text: University of Calgary

text: live

text: Generic

text: Tailing sample from MLSB tailing pond, M09-16 (central site) 13m below surface, MM13

text: hydrocarbon metagenome

text: Prokaryotic diversity at MLSB location M09-16 (central site) 13m below surface, MM13


status: PUBLIC

characteristic: External Id

text: University of Calgary

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: Tailing sample from MLSB tailing pond, M09-16 (central site) 18m below surface, MM18

characteristic: description

text: hydrocarbon metagenome

characteristic: organism

text: Prokaryotic diversity at MLSB location M09-16 (central site) 18m below surface, MM18

characteristic: title


text: University of Calgary

text: live

text: Generic

text: Tailing sample from MLSB tailing pond, M09-16 (central site) 23m below surface, MM23

text: hydrocarbon metagenome

text: Prokaryotic diversity at MLSB location M09-16 (central site) 23m below surface, MM23


text: University of Calgary

text: live

text: Generic

text: Tailing sample from MLSB tailing pond, M09-16 (central site) 28m below surface, MM28

text: hydrocarbon metagenome

text: Prokaryotic diversity at MLSB location M09-16 (central site) 28m below surface, MM28


text: University of Calgary

text: live

text: Generic

text: Tailing sample from MLSB tailing pond, M09-16 (central site) 33m below surface, MM33

text: hydrocarbon metagenome

text: Prokaryotic diversity at MLSB location M09-16 (central site) 33m below surface, MM33


text: University of Calgary

text: live

text: Generic

text: Tailing sample from MLSB tailing pond, M09-19 (south site) 2.5m below surface, MS2.5

text: hydrocarbon metagenome

text: Prokaryotic diversity at MLSB location M09-19 (south site) 2.5m below surface, MS2.5


text: University of Calgary

text: live

text: Generic

text: Tailing sample from MLSB tailing pond, M09-19 (south site) 7.5m below surface, MS7.5

text: hydrocarbon metagenome

text: Prokaryotic diversity at MLSB location M09-19 (south site) 7.5m below surface, MS7.5


text: University of Calgary

text: live

text: Generic

text: Tailing sample from MLSB tailing pond, M09-19 (south site) 12.5m below surface, MS12.5

text: hydrocarbon metagenome

text: Prokaryotic diversity at MLSB location M09-19 (south site) 12.5m below surface, MS12.5


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

text: live

text: Generic

text: Boechera holboellii

text: Boechera holboellii

text: Panther

tag: attribute

characteristic: strain

text: Generic sample from Boechera holboellii


text: Gydle Inc.

text: live

text: Generic

text: Tissue type: Shoot Apical buds, different development stages, seedlings

text: Picea glauca

text: Picea glauca, growth-related


ILMN-Phloem

text: Gydle Inc.

text: live

text: Generic

text: Tissue type: Stem:Phloem Phloem, seedlings

text: Picea glauca

text: Picea glauca, Phloem


ILMN-Xylem

text: Gydle Inc.

text: live

text: Generic

text: Tissue type: Stem:Xylem Xylem, seedlings

text: Picea glauca

text: Picea glauca, Xylem


text: Gydle Inc.

text: live

text: Generic

text: Phloem, xylem, needles, mature trees

text: Picea glauca

text: Picea glauca, individual F77111


text: Gydle Inc.

text: live

text: Generic

text: Phloem, xylem, needles, mature trees

text: Picea glauca

text: Picea glauca, individual M2388


Pc

text: Ghent University

text: live

text: Generic

text: Pratylenchus coffeae

text: Pratylenchus coffeae mixed stages


Salvelinus fontinalis cDNA

text: Université Laval

text: live

text: Generic

text: Salvelinus fontinalis (brook trout)

text: Salvelinus fontinalis

text: Salvelinus fontinalis cDNA


name: 1127964786849 Staphylococcus aureus IS-K 15K-RLB-RL025-01-669 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-K

