ATCC 33641

text: ATCC 33641

text: Generic sample from Yersinia frederiksenii ATCC 33641

text: type strain of Yersinia frederiksenii


text: live

text: Generic

text: Isolated from human urine. Reference Validation list no. 6. Int. J. Syst. Bacteriol. 31: 215-218, 1981 and Brenner D.J., et al. 1980. Yersinia intermedia: a new species of Enterobacteriaceae composed of rhamnose-positive, melibiose-positive, raffinose-positive strains (formerly called Yersinia enterocolitica or Yersinia enterocolitica-like). Curr. Microbiol. 4: 207-212.

text: Yersinia intermedia ATCC 29909

text: ATCC 29909

text: Generic sample from Yersinia intermedia ATCC 29909

text: type strain of Yersinia intermedia


controls

text: University of Calgary

text: live

text: Generic

text: Circulating nucleic acids from 2 control animals (#6 and #31) at various timepoints during a 25 month chronic wasting disease study.

text: Cervus elaphus

text: Generic sample from Cervus elaphus


inoculated

text: University of Calgary

text: live

text: Generic

text: Circulating nucleic acids from 10 CWD-infected animals (39, 19, 69, 33, 27, 35y, 37, 18, 28 and 8) taken at intervals during a 25 month infection study.

text: Cervus elaphus

text: Generic sample from Cervus elaphus


text: live

text: Generic

text: Yersinia kristensenii ATCC 33638

text: ATCC 33638

text: Generic sample from Yersinia kristensenii

text: type strain of Yersinia kristensenii


text: live

text: Generic

text: Yersinia mollaretii ATCC 43969

text: ATCC 43969

text: Generic sample from Yersinia mollaretii

text: type strain of Yersinia mollaretii


text: live

text: Generic

text: Yersinia ruckeri ATCC 29473

text: ATCC 29473

text: Generic sample from Yersinia ruckeri

text: type strain of Yersinia ruckeri


text: live

text: Generic

text: Yersinia rohdei ATCC 43380

text: ATCC 43380

text: Generic sample from Yersinia rohdei

text: type strain of Yersinia rohdei


text: BGI

text: live

text: Generic

text: Whole genome re-sequencing analysis of Zheng58, Mo17, 5003, 478, 178, and Chang7-2,six elite maize lines. This effort will illustrate the genomic changes that have occurred in the large and complex genome coincident with its genetic improvement

text: Zea mays

text: Zea mays


text: BGI

text: live

text: Generic

characteristic: maize line

text: Zea mays

text: Zea mays


text: Craig Mello, Program in Molecular Medicine, University of Massachusetts Medical School

text: live

text: Generic

text: Caenorhabditis elegans

text: oocytes

characteristic: sample type

text: oocytes

text: rom fem-1(hc17)


characteristic: External Id

text: live

text: Generic

text: Caenorhabditis elegans

text: WAGO-1 IP from Young adult worms

text: WAGO-1 IP from Young adult worms


text: live

text: Generic

text: Caenorhabditis elegans

characteristic: organism

text: Young adult worms

text: Young adult worms


text: live

text: Generic

text: Caenorhabditis elegans

text: gravid adult worms

text: gravid adult worms

characteristic: title


characteristic: INSDC center name

text: live

text: Generic

text: Caenorhabditis elegans

text: adult worms

text: adult worms

text: rrf-1(neC1) ego-1(om97)


characteristic: INSDC first public

text: live

text: Generic

text: Caenorhabditis elegans

text: adult worms

text: adult worms


characteristic: INSDC last update

text: live

text: Generic

text: Caenorhabditis elegans

text: CSR-1 immunopercipitate

text: CSR-1 immunopercipitate from wild type, N2

text: small RNAs that co-immunopercepitate with the argonaute CSR-1


characteristic: INSDC secondary accession

text: live

text: Generic

text: Caenorhabditis elegans

text: wild type adult animals

text: Wild type, N2

text: small RNAs from wild type worms input control for the IP experiment


text: live

characteristic: INSDC status

text: Generic

text: Caenorhabditis elegans

text: ego-1(om97) adult animals

text: small RNAs from ego-1 mutant animals


text: INRA

text: live

text: Generic

characteristic: NCBI submission package

text: Plasmodium falciparum

text: Generic sample from Plasmodium falciparum


text: University of Hawaii

text: live

text: Generic

text: Approximately 50 g of leaf tissue harvested from seedlings of Zea mays subsp. mays cv. B73, from which approximately 3 ug of immunoprecipitated DNA was obtained. This work was performed in the Jiming Jiang Laboratory at the University of Wisconsin.

characteristic: description

text: Zea mays

text: Generic sample from Zea mays


Pinus ponderosa chloroplast genome

text: Oregon St Univ - Center for Genome Research & Biocomputing

text: live

text: Generic

characteristic: SRA accession

text: Source was genomic DNA of Pinus ponderosa, accession POND06. The genomic DNA was subjected to Multiple Displacement Amplification with chloroplast-specific oligonucleotides (R. Cronn, unpublished).

text: Pinus ponderosa

text: Generic sample from Pinus ponderosa


text: Hubrecht Institute

text: live

text: Generic

text: adult

characteristic: developmental stage

text: cde-1 mutant

characteristic: genome/variation

text: Caenorhabditis elegans

text: whole animal

characteristic: tissue


text: Hubrecht Institute

text: live

text: Generic

characteristic: NCBI submission model

text: adult

text: cde-1 mutant

characteristic: ip antibody

text: Caenorhabditis elegans

text: whole animal


text: Hubrecht Institute

text: live

text: Generic

text: aged adult

text: cde-1 mutant

text: Caenorhabditis elegans

text: CDE1 aged adults

text: whole animal


text: Hubrecht Institute

text: live

text: Generic

text: young adult

text: cde-1 mutant

text: Caenorhabditis elegans

text: CDE1 young adults

text: whole animal


text: Hubrecht Institute

text: live

text: Generic

text: adult

text: wild type

text: Caenorhabditis elegans

text: whole animal


text: Hubrecht Institute

text: live

text: Generic

text: adult

text: wild type

text: Caenorhabditis elegans

text: whole animal


text: Hubrecht Institute

text: live

text: Generic

text: aged adult

text: wild type

text: Caenorhabditis elegans

text: whole animal


text: Hubrecht Institute

text: live

text: Generic

text: young adult

text: wild type

text: Caenorhabditis elegans

text: whole animal


text: Gerstein, MB&B, Yale University

text: live

text: Generic

characteristic: antibody

characteristic: cell line

text: myelogenous leukaemia

characteristic: cell type

text: Homo sapiens

characteristic: passage

text: K562 cells


Saccharomyces kudriavzevii IFO1802

characteristic: External Id

text: University of Colorado School of Medicine

characteristic: INSDC center name

text: live

text: Generic

text: Only used to establish maximum error rate of reference-based assemblies. Otherwise, the Sanger-based assemblies of Cliften et al. 2003 with modifications of Hittinger et al. 2004 were used.

text: Saccharomyces kudriavzevii IFO 1802

characteristic: organism

text: Generic sample from Saccharomyces kudriavzevii IFO 1802

characteristic: title


Saccharomyces kudriavzevii IFO10990

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: Reads used for reference-based genome assembly

text: Saccharomyces kudriavzevii

text: Generic sample from Saccharomyces kudriavzevii


Saccharomyces kudriavzevii IFO10991

text: live

text: Generic

characteristic: NCBI submission package

characteristic: SRA accession

characteristic: description

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii IFO1803

text: live

text: Generic

characteristic: NCBI submission model

text: Saccharomyces kudriavzevii


text: CSIRO Plant Industry

text: live

text: Generic

text: Crude lysate of 12 day old, long day grown Arabidopsis thaliana seedlings digested with MNase. The 150bp fragments corresponding to the expected sizes of nucleosome cores were gel purified and used to prepare a library for Illumina GS sequencing.

text: Arabidopsis thaliana

text: Generic sample from Arabidopsis thaliana


text: Stanford

text: live

text: Generic

text: Homo sapiens

text: Generic sample from Homo sapiens


name: Saccharomyces cerevisiae/Saccharomyces kudriavzevii hybrid W27

text: live

text: Generic

text: Positive control for hybrid detection (Fig. S2; FM1043 was isolated from a single colony of W27); not assembled

text: Generic sample from Saccharomyces cerevisiae x Saccharomyces kudriavzevii


text: Sorek, Molecular Genetics, Weizmann Institute of Science

text: live

text: Generic

text: Glucose + Brock’s mineral medium

characteristic: growth condition

text: RACE

characteristic: library preparation

text: Saccharolobus solfataricus P2

text: 5' ends of cDNA, strand-sensitive

characteristic: sequenced molecule

text: Sulfolobus solfataricus P2

text: DSMZ 1617

characteristic: strain


text: live

text: Generic

text: Cellobiose + Brock’s mineral medium

text: RACE

text: Saccharolobus solfataricus P2

text: 5' ends of cDNA, strand-sensitive

text: Sulfolobus solfataricus P2

text: DSMZ 1617


text: live

text: Generic

text: Cellulose + Brock’s mineral medium

text: RACE

text: Saccharolobus solfataricus P2

text: 5' ends of cDNA, strand-sensitive

text: Sulfolobus solfataricus P2

text: DSMZ 1617


text: live

text: Generic

text: Glucose + Brock’s mineral medium

text: cDNA

text: Saccharolobus solfataricus P2

text: cDNA, strand-insensitive

text: Sulfolobus solfataricus P2

text: DSMZ 1617


text: live

text: Generic

text: Cellobiose + Brock’s mineral medium

text: cDNA

text: Saccharolobus solfataricus P2

text: cDNA, strand-insensitive

text: Sulfolobus solfataricus P2

text: DSMZ 1617


text: live

text: Generic

text: Cellulose + Brock’s mineral medium

text: cDNA

text: Saccharolobus solfataricus P2

text: cDNA, strand-insensitive

text: Sulfolobus solfataricus P2

text: DSMZ 1617


text: Pritchard, Human Genetics, University of Chicago

text: live

text: Generic

text: Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA19238

characteristic: biomaterial provider

characteristic: cell line

text: YRI

characteristic: hapmap

text: Homo sapiens

text: lymphoblastoid cell line

text: YRI NA19238 HapMap RNA Seq


characteristic: External Id

characteristic: INSDC center name

text: live

text: Generic

text: Coriell Cell Repositories http://ccr.coriell.org/Sections/Search/Search.aspx?PgId=165&q=NA19239

text: YRI

text: Homo sapiens

characteristic: organism

text: lymphoblastoid cell line

text: YRI NA19239 HapMap RNA Seq


Saccharomyces kudriavzevii ZP591

characteristic: INSDC first public

characteristic: INSDC last update

text: live

text: Generic

text: Reads used for reference-based genome assembly and de novo assembly (FM1009 was isolated from a single colony of ZP591)

text: Saccharomyces kudriavzevii

characteristic: title


Saccharomyces kudriavzevii FM1071

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission package

text: Reads used for reference-based assembly (FM1071 is a monosporic deriviative of ZP591)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1072

text: live

text: Generic

characteristic: NCBI submission model

characteristic: SRA accession

text: Reads used for reference-based genome assembly (FM1072 is a monosporic derivative of ZP620)

characteristic: description

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1076

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1076 is a monosporic derivative of ZP629)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1078

text: University of Colorado School of Medicine

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1078 is a monosporic derivative of ZP594)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1069

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1069 is a monosporic derivative of ZP513)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1094

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1094 is a monosporic derivative of ZP537)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1077

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1077 is a monosporic derivative of ZP630)

text: Saccharomyces kudriavzevii

text: Generic sample from Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1079

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1079 is a monosporic derivative of ZP595)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1073

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1073 is a monosporic derivative of ZP621)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1074

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1074 is a monosporic derivative of ZP623)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1066

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1066 was isolated from a single colony of ZP634)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1062

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1062 was isolated from a single colony of ZP625)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1057

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1057 was isolated from a single colony of ZP542)

text: Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1056

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1056 was isolated from a single colony of ZP537)

text: Saccharomyces kudriavzevii


name: Saccharomyces cerevisiae/Saccharomyces kudriavzevii hybrid CBS679

text: live

text: Generic

text: Discovered to be a hybrid (Fig. S2; FM1054 was isolated from a single colony of CBS679); not assembled

text: Generic sample from Saccharomyces cerevisiae x Saccharomyces kudriavzevii


Saccharomyces kudriavzevii FM1075

text: live

text: Generic

text: Reads used for reference-based genome assembly (FM1075 is a monosporic derivative of ZP627)

text: Saccharomyces kudriavzevii


text: Iowa State University

text: live

text: Generic

text: 14 days after planting

characteristic: age

characteristic: genotype

text: Zea mays

text: above ground Seedling

characteristic: tissue


Vibrio cholerae NG288-36 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae NG288-36 using 454 technology

text: Vibrio cholerae NG288-36

characteristic: strain

text: Generic sample from Vibrio cholerae NG288-36


Vibrio cholerae PS15 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae PS15 using 454 technology

text: Vibrio cholerae PS15

text: Generic sample from Vibrio cholerae PS15


Vibrio cholerae 5052 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae 5052 using 454 technology

text: Vibrio cholerae 5052

text: Generic sample from Vibrio cholerae 5052


Vibrio cholerae O139-ARG Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae O139-ARG using 454 technology

text: Vibrio cholerae 0139-ARG

text: Generic sample from Vibrio cholerae 0139-ARG


Vibrio cholerae PG38 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae PG38 using 454 technology

text: Vibrio cholerae PG38

text: Generic sample from Vibrio cholerae PG38


Vibrio cholerae T5957 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae T5957 using 454 technology

text: Vibrio cholerae NG288-36


Vibrio cholerae NG288-36 Sample_1

text: J. Craig Venter Institute

text: live

text: Generic

text: Vibrio cholerae T5957

text: Generic sample from Vibrio cholerae T5957


Vibrio cholerae O145B Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae O145B using 454 technology

text: Vibrio cholerae O145B

text: Generic sample from Vibrio cholerae O145B


Vibrio cholerae CS351 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. cholerae CS351 using 454 technology

text: Vibrio cholerae CS351

text: Generic sample from Vibrio cholerae CS351


Vibrio cholerae NG288-36 Sample_1_2

text: J. Craig Venter Institute

text: live

text: Generic

text: Vibrio cholerae NG288-36


Salmonella clearance

text: Institute of Molecular Biology University of Zurich

text: live

text: Generic

text: pool sample: Non-typhoidal Salmonella infections are a major cause of diarrhea. Acute symptoms cease rapidly, but some patients keep shedding NTS for weeks or months - representing subclinical carriers and transmitters. The factors preventing this 'asymptomatic excretor' state are poorly understood, but of high clinical and epidemiological importance. Here, we analyzed the parameters controlling clearance of an acute NTS infection in mice. BARCODE_INDEX = {1:TAGC, 2:TCGA, 3:TCGC, 4:TAGA, 5:TGCA, 6:ATCG, 7:AGCT, 8:AGCG, 9:ATCT, 10:ACGT, 11:GATC, 12:GCTA, 13:GCTC, 14:GATA, 15:GTCA, 16:CAGT, 17:CTGA, 18:CAGA, 19:CTGT, 20:CGTA} REGION_1 = {1:Input_RK69, 2:Pellet_RK69, 3:Donor_I_TV1012_CON, 4:Beads_RK69, 5:Eluat_Reg_RK69, 6:Beads_RK69, 7:Eluat_Reg_RK69, 8:US_RK75, 9:B727-1_CON, 10:B728-1_CON, 11:B729-1_CON, 12:B730-1_CON, 13:B731-1_CON, 14:B732-1_CON, 15:FB727-Day_1_BSA, 16:FB728-Day_1_BSA, 17:FB729-Day_1_BSA, 18:FB730-Day_1_RegIIIbeta, 19:FB731-Day_1_RegIIIbeta, 20:FB732-Day_1_RegIIIbeta} REGION_2 = {1:Donor_1_TV973_C_donor_day_0, 2:Donor_TV973_C_donor_day_83, 3:B896_TV973_L-C_day_80, 4:B897_TV973_L-C_day_80, 5:B899_TV973_L-C_day_80, 6:B900_TV973_L-C_day_80, 7:B902_TV973_L-C_day_80, 8:B903_TV973_L-C_day_80, 9:B905_TV973_L_day_80, 10:B906_TV973_L_day_80, 11:B907_TV973_L_day_80, 12:B908_TV973_L_day_80, 13:B208_day_2_TV907_L_day_2, 14:B209_day_2_TV907_L_day_2, 15:B210_day_2_TV907_L_day_2, 16:B211_day_2_TV907_L_day_2, 17:B213_day_40_TV907_L_day_40, 18:B214_day_40_TV907_L_day_40, 19:B214_day_40_TV907_L_day_40, 20:B214_day_40_TV907_L_day_40}