text: Staphylococcus epidermidis IS-K

text: IS-K

text: Generic sample from Staphylococcus aureus subsp. aureus IS-K


text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-250

text: Staphylococcus epidermidis IS-250

text: Generic sample from Staphylococcus aureus subsp. aureus IS-250


text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-278

text: Generic sample from Staphylococcus aureus subsp. aureus IS-278


name: 1127981694100 Staphylococcus aureus IS-55 1555-RLB-RL029-01-677 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-55

text: Generic sample from Staphylococcus aureus subsp. aureus IS-55


name: 1127979754140 Staphylococcus aureus IS-3 153-RLB-RL027-01-763 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-3

text: Generic sample from Staphylococcus aureus subsp. aureus IS-3


name: 1128083784021 Staphylococcus aureus IS-88 1588-RLB-RL030-01-743 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-88

text: Generic sample from Staphylococcus aureus subsp. aureus IS-88


name: 1128031164533 Staphylococcus aureus IS-99 1599-RLB-RL032-01-677 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-99

text: Generic sample from Staphylococcus aureus subsp. aureus IS-99


name: 1127985853570 Staphylococcus aureus IS-91 1591-RLB-RL031-01-619 Sample

text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-91

text: Generic sample from Staphylococcus aureus subsp. aureus IS-91


text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-105

text: Generic sample from Staphylococcus aureus subsp. aureus IS-105


text: J. Craig Venter Institute

text: live

text: IRQ

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-111

text: Staphylococcus

characteristic: genus

characteristic: isolate

text: Wound

text: skin or soft tissue

text: Generic sample from Staphylococcus aureus subsp. aureus IS-111

type: AMR curated data - CABBAGE

value: gentamicin

value: CLSI

value: susceptible

value: Staphylococcus aureus

value: vancomycin

value: trimethoprim-sulfamethoxazole

value: ciprofloxacin

value: intermediate

value: rifampin

value: clindamycin

value: amoxicillin-clavulanic acid

value: resistant

value: oxacillin

value: erythromycin

value: ofloxacin

value: chloramphenicol

value: cephalothin

value: ampicillin

value: tetracycline


text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-122

text: Generic sample from Staphylococcus aureus subsp. aureus IS-122


text: J. Craig Venter Institute

text: live

text: IRQ

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-160

text: Staphylococcus

text: Wound

text: skin or soft tissue

text: Generic sample from Staphylococcus aureus subsp. aureus IS-160

value: susceptible

value: CLSI

value: gentamicin


name: 1128056951519 Staphylococcus aureus IS-M 15M-RLB-RL026-01-659 Sample

text: J. Craig Venter Institute

text: live

text: IRQ

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-M

text: Staphylococcus

text: IS-M

text: Blood

text: blood

text: IS-M

text: Generic sample from Staphylococcus aureus subsp. aureus IS-M

value: Staphylococcus aureus

value: trimethoprim-sulfamethoxazole

value: vancomycin


FGSC 5914

text: UC Berkeley

text: live

text: Generic

text: FGSC 5914/JW57

text: Neurospora crassa

text: FGSC 5914


FGSC 3200

text: UC Berkeley

text: live

text: Generic

text: FGSC 3200/JW59

text: Neurospora crassa

text: FGSC 3200


text: J. Craig Venter Institute

text: live

text: Generic

text: Total DNA isolated from Staphylococcus aureus IS-157

text: Generic sample from Staphylococcus aureus subsp. aureus IS-157


FGSC 3211

text: UC Berkeley

text: live

text: Generic

text: FGSC 3211/JW66

text: Neurospora crassa

text: FGSC 3211


FGSC 3199

text: UC Berkeley

text: live

text: Generic

text: FGSC 3199/JW70

text: Neurospora crassa

text: FGSC 3199


FGSC 3943

text: UC Berkeley

text: live

text: Generic

text: FGSC 3943/JW75

text: Neurospora crassa

text: FGSC 3943


FGSC 6203

text: UC Berkeley

text: live

text: Generic

text: FGSC 6203/JW77

text: Neurospora crassa

text: FGSC 6203


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome


Soilgene Pampa

text: INDEAR

text: live

text: Generic

text: Soil samples were collected from three different agricultural sites of La Pampa Ondulada region in Buenos Aires, Argentina. Sites are called: La Estrella (le),La Negrita(ln) and Criadero Klein (ck). For each site two types of soil were sampled: no- till farming (Agro or A) and undisturbed (No Agro or N). Three no-till farming sites and three nearby undisturbed sites were multiplexed in the following way: (sample, MID) leAV4, ACGAGTGCGT; leNV4, ACGCTCGACA; lnAV4, AGACGCACTC; lnNV4, AGCACTGTAG; ckAV4, ATCAGACACG; ckNV4, ATATCGCGAG. References: le, La estrella; A, agro; N, no agro(undisturbed) ln, La Negrita; A, agro, N, no agro ck, Criadero Klein; A, agro; N, no agro