text: mouse gut metagenome

text: Generic sample from mouse gut metagenome


LCM mouse model

text: live

text: Generic

text: pool sample: 16S rRNA gene amplicons from a mouse model with low complexity gut microbiota to study colonization resistance BARCODE_INDEX = {1:TAGC, 2:TCGA, 3:TCGC, 4:TAGA, 5:TGCA, 6:ATCG, 7:AGCT, 8:AGCG, 9:ATCT, 10:ACGT, 11:GATC, 12:GCTA, 13:GCTC, 14:GATA, 15:GTCA, 16 :CAGT, 17:CTGA, 18:CAGA, 19:CTGT, 20:CGTA} REGION_1 = {1:9855_CON_day_0, 2:9855_CON_day_3, 3:9856_CON_day_0, 4:9856_CON_day_3, 5:9865_LCM-CON_day_0, 6:9865_LCM-CON_day_3, 7:9866_LCM-CON_da y_0, 8:9866_LCM-CON_day_3, 9:LCM-CON_3_day_24, 10:LCM-CON_4_day_24, 11:LCM-CON_5_day_24, 12:LCM-CON_6_day_24} REGION_2 = {1:CON_1_day_0, 2:CON_1_day_21, 3:CON_1_day_24, 4:LCM-CON_1_day_0, 5:LCM-CON_1_day_21, 6:LCM-CON_1_day_24, 7:LCM-CON_2_day_0, 8:LCM-CO N_2_day_21, 9:LCM-CON_2_day_24, 10:CON_2_day_0, 11:CON_2_day_21, 12:CON_2_day_24 13:LCM-CON_3_day_0, 14:LCM-CON_3_day_21, 15:LCM-CON_4_day_0, 16:LCM-C ON_4_day_21, 17:LCM-CON_5_day_0, 18:LCM-CON_5_day_21, 19:LCM-CON_6_day_0, 20:LCM-CON_6_day_21}

text: mouse gut metagenome


Harlan

text: Virginia Tech

text: live

text: Generic

text: Cimex lectularius

text: Generic sample from Cimex lectularius


Richmond

text: Virginia Tech

text: live

text: Generic

text: Cimex lectularius

text: Generic sample from Cimex lectularius


text: Cold Spring Harbor Laboratory

text: live

text: Generic

text: Vitis vinifera

text: Generic sample from Vitis vinifera


text: Gerstein, MB&B, Yale University

text: live

text: Generic

text: emrbyo

characteristic: growth stage

text: Caenorhabditis elegans

text: pha-4 transgenic worm OP37

text: Pha-4 emb input


characteristic: External Id

text: Gerstein, MB&B, Yale University

text: live

text: Generic

text: Caenorhabditis elegans

text: pha-4 transgenic worm OP37

text: Pha-4 starved L1 input


text: Cold Spring Harbor Laboratory

characteristic: INSDC center name

text: live

text: Generic

text: Vitis

text: Generic sample from Vitis


text: Cold Spring Harbor Laboratory

text: live

text: Generic

text: Vitis amurensis

characteristic: organism

text: Generic sample from Vitis amurensis


text: Cold Spring Harbor Laboratory

characteristic: INSDC first public

text: live

text: Generic

text: Vitis labrusca

text: Generic sample from Vitis labrusca


text: Cold Spring Harbor Laboratory

characteristic: INSDC last update

text: live

text: Generic

text: Vitis rotundifolia

text: Generic sample from Vitis rotundifolia


text: UVA

text: live

text: Generic

text: We obtained one female mouse each from the C57BL/6J (B6) and DBA/2J (DBA) inbred strains (Jackson Laboratory, Bar Harbor, ME). The B6 individual was obtained in January, 2006. This mouse was a retired foundation stock breeder (F226), and is thus derived from the colony nucleus and should be minimally diverged from the reference genome (Waterston et al. 2002). The DBA mouse was obtained in December, 2004. This mouse was ordered through the standard mechanism and is not pedigreed. These are precisely the same samples analyzed in our previous aCGH study (Egan et al. 2007). DNA preparation. DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications. Livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. After isolation of crude DNA from liver and tail, further extractions were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.

text: Mus musculus

text: Generic sample from Mus musculus

characteristic: title


text: UVA

characteristic: INSDC secondary accession

text: live

text: Generic

text: We obtained one female mouse each from the C57BL/6J (B6) and DBA/2J (DBA) inbred strains (Jackson Laboratory, Bar Harbor, ME). The B6 individual was obtained in January, 2006. This mouse was a retired foundation stock breeder (F226), and is thus derived from the colony nucleus and should be minimally diverged from the reference genome (Waterston et al. 2002). The DBA mouse was obtained in December, 2004. This mouse was ordered through the standard mechanism and is not pedigreed. These are precisely the same samples analyzed in our previous aCGH study (Egan et al. 2007). DNA was isolated using the Puregene Kit (Gentra Systems), with the following modifications. Livers were flash frozen in liquid nitrogen, ground with mortar and pestle, and dounce-homogenized in 20 ml cell lysis solution. After isolation of crude DNA from liver and tail, further extractions were performed with phenol/chloroform/isoamyl alcohol, and chloroform/isoamyl alcohol, and DNA was precipitated with 2 volumes isopropanol and 1/10 volume sodium acetate.

text: Mus musculus

text: Generic sample from Mus musculus


text: Center for Comparative Microbial Ecology

text: live

characteristic: INSDC status

text: Metagenome or environmental

characteristic: PalmSize

text: female right palm

text: right

characteristic: dominant hand

text: R

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

characteristic: host age

text: female

characteristic: host sex

text: less than 2

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Male left palm

characteristic: description

text: right

text: L

text: Homo sapiens

text: male

text: greater than 4 hours

text: human skin metagenome

text: human hand microbiome


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: Male left palm

text: right

text: L

text: Homo sapiens

text: male

text: between 2 and 4

text: human skin metagenome

characteristic: organism

text: human hand microbiome


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Metagenome or environmental

text: Male right palm

text: left

text: R

text: Homo sapiens

text: male

text: greater than 4 hours

text: human skin metagenome

text: human hand microbiome

characteristic: title


text: live

text: Metagenome or environmental

characteristic: PalmSize

text: Male left palm

text: left

characteristic: dominant hand

text: L

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

text: male

text: greater than 4 hours

text: human skin metagenome

text: human hand microbiome


text: live

text: Metagenome or environmental

text: female right palm

text: right

text: R

text: Homo sapiens

characteristic: host age

text: female

characteristic: host sex

text: greater than 4 hours

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: female left palm

characteristic: description

text: right

text: L

text: Homo sapiens

text: female

text: greater than 4 hours

text: human skin metagenome

text: human hand microbiome


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: Male right palm

text: right

text: R

text: Homo sapiens

text: male

text: between 2 and 4

text: human skin metagenome

characteristic: organism

text: human hand microbiome


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Metagenome or environmental

text: Male right palm

text: right

text: R

text: Homo sapiens

text: male

text: greater than 4 hours

text: human skin metagenome

text: human hand microbiome

characteristic: title


text: live

text: Metagenome or environmental

characteristic: PalmSize

text: female right palm

text: right

characteristic: dominant hand

text: R

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

text: female

text: between 2 and 4

text: human skin metagenome

text: human hand microbiome


text: live

text: Metagenome or environmental

text: female left palm

text: right

text: L

text: Homo sapiens

characteristic: host age

text: female

characteristic: host sex

text: between 2 and 4

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Male right palm

characteristic: description

text: right

text: R

text: Homo sapiens

text: male

text: less than 2

text: human skin metagenome

text: human hand microbiome


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: Male left palm

text: right

text: L

text: Homo sapiens

text: male

text: less than 2

text: human skin metagenome

characteristic: organism

text: human hand microbiome


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Metagenome or environmental

text: female left palm

text: left

text: L

text: Homo sapiens

text: female

text: greater than 4 hours

text: human skin metagenome

text: human hand microbiome

characteristic: title


text: live

text: Metagenome or environmental

characteristic: PalmSize

text: female right palm

text: ambidextrous

characteristic: dominant hand

text: R

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

text: female

text: less than 2

text: human skin metagenome

text: human hand microbiome


text: live

text: Metagenome or environmental

text: female left palm

text: ambidextrous

text: L

text: Homo sapiens

characteristic: host age

text: female

characteristic: host sex

text: less than 2

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: female left palm

characteristic: description

text: right

text: L

text: Homo sapiens

text: female

text: less than 2

text: human skin metagenome

text: human hand microbiome


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: female right palm

text: right

text: R

text: Homo sapiens

text: female

text: less than 2

text: human skin metagenome

characteristic: organism

text: human hand microbiome


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Metagenome or environmental

text: Male right palm

text: left

text: R

text: Homo sapiens

text: male

text: less than 2

text: human skin metagenome

text: human hand microbiome

characteristic: title


text: live

text: Metagenome or environmental

characteristic: PalmSize

text: Male left palm

text: left

characteristic: dominant hand

text: L

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

text: male

text: less than 2

text: human skin metagenome

text: human hand microbiome


text: live

text: Metagenome or environmental

text: female right palm

text: left

text: R

text: Homo sapiens

characteristic: host age

text: female

characteristic: host sex

text: between 2 and 4

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Male left palm

characteristic: description

text: right

text: L

text: Homo sapiens

text: male

text: between 2 and 4

text: human skin metagenome

text: human hand microbiome


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: Male left palm

text: left

text: L

text: Homo sapiens

text: male

text: greater than 4 hours

text: human skin metagenome

characteristic: organism

text: human hand microbiome


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Metagenome or environmental

text: female right palm

text: left

text: R

text: Homo sapiens

text: female

text: less than 2

text: human skin metagenome

text: human hand microbiome

characteristic: title


text: live

text: Metagenome or environmental

characteristic: PalmSize

text: female left palm

text: left

characteristic: dominant hand

text: L

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

text: female

text: less than 2

text: human skin metagenome

text: human hand microbiome


text: live

text: Metagenome or environmental

text: female left palm

text: ambidextrous

text: L

text: Homo sapiens

characteristic: host age

text: female

characteristic: host sex

text: between 2 and 4

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Male right palm

characteristic: description

text: left

text: R

text: Homo sapiens

text: male

text: between 2 and 4

text: human skin metagenome

text: human hand microbiome


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: Male left palm

text: left

text: L

text: Homo sapiens

text: male

text: between 2 and 4

text: human skin metagenome

characteristic: organism

text: human hand microbiome


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Metagenome or environmental

text: female right palm

text: right

text: R

text: Homo sapiens

text: female

text: between 2 and 4

text: human skin metagenome

text: human hand microbiome

characteristic: title


text: live

text: Metagenome or environmental

characteristic: PalmSize

text: Male right palm

text: right

characteristic: dominant hand

text: R

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

text: male

text: less than 2

text: human skin metagenome

text: human hand microbiome


text: live

text: Metagenome or environmental

text: Male right palm

text: right

text: R

text: Homo sapiens

characteristic: host age

text: male

characteristic: host sex

text: between 2 and 4

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Male left palm

characteristic: description

text: right

text: L

text: Homo sapiens

text: male

text: less than 2

text: human skin metagenome

text: human hand microbiome


characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Metagenome or environmental

text: Male left palm

text: right

text: L

text: Homo sapiens

text: male

text: greater than 4 hours

text: human skin metagenome

characteristic: organism

text: human hand microbiome


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Metagenome or environmental

text: Male right palm

text: right

text: R

text: Homo sapiens

text: male

text: greater than 4 hours

text: human skin metagenome

text: human hand microbiome

characteristic: title


text: live

text: Metagenome or environmental

characteristic: PalmSize

text: female right palm

text: right

characteristic: dominant hand

text: R

characteristic: hand (R/L)

text: Homo sapiens

characteristic: host

text: female

text: less than 2

text: human skin metagenome

text: human hand microbiome


text: live

text: Metagenome or environmental

text: female left palm

text: right

text: L

text: Homo sapiens

characteristic: host age

text: female

characteristic: host sex

text: less than 2

characteristic: hours since wash

text: human skin metagenome

characteristic: subject

text: human hand microbiome


text: live

text: Metagenome or environmental

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Male right palm

characteristic: description

text: left

text: R

text: Homo sapiens

text: male

text: less than 2

text: human skin metagenome

text: human hand microbiome


name: Caenorhabditis elegans N2 exposed to Harposporium 24hrs RNA sample 1

characteristic: External Id

text: University of Washington Genome Sciences

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Generic

text: Jonathan Ewbank lab grew up the worms. In the Valerie Reinke lab, they grew up the E. coli OP50 (as a control experiment) and Harposporium infected samples. The control experiment is stored in the trace archive under sample alias Caenorhabditis elegans N2 control for Harposporium exposed to E. coli OP50 24hrs RNA sample 1. Worms: Eggs from C. elegans N2 worms cultivated at 25 C were allowed to hatch in the absence of food at 25 C. Synchronized larvae were transferred after 19-24 h to NGM agar plates lawned with OP50 and cultivated at 25 C until the young adult stage (43-45h). Preparation of plates: Culture OP50/Harposporium in liquid LB at 37 C overnight, put on NGM plates for 24 h at 25 C, then another 20h at 25 C. Infection: Synchronized N2 worms at young adult stage were transferred to NGM plates lawned with OP50/Harposporium and cultivated at 25 C for 24 hours. worms were collected and washed 2 times in M9 buffer before being resuspend in Trizol. Harvesting: worms were harvested and washed 2 times in M9, as far as possible undesirable larvae were separated from adult during washing. the supernatant was removed and discarded. the volume of the pellet was measured and 10 volumes of Trizol added. Tubes were vortexed for 45 sec, placed in liquid Nitrogen flash freeze completely, then thawed completely in 37C water bath. this freeze/thaw process was repeated 4 times. worms and Trizol homogenate was frozen at -80 C. Local library name: HP_2_24 for 2nd assay infected at 24 hours Quality values are GAPipeline1.4 solexa/illumina values.

text: Caenorhabditis elegans

characteristic: organism

text: Generic sample from Caenorhabditis elegans


name: Caenorhabditis elegans N2 control for Harposporium exposed to E. coli OP50 24hrs RNA sample 1

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: Jonathan Ewbank lab grew up the worms. In the Valerie Reinke lab, they grew up the E. coli OP50 (as a control experiment) and Harposporium infected samples. This is the control experiment for trace archive data stored under sample Caenorhabditis elegans N2 exposed to Harposporium 24hrs RNA sample 1. Worms: Eggs from C. elegans N2 worms cultivated at 25 C were allowed to hatch in the absence of food at 25 C. Synchronized larvae were transferred after 19-24 h to NGM agar plates lawned with OP50 and cultivated at 25 C until the young adult stage (43-45h). Preparation of plates: Culture OP50/Harposporium in liquid LB at 37 C overnight, put on NGM plates for 24 h at 25 C, then another 20h at 25 C. Infection: Synchronized N2 worms at young adult stage were transferred to NGM plates lawned with OP50/Harposporium and cultivated at 25 C for 24 hours. worms were collected and washed 2 times in M9 buffer before being resuspend in Trizol. Harvesting: worms were harvested and washed 2 times in M9, as far as possible undesirable larvae were separated from adult during washing. the supernatant was removed and discarded. the volume of the pellet was measured and 10 volumes of Trizol added. Tubes were vortexed for 45 sec, placed in liquid Nitrogen flash freeze completely, then thawed completely in 37C water bath. this freeze/thaw process was repeated 4 times. worms and Trizol homogenate was frozen at -80 C. Local library name: UI_2_24 for 2nd assay infected at 24 hours Quality values are GAPipeline1.4 solexa/illumina values.

text: Caenorhabditis elegans

characteristic: title


name: Caenorhabditis elegans N2 exposed to S. macescens Db10 24hrs RNA sample 1

text: live

text: Generic

text: Jonathan Ewbank lab grew up the worms. In the Valerie Reinke lab, they grew up the E. coli OP50 (as a control experiment) and Serratia macescens strain Db10 infected samples. The control experiment is stored in the trace archive under sample alias Caenorhabditis elegans N2 control for S. macescens Db10 exposed to E. coli OP50 24hrs RNA sample 1. Worms: Eggs from C. elegans N2 worms cultivated at 25 C were allowed to hatch in the absence of food at 25 C. Synchronized larvae were transferred after 19-24 h to NGM agar plates lawned with OP50 and cultivated at 25 C until the young adult stage (43-45h). Preparation of plates: Culture OP50/Db10 in liquid LB at 37 C overnight, put on NGM plates for 24 h at 25 C, then another 20h at 25 C. Infection: Synchronized N2 worms at young adult stage were transferred to NGM plates lawned with OP50/Db10 and cultivated at 25 C for 24 hours. worms were collected and washed 2 times in M9 buffer before being resuspend in Trizol. Harvesting: worms were harvested and washed 2 times in M9, as far as possible undesirable larvae were separated from adult during washing. the supernatant was removed and discarded. the volume of the pellet was measured and 10 volumes of Trizol added. Tubes were vortexed for 45 sec, placed in liquid Nitrogen flash freeze completely, then thawed completely in 37C water bath. this freeze/thaw process was repeated 4 times. worms and Trizol homogenate was frozen at -80 C. Local library name: DB_1_24 for 1st assay infected at 24 hours Quality values are GAPipeline1.4 solexa/illumina values.