text: soil metagenome

text: microbial diversity of Argentinian soils as revealed by 16sRNA pyrosequencing


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_002_003_001_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_001_003_001_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_003_003_001_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_002_003_002_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_001_003_002_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_003_003_002_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_002_003_003_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_001_003_003_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_001_002_ME_003_003_003_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_002_003_001_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_001_003_001_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_003_003_001_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_002_003_002_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_001_003_002_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_003_003_002_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_002_003_003_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_001_003_003_020210


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: KB_TR_CB_CT_002_002_ME_003_003_003_020210


Toluene-degrading culture

text: University of Calgary - Sun Center of Excellence for Visual Genomics

text: live

text: Generic

text: Methanogenic consortium that biodegrades toluene enriched from a gas condensate-contaminated aquifer near Ft. Lupton, Colorado. Aquifer sediments from the site were added to an anaerobic mineral salts medium and amended with toluene. Multiple transfers yielded a sediment-free enrichment culture that is maintained by transfers every 2 to 4 months.

text: hydrocarbon metagenome

text: Methanogenic Hydrocarbon-Degrading Enrichment Cultures


text: live

text: Generic

text: Methanogenic consortium not amended with a carbon source that serves as a background control for methanogenesis from naphthalene substrates. The unamended culture was initially derived from a gas condensate-contaminated aquifer near Ft. Lupton, Colorado. Aquifer sediments from the site were added to an anaerobic mineral salts medium and multiple transfers yielded a sediment-free culture. The unamended culture was initially incubated with 2-methylnaphthalene but was transferred without substrate to serve as an unamended control.

text: hydrocarbon metagenome


text: live

text: Generic

text: Methanogenic consortium that biodegrades 2,6-dimethyl naphthalene enriched from a gas condensate-contaminated aquifer near Ft. Lupton, Colorado. Aquifer sediments from the site were added to an anaerobic mineral salts medium without electron acceptors and amended with 2,6-dimethylnaphthalene. Multiple transfers yielded a sediment-free enrichment culture that is maintained by transfers every 2 to 4 months.

text: hydrocarbon metagenome


text: live

text: Generic

text: Methanogenic consortium that biodegrades 2-methyl naphthalene enriched from a gas condensate-contaminated aquifer near Ft. Lupton, Colorado. Aquifer sediments from the site were added to an anaerobic mineral salts medium without electron acceptors and amended with 2-methylnaphthalene. Multiple transfers yielded a sediment-free enrichment culture that is maintained by transfers every 2 to 4 months.

text: hydrocarbon metagenome


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

text: live

text: Generic

text: Salix purpurea L

text: Salix purpurea

characteristic: sample number

text: L

text: Salix purpurea strain L


text: Research Institute of Physico-Chemical Medicine

text: live

text: Generic

text: Sample was prepared from the frontal part of the superior frontal gyrus of postmortem brains of 5 humans (from 88 to 98 years, 4 males and 1 females) by pooling equal quantities of total RNA. Samples were obtained from the NICHD Brain and Tissue Bank for Developmental Disorders at the University of Maryland, USA, the Netherlands Brain Bank, Amsterdam, Netherlands and the Chinese Brain Bank Center, Wuhan, China. Informed consent for use of human tissues for research was obtained in writing from all donors or from their next of kin. All subjects were defined as normal by forensic pathologists at the corresponding brain bank. All subjects suffered sudden death with no prolonged agonal state. All samples contained an approximately 2:1 gray matter to white matter volume ratio.