text: Caenorhabditis elegans


name: Caenorhabditis elegans N2 control for S. macescens Db10 exposed to E. coli 24hrs RNA sample 1

text: live

text: Generic

text: Jonathan Ewbank lab grew up the worms. In the Valerie Reinke lab, they grew up the E. coli OP50 (as a control experiment) and Serratia macescens strain Db10 infected samples. This is the control experiment to the experiment stored in the trace archive under sample alias Caenorhabditis elegans N2 exposed to S. macescens Db10 24hrs RNA sample 1. Worms: Eggs from C. elegans N2 worms cultivated at 25 C were allowed to hatch in the absence of food at 25 C. Synchronized larvae were transferred after 19-24 h to NGM agar plates lawned with OP50 and cultivated at 25 C until the young adult stage (43-45h). Preparation of plates: Culture OP50/Db10 in liquid LB at 37 C overnight, put on NGM plates for 24 h at 25 C, then another 20h at 25 C. Infection: Synchronized N2 worms at young adult stage were transferred to NGM plates lawned with OP50/Db10 and cultivated at 25 C for 24 hours. worms were collected and washed 2 times in M9 buffer before being resuspend in Trizol. Harvesting: worms were harvested and washed 2 times in M9, as far as possible undesirable larvae were separated from adult during washing. the supernatant was removed and discarded. the volume of the pellet was measured and 10 volumes of Trizol added. Tubes were vortexed for 45 sec, placed in liquid Nitrogen flash freeze completely, then thawed completely in 37C water bath. this freeze/thaw process was repeated 4 times. worms and Trizol homogenate was frozen at -80 C. Local library name: OP_1_24 for 1st assay infected at 24 hours Quality values are GAPipeline1.4 solexa/illumina values.

text: Caenorhabditis elegans


name: Caenorhabditis elegans strain JK1107 mid-L4 male soma only no DNaseI RNA sample 1

text: live

text: Generic

text: Animals were synchronized by treating a mixed population with bleach to collect embryos. The embryos were incubated without food, causing the larvae to arrest at the L1 stage upon hatching. Starved L1 larvae were plated in the presence of food and raised at 25 degrees Celsius. Staging was determined by examining a subset of animals under Nomarski optics at intervals for vulval and germline development. Animals were collected at mid-L4 stage and washed in S basal buffer. These are from the strain JK1107. They are soma only from the L4 stage. They were not DNaseI treated. Local Library Name: JKL4_4_NDT Quality values are GAPipeline1.4 solexa/illumina values.

text: Caenorhabditis elegans


marsh fritillary transcriptome

text: University of Exeter - Center for Ecology and Conservation

text: live

text: Generic

text: Euphydryas aurinia

text: Generic sample from Euphydryas aurinia


Pinus chloroplast genomes mixed 1

text: Oregon St Univ - Center for Genome Research & Biocomputing

text: live

text: Generic

text: Pinus thunbergii THUN05

characteristic: barcode AAT

text: Pinus ponderosa POND06

characteristic: barcode CCT

text: Pinus taeda TAED06

characteristic: barcode CGT

text: Pinus pinaster PINA04

characteristic: barcode GGT

text: Genomic DNA was extracted from fresh needles or seed megagametophyte tissue using the FastDNA Kit or the DNeasy Plant Mini Kit. Chloroplast genomes were amplified in 35 separate PCR reactions. For each species, the PCR reactions were quantified, pooled into equal-molar mixtures, and converted into barcoded Illumina sequencing libraries. Individual libraries were pooled into multiplex sequencing libraries ranging from 4X-6X.

text: Pinus

text: Generic sample from Pinus


Pinus chloroplast genomes mixed 2

text: live

text: Generic

text: Pinus krempfii KREM03

text: Pinus lambertiana N LAMB08

characteristic: barcode ATT

text: Pinus contorta CONT40

text: Pinus gerardiana GERA03

text: Pinus

text: Generic sample from Pinus


Pinus chloroplast genomes mixed 3

text: live

text: Generic

characteristic: NCBI submission model

text: Pinus nelsonii NELS03

text: Picea sitchensis PICSIT04

text: Pinus longaeva LONG01

text: Pinus monophylla MONO10

text: Genomic DNA was extracted from fresh needles or seed megagametophyte tissue using the FastDNA Kit or the DNeasy Plant Mini Kit. Chloroplast genomes were amplified in 35 separate PCR reactions. For each species, the PCR reactions were quantified, pooled into equal-molar mixtures, and converted into barcoded Illumina sequencing libraries. Individual libraries were pooled into multiplex sequencing libraries ranging from 4X-6X. barcode ATT Picea sitchensis PICSIT04 barcode CCT Pinus longaeva LONG01 barcode GGT Pinus monophylla MONO10 barcode AAT Pinus nelsonii NELS03

text: Pinaceae

text: Generic sample from Pinaceae


Pinus chloroplast genomes mixed 4

text: live

text: Generic

characteristic: NCBI submission package

text: Pinus merkusii MERK04

text: Larix occidentalis LAROCC01

text: Genomic DNA was extracted from fresh needles or seed megagametophyte tissue using the FastDNA Kit or the DNeasy Plant Mini Kit. Chloroplast genomes were amplified in 35 separate PCR reactions. For each species, the PCR reactions were quantified, pooled into equal-molar mixtures, and converted into barcoded Illumina sequencing libraries. Individual libraries were pooled into multiplex sequencing libraries ranging from 4X-6X. barcode GGT Larix occidentalis LAR0CC01 228017363 barcode ATT Pinus merkusii MERK04 228017432

text: Pinaceae

text: Generic sample from Pinaceae


Pinus chloroplast genomes mixed 5

text: live

text: Generic

characteristic: SRA accession

text: Larix occidentalis LAR0CC01

text: Larix occidentalis

text: Generic sample from Larix occidentalis


Loricaria gr. cataphracta

text: University of Geneva

text: live

text: Generic

text: Loricaria cf. cataphracta YSG-2010

text: Loricaria cf. cataphracta YSG-2010


Heliconius numata Pool1

text: live

text: Generic

text: Heliconius numata

text: Generic sample from Heliconius numata


Heliconius numata Pool2

text: live

text: Generic

text: Heliconius numata

text: Generic sample from Heliconius numata


MBfR-NS

text: Arizona State University

text: live

text: Generic

text: bioreactor metagenome

text: Generic sample from Bacteria


MBfR-TCE

text: Arizona State University

text: live

text: Generic

text: bioreactor metagenome

text: Generic sample from Bacteria


MBfR-Mix

text: Arizona State University

text: live

text: Generic

text: bioreactor metagenome

text: Generic sample from Bacteria


text: Cancer Research UK (CRUK)

text: live

text: Generic

text: MCF-7 cell line, full media, anti-ER antibody sc-543 from Santa Cruz Biotechnologies, followed by anti-ER antibody sc-543 from Santa Cruz Biotechnologies.

characteristic: description

text: Homo sapiens

text: Generic sample from Homo sapiens


characteristic: External Id

text: Cancer Research UK (CRUK)

text: live

text: Generic

text: MCF-7 cell line, full media, anti-ER antibody sc-543 from Santa Cruz Biotechnologies, followed by anti-IgG (rabbit) antibody sc-2072 from Santa Cruz Biotechnologies for use as a control.

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Cancer Research UK (CRUK)

characteristic: INSDC center name

text: live

text: Generic

text: MCF-7 cell line, full media, anti-ER antibody sc-543 from Santa Cruz Biotechnologies, followed by anti-RARA antibody sc-551 from Santa Cruz Biotechnologies.

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Cancer Research UK (CRUK)

characteristic: INSDC first public

text: live

text: Generic

text: MCF-7 cell line, full media, anti-ER antibody sc-543 from Santa Cruz Biotechnologies.

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Cancer Research UK (CRUK)

text: live

text: Generic

text: MCF-7 cell line, full media, anti-RARA antibody sc-551 from Santa Cruz Biotechnologies.

text: Homo sapiens

characteristic: organism

text: Generic sample from Homo sapiens


text: Cancer Research UK (CRUK)

characteristic: INSDC last update

text: live

text: Generic

text: MCF-7 cell line, treated with ICI 182780 (Fulvestrant), anti-RARA antibody sc-551 from Santa Cruz Biotechnologies.

text: Homo sapiens

text: Generic sample from Homo sapiens


text: Cancer Research UK (CRUK)

characteristic: INSDC secondary accession

text: live

text: Generic

text: MCF-7 cell line, full media, un-immunoprecipitated for use as Input.

text: Homo sapiens

text: Generic sample from Homo sapiens


LaSelva Nematode Sample

text: University of New Hampshire

text: live

characteristic: INSDC status

text: Generic

text: Caenorhabditis elegans

text: Generic sample from Caenorhabditis elegans


Postia placenta RNA sample 1

text: Clemson University

text: live

text: Generic

text: Postia placenta

text: Generic sample from Postia placenta

characteristic: title


text: Joint Genome Institute, U.S. Department of Energy

text: live

text: Generic

text: Burkholderia sp. CCGE1002

text: Paraburkholderia atlantica

characteristic: strain

text: Generic sample from Burkholderia sp. CCGE1002


E. coil ETEC WS3080A Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC WS3080A using 454 technology

text: Escherichia coli ETEC WS3080A

text: ETEC WS3080A

text: Generic sample from Escherichia coli ETEC WS3080A


E. coli ETEC TW03576 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coli ETEC TW03576 using 454 technology

text: Escherichia coli ETEC TW03576

text: ETEC TW03576

text: Generic sample from Escherichia coli ETEC TW03576


text: live

text: Generic

text: A wild soybean accession PI468916 was used for the re-sequencing and the whole genome sequence of Williams 82 were used as a reference sequence

text: Glycine max

text: Generic sample from Glycine max


text: live

text: Generic

text: Methanocaldococcus strain FS406-22

text: Methanocaldococcus sp. FS406-22

text: Generic sample from Methanocaldococcus sp. FS406-22


text: DOE-CSP 2008

characteristic: Funding Program

characteristic: GOLD Stamp ID

text: Gram+

characteristic: Gram Staining

characteristic: Greengenes ID

text: live

text: Generic

text: Sporulating

characteristic: Sporulation

text: Yes

characteristic: Type Strain

text: free living

characteristic: biotic relationship

text: Keywords: GSC:MIGS:2.1

text: Soil

characteristic: environment

characteristic: investigation type

text: Soil

characteristic: isolation site

text: Micromonospora aurantiaca ATCC 27029

text: Micromonospora aurantiaca ATCC 27029

characteristic: project name

text: ATCC 27029, DSM 43813

text: aerobe

text: ATCC 27029

characteristic: temperature optimum

text: Mesophile

characteristic: temperature range

text: Micromonospora aurantiaca ATCC 27029, complete genome.

text: type strain of Micromonospora aurantiaca

characteristic: type material


name: DBY10147 whole genome sequencing CA0001.SAM1

characteristic: External Id

text: University of Washington Genome Sciences

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: DBY11331 (S2c1) was isolated after ~188 generations of a sulfate-limited continuous culture seeded with the prototrophic haploid strain DBY10147, as previously described [1]. Illumina sequencing libraries were constructed from DBY11331 and DBY10147 genomic DNA following standard procedures and published recommendations [2]. We collected 13,555,852 and 13,901,121 single-end, 36 bp, quality-filtered reads from DBY11331 and DBY10147, respectively, using the Illumina Genome Analyzer II platform. References: 1. Gresham D, Desai M, Tucker C, Jenq H, Pai D, Ward A, Desevo C, Botstein D, Dunham M: The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genetics 2008, 4:e1000303. 2. Quail MA, Kozarewa I, Smith F, Scally A, Stephens PJ, Durbin R, Swerdlow H, Turner DJ: A large genome center's improvements to the Illumina sequencing system. Nature methods 2008, 5:1005-1010.

characteristic: description

text: Saccharomyces cerevisiae

characteristic: organism

text: Generic sample from Saccharomyces cerevisiae


name: DBY11331 whole genome sequencing CA0001.SAM2

text: live

text: Generic

text: Saccharomyces cerevisiae

characteristic: title


Vibrio mimicus 7555 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of V. mimicus 7555 using 454 technology

text: Vibrio mimicus 7555

characteristic: strain

text: Generic sample from Vibrio mimicus 7555


HeLaMOCK

text: UMass Medical School

text: live

text: Generic

text: Total small RNAs prepared from HeLa cells 48h post MOCK transfection with Dharmafect4 (Dharmacon). Total RNA was extracted using Trizol (Invitrogen), then short (18-29 nt) RNAs were gel-purified. Library was constructed as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)).

text: Homo sapiens

text: Generic sample from Homo sapiens


text: UMass Medical School

text: live

text: Generic

text: Total small RNAs prepared from HeLa cells 48h post transfection of 1 nM antagomir miR-16with Dharmafect4 (Dharmacon). Total RNA was extracted using Trizol (Invitrogen), then short (18-29 nt) RNAs were gel-purified. Library was constructed as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)

text: Homo sapiens

text: HeLa cells transfected with 1 nM antagomir against miR-16


text: UMass Medical School

text: live

text: Generic

text: Total small RNAs prepared from HeLa cells 48h post transfection of 10 nM antagomiR against miR-21 with Dharmafect4 (Dharmacon). Total RNA was extracted using Trizol (Invitrogen), then short (18-29 nt) RNAs were gel-purified. Library was constructed as described in Seitz et al. (Curr. Biol. 18:147-151 (2008)

text: Homo sapiens

text: mock transfected HeLa cells


E. coil ETEC TW03741 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC TW03741 using 454 technology

text: Escherichia coli ETEC TW03741

text: ETEC TW03741

text: Generic sample from Escherichia coli ETEC TW03741


E. coil ETEC DS168-1 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC DS168-1 using 454 technology

text: Escherichia coli ETEC DS168-1

text: ETEC DS168-1

text: Generic sample from Escherichia coli ETEC DS168-1


E. coil ETEC TW03574 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC TW03574 using 454 technology

text: Escherichia coli ETEC TW03574

text: ETEC TW03574

text: Generic sample from Escherichia coli ETEC TW03574


E. coil ETEC TW03585 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC TW03585 using 454 technology

text: Escherichia coli ETEC TW03585

text: ETEC TW03585

text: Generic sample from Escherichia coli ETEC TW03585


E. coil ETEC TW03439 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC TW03439 using 454 technology

text: Escherichia coli ETEC TW03439

text: ETEC TW03439

text: Generic sample from Escherichia coli ETEC TW03439


E. coil ETEC TW03452 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC TW03452 using 454 technology

text: Escherichia coli ETEC TW03452

text: ETEC TW03452

text: Generic sample from Escherichia coli ETEC TW03452


E. coil ETEC WS2068A Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC WS2068A using 454 technology

text: Escherichia coli ETEC WS2068A

text: ETEC WS2068A

text: Generic sample from Escherichia coli ETEC WS2068A


E. coil ETEC TW14691 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC TW14691 using 454 technology

text: Escherichia coli ETEC TW14691

text: ETEC TW14691

text: Generic sample from Escherichia coli ETEC TW14691


E. coil ETEC WS1896A Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Partial genome sequencing of E. coil ETEC WS1896A using 454 technology

text: Escherichia coli ETEC WS1896A

text: ETEC WS1896A

text: Generic sample from Escherichia coli ETEC WS1896A


text: Center for Comparative Microbial Ecology

text: live

text: Generic

text: Human palm microbiome, default sample for unclassified reads

text: human skin metagenome

text: human hand microbiome


text: Cornell University

text: live

text: Generic

text: Clostridium difficile is a gram positive spore forming pathogen with a wide host range. Microarray based comparative genome hybridizations (Janvilisri et al, J Bacteriol. 2009 Jun;191(12):3881-91) have shown that the core genome of this species could be as low as 16% of the total genome. The objective of this project is to perform comparative genome sequencing of new C. difficile isolates and compare the new genomes to the reference strain C. difficile 630 (Genbank ID: AM180355). Based on microarray based comparative genome hybridizations of 80 C. difficile isolates from different hosts and geographical areas, strains showing large degree of genome variation was selected for shot gun sequencing. Strain 6466 sequenced in this study is a non-epidemic human isolate and will be used for comparative sequence analysis.

text: Clostridioides difficile 6466

text: Generic sample from Clostridium difficile 6466


text: University of Melbourne

text: live

text: Generic

text: Patient isolate of Enterococcus faecium

text: Enterococcus faecium

text: Ef AUS0004 sample


text: University of Melbourne

text: live

text: Generic

text: Patient isolate of Enterococcus faecium

text: Enterococcus faecium

text: EFAUS0085 sample


text: Gene Expression Omnibus

text: live

text: Generic

characteristic: batch

text: Cellular Dynamics International

characteristic: biomaterial provider

text: Cell Line

characteristic: biomaterial type

text: human embryonic stem cells WA01

text: undifferentiated

characteristic: differentiation stage

characteristic: line

text: genomic DNA

characteristic: molecule

text: Homo sapiens

text: male

characteristic: sex

text: Generic sample from Homo sapiens


HMP100-454 Sample

characteristic: External Id

text: J. Craig Venter Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: live

text: MIGS.ba

text: not determined

characteristic: assembly

text: terrestrial biome [ENVO:00000446]

characteristic: biome

text: not determined

characteristic: collection date

text: This strain was isolated from the human vaginal cavity.