text: Homo sapiens

text: hs, 76nt, s7, ctx


text: live

text: Generic

text: Thalassiosira pseudonana TAG accumulation

text: Thalassiosira pseudonana

text: TAG accumulation

text: Generic sample from Thalassiosira pseudonana


text: Baylor College of Medicine

text: live

text: MIGS.ba

text: Newbler v. 2.3-10192009

characteristic: assembly

text: terrestrial biome [ENVO:00000446]

characteristic: biome

text: not determined

characteristic: collection date

characteristic: culture-collection

text: Streptococcus pyogenes strain ATCC 10782

characteristic: estimated size

text: Homo sapiens-associated habitat [ENVO:00009003]

characteristic: feature

text: Level 2: High-Quality Draft33x;90

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: Nasal

characteristic: misc_param: HMP body site

text: airways

characteristic: misc_param: HMP supersite

text: not determined

characteristic: nucleic acid extraction

text: not determined

text: Streptococcus pyogenes ATCC 10782

text: Streptococcus pyogenes ATCC 10782

characteristic: project name

text: Reference Genome

text: not determined

characteristic: sequencing method

characteristic: sop

text: ATCC 10782, CIP 56.61

text: Homo sapiens

characteristic: specific host

text: ATCC 10782

text: MIGS Cultured Bacterial/Archaeal sample from Streptococcus pyogenes ATCC 10782


characteristic: External Id

text: Baylor College of Medicine

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: MIGS.ba

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Newbler v. 2.0-01162009

characteristic: assembly

text: terrestrial biome [ENVO:00000446]

characteristic: biome

text: not determined

text: Mycobacterium parascrofulaceum strain ATCC BAA-614

characteristic: description

text: Level 2: High-Quality Draft52.9x;405

text: not determined

text: not determined

text: not determined

text: biological product [ENVO:02000043]

text: Vaginal

text: not determined

text: not determined

characteristic: organism

text: Reference Genome

text: not determined

text: ATCC BAA-614

text: Homo sapiens

text: ATCC BAA-614

characteristic: strain

text: MIGS Cultured Bacterial/Archaeal sample from Mycobacterium parascrofulaceum ATCC BAA-614

characteristic: title


Perkins 4450

text: UC Berkeley

text: live

text: Generic

text: Perkins 4450

text: Neurospora crassa

text: Perkins 4450


Perkins 4452

text: UC Berkeley

text: live

text: Generic

text: Perkins 4452

text: Neurospora crassa

text: Perkins 4452


Perkins 4455

text: UC Berkeley

text: live

text: Generic

text: Perkins 4455

text: Neurospora crassa

text: Perkins 4455


text: NIAAA/NIH

text: live

text: Generic

text: Macaca mulatta

text: Peer-reared K42


Perkins 4465

text: UC Berkeley

text: live

text: Generic

text: Perkins 4465

text: Neurospora crassa

text: Perkins 4465


Perkins 4476

text: UC Berkeley

text: live

text: Generic

text: Perkins 4476

text: Neurospora crassa

text: Perkins 4476


Perkins 4496

text: UC Berkeley

text: live

text: Generic

text: Perkins 4496

text: Neurospora crassa

text: Perkins 4496


pampa v4 timepoints

text: INDEAR

text: live

text: Generic

text: default sample

text: soil metagenome

text: Default Sample - Dynamical changes of soil microbiota during a one-year period timeframe and crop rotation under No Till farming


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: LnCaP Cell Line - Androgen Time Course Study 0h Timepoint (AS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: LnCaP Cell Line - Androgen Time Course Study 24h Timepoint (AS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: LnCaP Cell Line - Androgen Time Course Study 48h Timepoint (AS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: LnCaP Cell Line - Androgen Time Course Study 0h Timepoint (SMS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: LnCaP Cell Line - Androgen Time Course Study 24h Timepoint (SMS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: LnCaP Cell Line - Androgen Time Course Study 48h Timepoint (SMS)