characteristic: estimated size

text: human-associated habitat [ENVO:00009003]

characteristic: feature

text: Level 6: Finished36x

characteristic: finishing strategy (depth of coverage)

text: not determined

characteristic: geo loc name

characteristic: host taxid

text: not determined

text: not determined

characteristic: lat lon

text: biological product [ENVO:02000043]

characteristic: material

text: Vaginal

characteristic: misc_param: HMP body site

characteristic: misc_param: HMP supersite

text: not determined

characteristic: nucleic acid extraction

text: not determined

text: Mageeibacillus indolicus UPII9-5

text: Clostridiales genomosp. BVAB3 UPII9-5

characteristic: project name

text: Reference Genome

text: not determined

characteristic: sequencing method

characteristic: sop

text: BEI Shipping

text: Homo sapiens

characteristic: specific host

text: MIGS Cultured Bacterial/Archaeal sample from Clostridiales genomosp. BVAB3 str. UPII9-5


characteristic: External Id

text: Joint Genome Institute, U.S. Department of Energy

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Rhodopseudomonas palustris DX-1

characteristic: description

text: Rhodopseudomonas palustris DX-1

characteristic: organism

characteristic: strain

text: Generic sample from Rhodopseudomonas palustris DX-1

characteristic: title


text: Cornell University

text: live

text: Generic

text: Clostridioides difficile 6503

text: Generic sample from Clostridium difficile 6503


text: Cornell University

text: live

text: Generic

text: Clostridium difficile is a gram positive spore forming pathogen with a wide host range. Microarray based comparative genome hybridizations (Janvilisri et al, J Bacteriol. 2009 Jun;191(12):3881-91) have shown that the core genome of this species could be as low as 16% of the total genome. The objective of this project is to perform comparative genome sequencing of new C. difficile isolates and compare the new genomes to the reference strain C. difficile 630 (Genbank ID: AM180355). Based on microarray based comparative genome hybridizations of 80 C. difficile isolates from different hosts and geographical areas, strains showing large degree of genome variation was selected for shot gun sequencing. Strain 6534 sequenced in this study is a non-epidemic bovine isolate and will be used for comparative sequence analysis.

text: Clostridioides difficile 6534

text: Generic sample from Clostridium difficile 6534


text: Cornell University

text: live

text: Generic

text: Clostridium difficile is a gram positive spore forming pathogen with a wide host range. Microarray based comparative genome hybridizations (Janvilisri et al, J Bacteriol. 2009 Jun;191(12):3881-91) have shown that the core genome of this species could be as low as 16% of the total genome. The objective of this project is to perform comparative genome sequencing of new C. difficile isolates and compare the new genomes to the reference strain C. difficile 630 (Genbank ID: AM180355). Based on microarray based comparative genome hybridizations of 80 C. difficile isolates from different hosts and geographical areas, strains showing large degree of genome variation was selected for shot gun sequencing. Strain 6407 sequenced in this study is non-epidemic Equine isolate and will be used for comparative sequence analysis.

text: Clostridioides difficile 6407

text: Generic sample from Clostridium difficile 6407


Papilio dardanus

text: University of Exeter - Center for Ecology and Conservation

text: live

text: Generic

text: Papilio dardanus

text: Generic sample from Papilio dardanus


text: Arizona Cancer Center

text: live

text: Generic

text: Homo sapiens

text: Generic sample from Homo sapiens


Anopheles gambiae SUA2La poly-A RNA

text: University of Colorado School of Medicine

text: live

text: Generic

text: Anopheles gambiae SUA2La poly-A RNA

text: Anopheles gambiae

text: Generic sample from Anopheles gambiae


Aedes aegypti LVP-IB12 poly-A RNA

text: live

text: Generic

text: Aedes aegypti LVP-IB12 poly-A RNA

text: Aedes aegypti

text: Generic sample from Aedes aegypti


Anopheles albimanus, poly-A RNA

text: live

text: Generic

text: Anopheles albimanus, poly-A RNA

text: Anopheles albimanus

text: Generic sample from Anopheles albimanus


text: Richard Young, Biology, Whitehead Instute - MIT

text: live

text: Generic

characteristic: chip antibody

text: Mus musculus

text: no

characteristic: shrna

text: V6.5 mES cells

text: V6.5 mES cells

characteristic: tag


text: live

text: Generic

text: H3K9me3 (Ab8898)

text: Mus musculus

text: no

text: V6.5 mES cells

text: V6.5 mES cells


text: live

text: Generic

text: H3K9me3 (Up07222)

text: Mus musculus

text: no

text: V6.5 mES cells

text: V6.5 mES cells


text: live

text: Generic

text: H3K9me3 (Ab8898)

text: Mus musculus

text: GFP

text: V6.5 mES cells

text: V6.5 mES cells


text: live

text: Generic

text: H3K9me3 (Ab8898)

text: Mus musculus

text: V6.5 mES cells

text: V6.5 mES cells


text: live

text: Generic

text: WCE

text: Mus musculus

text: no

text: V6.5 mES cells

text: V6.5 mES cells


Anopheles arabiensis, poly-A RNA

text: live

text: Generic

text: Anopheles arabiensis, poly-A RNA

text: Anopheles arabiensis

text: Generic sample from Anopheles arabiensis


Pinus chloroplast genomes mixed 6

text: Oregon St Univ - Center for Genome Research & Biocomputing

text: live

text: Generic

text: Pinus attenuata ATTE06

characteristic: barcode ACGT

text: Pinus banksiana BANK03

characteristic: barcode AGCT

text: Pinus canariensis CANA01

characteristic: barcode CCCT

text: Pinus chihuahuana CHIH03

characteristic: barcode CTGT

text: Pinus resinosa RESI02

characteristic: barcode GGGT

text: Genomic DNA was extracted from fresh needles or seed megagametophyte tissue using the FastDNA Kit or the DNeasy Plant Mini Kit. Chloroplast genomes were amplified in 35 separate PCR reactions. For each species, the PCR reactions were quantified, pooled into equal-molar mixtures, and converted into barcoded Illumina sequencing libraries. Individual libraries were pooled into multiplex sequencing libraries ranging from 4X-6X.

text: Pinus

text: Generic sample from Pinus


characteristic: External Id

text: Genome Institute of Singapore

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: rabbit polyclonal anti-Eset antibody