PrCa-AdjNorm

text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: Prostate cancer adjacent normal matched tissue sample


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: VCaP Cell Line - Androgen Time Course Study 0h Timepoint (AS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: VCaP Cell Line - Androgen Time Course Study 24h Timepoint (AS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: VCaP Cell Line - Androgen Time Course Study 48h Timepoint (AS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: VCaP Cell Line - Androgen Time Course Study 0h Timepoint (SMS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: VCaP Cell Line - Androgen Time Course Study 24h Timepoint (SMS)


text: University of Michigan

text: live

text: Generic

text: Homo sapiens

text: VCaP Cell Line - Androgen Time Course Study 48h Timepoint (SMS)


text: Huazhong Agricultural University

text: live

text: Generic

text: nymphs of third and fourth instar

characteristic: dev-stage

text: rice varieties of TN1

characteristic: lab-host

text: Nilaparvata lugens

text: Nilaparvata lugens normalised-cDNA-library


characteristic: External Id

text: Kunming University of Science and Technology

text: live

text: Generic

characteristic: cultivar

text: exposed to Al solution for 12h,24h,48h,72h respectively

text: E. coli DH5alpha

text: Vicia faba

text: leaves

characteristic: tissue-type

text: Leaves Supression Substractive Hybridization cDNA Library of Yunnan Broadbeans 83324

text: pGEM-T Easy Vector

characteristic: vector


text: National Institute of Health

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: live

text: Generic

text: plerocercoid larva

text: Spirometra erinaceieuropaei

text: whole body

text: whole body worms (Spirometra erinacei) library


text: Universidad de los Andes

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

text: Different sexual and apomictic cultivars

text: Three different subtractive hybridization methods were used: Subtractive suppression hybridization (Diatchenko et al., 1996), mirror orientation selection (Rebrikov et al., 2000) and differential subtraction chain (DSC) (Luo et al., 1999). In each method, the apomictic and sexual cDNA bulks were used both as tester and driver, in order to isolate the cDNA sequences found only in the apomictic or only in the sexual cDNA bulk. The subtracted cDNA ultimately obtained with each method was used to construct subtractive libraries of 384 clones each.

text: Embryo sac formation

text: Ovaries

characteristic: organ

text: Urochloa brizantha/decumbens/ruziziensis mixed EST library

text: Sexual and apomictic cultivars

characteristic: sex

text: Substractive libraries from Brachiaria hybrid cultivar apomictic and sexual ovaries

text: Plasmid


text: DOE Joint Genome Institute

text: live

text: Generic

text: The library was made from oligo(dT) primed cDNA and cloned into the pCMV-SPORT6 vector (Invitrogen Corp., Carlsbad, CA). PolyA RNA was primed with an oligo dT primer (5'-GACTAGTTCTAGATCGCGAGCGGCCGCCCTTTTTTTTTTTTTTT-3'), ligated to a SalI adapter (5'-TCGACCCACGCGTCCG and 5'- CGGACGCGTGGG) and digested with NotI. cDNA was size selected from 0.6-2kb using 1.1% agarose gel electrophoresis then ligated into NotI and SalI-digested pCMV-SPORT6 vector. The library was constructed and sequencing performed at the DOE Joint Genome Institute (Walnut Creek, CA).