characteristic: antibody

characteristic: cell line

text: embryonic stem cells

characteristic: cell type

text: unperturbed

characteristic: knockdown

text: Mus musculus

text: embryonic stem cells, unperturbed


text: Genome Institute of Singapore

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: anti-H3K9Me3 antibody

text: embryonic stem cells

text: control

text: Mus musculus

characteristic: organism

text: embryonic stem cells, control shRNA

text: H3K9me3-Control shRNA_ChIPseq

characteristic: title


text: Genome Institute of Singapore

text: live

text: Generic

text: anti-H3K9Me3 antibody

text: embryonic stem cells

text: Eset

text: Mus musculus

text: embryonic stem cells, Eset shRNA

text: H3K9me3-Eset shRNA_ChIPseq


Pinus chloroplast genomes mixed 7

text: live

text: Generic

text: Pinus aristata ARIS02

characteristic: barcode ACGT

text: Pinus albicaulis ALBI05

characteristic: barcode AGCT

text: Pinus ayacahuite AYAC01

characteristic: barcode CCCT

text: Pinus cembra CEMB03

characteristic: barcode CTGT

text: Pinus flexilis FLEX13

text: Pinus peuce PEUC03

characteristic: barcode TACT

characteristic: description

text: Pinus

text: Generic sample from Pinus


Pinus chloroplast genomes mixed 8

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: Pinus wallichiana WALL02

text: Pinus armandii ARMA04

text: Pinus parviflora var. pentaphylla PARV14

text: Pinus sibirica SIBI02

text: Pinus strobus STRO27

characteristic: barcode GGGT

text: Pinus squamata SQUA02

text: Pinus

text: Pinus chloroplast genomes


Pinus chloroplast genomes mixed 9

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

text: Picea sitchensis PICSIT04

characteristic: barcode AATT

text: Pinus torreyana ssp. insularis T0RR03

text: Pinus lambertiana N LAMB08

characteristic: barcode ATT

text: Pinus monticola MONT05

text: Pinus rzedowskii RZED01

text: Pinaceae

text: Generic sample from Pinaceae


Pinus chloroplast genomes mixed 10

text: live

text: Generic

characteristic: NCBI submission package

characteristic: SRA accession

text: Cedrus deodara CEDDEO01

text: Pinaceae

characteristic: organism

text: Generic sample from Pinaceae

characteristic: title


Pinus chloroplast genomes mixed 11

text: live

text: Generic

text: Pinus thunbergii THUN05

characteristic: barcode AAT

text: Pinus lambertiana S LAMB01

characteristic: barcode CCCT

text: Pinus taeda TAED06

characteristic: barcode CGT

text: Pinus

text: Generic sample from Pinus


Pinus chloroplast genomes mixed 12

characteristic: External Id

text: live

text: Generic

text: Pinus nelsonii NELS03

text: Abies firma ABIFIR01

characteristic: barcode AGCT

text: Pinus merkusii MERK04

text: Pinus contorta CONT40

characteristic: barcode CCT

text: Pinus torreyana ssp. torreyana TORR02

characteristic: barcode CTGT

characteristic: description

text: Pinaceae

text: Generic sample from Pinaceae


Pinus chloroplast genomes mixed 13

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: Pinus monticola MONT26E1

characteristic: barcode ATGT

text: Pinus monticola MONT36E2

text: Pinus monticola MONT30E2

characteristic: barcode CGTT

text: Pinus monticola MONT38E1

characteristic: barcode GTAT

text: Pinus monticola MONT49E1

characteristic: barcode TACT

text: Pinus monticola

text: Generic sample from Pinus monticola


Pinus chloroplast genomes mixed 14

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Pinus monticola MONT06E1

characteristic: barcode AACT

text: Pinus monticola MONT07E2

text: Pinus monticola MONT08E1

characteristic: barcode CACT

text: Pinus monticola MONT14E1

characteristic: barcode GGGT

text: Pinus monticola MONT12E1

text: Pinus monticola

characteristic: organism

text: Generic sample from Pinus monticola

characteristic: title


Anopheles dirus, poly-A RNA

characteristic: External Id

characteristic: INSDC center name

text: live

text: Generic

text: Anopheles dirus, poly-A RNA

characteristic: description

text: Anopheles dirus

text: Generic sample from Anopheles dirus


text: Weng, Program in Bioinformatics and Integrative Biology, UMASSMED

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: Oregon R strain

characteristic: genotype

text: Drosophila melanogaster

text: fly heads

text: head

characteristic: tissue

text: Total small RNAs from Oregon R


text: live

characteristic: INSDC status

text: Generic

text: Oregon R strain

text: Drosophila melanogaster

text: fly heads

text: head

text: 2´-O-methylated small RNAs from Oregon R


text: live

text: Generic

characteristic: NCBI submission model

text: Oregon R strain

text: Drosophila melanogaster

text: fly heads

text: head

text: Ago1-associated small RNAs from Oregon R


text: live

text: Generic

characteristic: NCBI submission package

text: CyO-balanced dcr-2^L811fsX mutant strain (described in Lee et al., 2004, Cell 117:69)

text: Drosophila melanogaster

text: fly heads

text: head

text: Total small RNAs from dcr-2 heterozygous flies


text: live

text: Generic

characteristic: SRA accession

text: Drosophila melanogaster

text: fly heads

text: head

text: 2´-O-methylated small RNAs from dcr-2 heterozygous flies


text: live

text: Generic

text: dcr-2^L811fsX mutant strain (described in Lee et al., 2004, Cell 117:69)

text: Drosophila melanogaster

text: fly heads

text: head

text: Total small RNAs from dcr-2 homozygous flies


text: live

text: Generic

text: Drosophila melanogaster

text: fly heads

text: head

text: 2´-O-methylated small RNAs from dcr-2 homozygous flies


text: live

text: Generic

text: CyO-balanced r2d2^1 mutant strain (described in Liu et al., 2006, RNA 12:1514)

text: Drosophila melanogaster

text: fly heads

text: head

text: Total small RNAs from r2d2 heterozygous flies


text: live

text: Generic

text: Drosophila melanogaster

text: fly heads

text: head

text: 2´-O-methylated small RNAs from r2d2 heterozygous flies


text: live

text: Generic

text: r2d2^1 mutant strain (described in Liu et al., 2006, RNA 12:1514)

text: Drosophila melanogaster

text: fly heads

text: head

text: Total small RNAs from r2d2 homozygous flies


text: live

text: Generic

text: Drosophila melanogaster

text: fly heads

text: head

text: 2´-O-methylated small RNAs from r2d2 homozygous flies


Anopheles farauti, poly-A RNA

text: University of Colorado School of Medicine

text: live

text: Generic

text: Anopheles farauti, poly-A RNA

text: Anopheles farauti

text: Generic sample from Anopheles farauti


text: Genetics and Genome Sciences, University of Connecticut Health Center

text: live

text: Generic

characteristic: cell line

text: Drosophila melanogaster


Anopheles freeborni, poly-A RNA

text: live

text: Generic

text: Anopheles freeborni, poly-A RNA

text: Anopheles freeborni

text: Generic sample from Anopheles freeborni


Anopheles quadriannulatus, poly-A RNA

text: live

text: Generic

text: Anopheles quadriannulatus, poly-A RNA

text: Anopheles quadriannulatus

text: Generic sample from Anopheles quadriannulatus


Anopheles quadrimaculatus, poly-A RNA

text: live

text: Generic

text: Anopheles quadrimaculatus, poly-A RNA

text: Anopheles quadrimaculatus

text: Generic sample from Anopheles quadrimaculatus


Anopheles stephensi, poly-A RNA

text: live

text: Generic

text: Anopheles stephensi, poly-A RNA

text: Anopheles stephensi

text: Generic sample from Anopheles stephensi


text: Joint Genome Institute, U.S. Department of Energy

text: live

text: Generic

text: callus

text: Brachypodium distachyon callus

text: tissue culture

characteristic: in vivo conditions

text: standard

characteristic: library description

text: standard

characteristic: library type

text: Brachypodium distachyon

characteristic: strain

text: Generic sample from Brachypodium distachyon


characteristic: External Id

text: live

text: Generic

text: root

text: Brachypodium distachyon diurnally sampled roots

text: 28 days post germination

text: 12:12 light/dark cycles

text: normalized

text: normalized

text: Brachypodium distachyon

characteristic: organism

characteristic: title


characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Generic

text: leaves and stems

text: Brachypodium distachyon diurnally sampled leaves and stems

characteristic: description

text: 28 days post germination

text: 12:12 light/dark cycles

text: normalized

text: normalized

text: Brachypodium distachyon


characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: flower spikes

text: Brachypodium distachyon diurnally sampled flower spikes

text: 12:12 light/dark cycles

text: normalized

text: normalized

text: Brachypodium distachyon


text: live

characteristic: INSDC status

text: Generic

text: callus

text: Brachypodium distachyon callus

text: tissue culture

text: normalized

text: normalized

text: Brachypodium distachyon


text: live

text: Generic

characteristic: NCBI submission model

text: Cochliobolus heterostrophus C5 ESTs

text: normalized 454 library

text: normalized

text: Bipolaris maydis C5

text: Generic sample from Cochliobolus heterostrophus C5


characteristic: Coriell panel

text: ORK

characteristic: Coriell plate

characteristic: DNA id

text: NCBI

text: live

text: Generic

characteristic: NCBI submission package

text: British From England and Scotland, UK

characteristic: Population Description

text: EUR

characteristic: Super Population Code

text: European

characteristic: Super Population Description

characteristic: culture collection

text: Human 1000 genomes individual HG00118

text: Homo sapiens

text: GBR

characteristic: population

text: female

characteristic: sex

text: Coriell HG00118


text: ORK

characteristic: External Id

text: NCBI

characteristic: INSDC center name

text: live

text: Generic

text: British From England and Scotland, UK

characteristic: SRA accession

text: EUR

text: European

text: Human 1000 genomes individual HG00119

text: Homo sapiens

characteristic: organism

text: GBR

text: male

text: Coriell HG00119

characteristic: title


text: ORK

text: NCBI

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: British From England and Scotland, UK

text: EUR

text: European

text: Human 1000 genomes individual HG00121

characteristic: description

text: Homo sapiens

text: GBR

text: female

text: Coriell HG00121


characteristic: Coriell panel

text: ORK

characteristic: Coriell plate

characteristic: DNA id

text: NCBI

text: live

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

text: British From England and Scotland, UK

text: EUR

text: European

text: Human 1000 genomes individual HG00122

text: Homo sapiens

text: GBR

text: female

text: Coriell HG00122


text: ORK

text: NCBI

text: live

text: Generic

text: British From England and Scotland, UK

characteristic: Population Description

text: EUR

characteristic: Super Population Code

text: European

characteristic: Super Population Description

characteristic: culture collection

text: Human 1000 genomes individual HG00123

text: Homo sapiens

text: GBR

characteristic: population

text: female

text: Coriell HG00123