characteristic: description

text: Pleurotus ostreatus

characteristic: organism

text: SalI

text: NotI

text: N001 and PC9

text: vegetative mycelia

text: CCFC Pleurotus ostreatus N001 and PC9 vegetative mycelia (L)


text: DOE Joint Genome Institute

text: live

text: Generic

text: The library was made from oligo(dT) primed cDNA and cloned into the pCMV-SPORT6 vector (Invitrogen Corp., Carlsbad, CA). PolyA RNA was primed with an oligo dT primer (5'-GACTAGTTCTAGATCGCGAGCGGCCGCCCTTTTTTTTTTTTTTT-3'), ligated to a SalI adapter (5'-TCGACCCACGCGTCCG and 5'- CGGACGCGTGGG) and digested with NotI. cDNA was size selected >2kb using 1.1% agarose gel electrophoresis then ligated into NotI and SalI-digested pCMV-SPORT6 vector. The library was constructed and sequencing performed at the DOE Joint Genome Institute (Walnut Creek, CA).

text: Pleurotus ostreatus

text: SalI

text: NotI

text: N001 and PC9

characteristic: strain

text: vegetative mycelia

text: CCFF Pleurotus ostreatus N001 and PC9 vegetative mycelia (H)

characteristic: title


text: DOE Joint Genome Institute

text: live

text: Generic

characteristic: lab-host

text: Pleurotus ostreatus

text: SalI

text: NotI

text: fruit bodies

text: CCFG Pleurotus ostreatus N001 fruit bodies (H)


characteristic: External Id

text: DOE Joint Genome Institute

text: live

text: Generic

text: Pleurotus ostreatus

text: SalI

text: NotI

text: fruit bodies

text: CCFH Pleurotus ostreatus N001 fruit bodies (L)


text: DOE Joint Genome Institute

text: live

text: Generic

text: DH10B T1-resistant

text: Wrightia tinctoria

text: SalI

text: NotI

text: developing embryos

text: CCPN Wrightia tinctoria developing embryos (L)


text: DOE Joint Genome Institute

text: live

text: Generic

text: DH10B T1-resistant

text: Wrightia tinctoria

text: SalI

text: NotI

text: developing embryos

text: CCPO Wrightia tinctoria developing embryos (H)


Common bean RNA

text: University of Illinois at Urbana-Champaign

characteristic: INSDC secondary accession

text: live

text: Generic

characteristic: SRA accession

text: Venu Kalavacharla, Zhanji Liu, Blake C Meyers, Jyothi Thimmapuram and Kalpalatha Melmaiee. 2011. Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biology, 11:135

text: Phaseolus vulgaris var. nanus

text: Common bean transcriptome


text: University of Calgary

text: live

text: Generic

text: Sample was obtained from a core sample drilled at a Northern Alberta reservoir in February 2008. The core sample represented from 595 to 625 metres below surface. Subsamples were collected from this core by taking 4 cm sections from selected depths. Material for use in DNA extraction was scrapred from the center area of the 4cm subsample. DNA was extracted from 1-2 g of this scraped material using the MP Biomedicals FastDNA Spin Kit for Soil. 2 rounds of PCR were used, one with universal non-bar coded primers and the second round with titanium amplicon primers, to generate amplicons from the obtained DNA.

text: hydrocarbon metagenome


text: University of Calgary

text: live

text: Generic

text: hydrocarbon metagenome

text: Microbial community variations within defined zones of an oil sand reservoir.


name: PRJNA172065.Anopheles gambiae 18 male testes

text: Broad Institute

text: live

text: Generic

text: mosquito metagenome

text: Anopheles gambiae 18 male testes

characteristic: sample name

text: Generic sample from mosquito metagenome


text: Broad Institute

characteristic: INSDC center name

text: live

text: Generic

characteristic: collection date

text: Atlantic: W Sargasso Sea

text: DNA:ds Viral DNA

characteristic: isolation source

text: mixed DNA library

text: Synechococcus sp.

characteristic: specific host

text: Generic sample from mixed DNA library


name: PRJNA172065.Anopheles gambiae 19 female gut

text: Broad Institute

characteristic: INSDC first public

characteristic: INSDC last update

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

text: mosquito metagenome

text: Anopheles gambiae 19 female gut

text: Generic sample from mosquito metagenome


PRJNA47891.phi SM

text: Broad Institute

text: live

text: Generic

characteristic: NCBI submission package

text: Atlantic: Baltic Sea

text: DNA:ds Viral DNA

text: Cellulophaga phage phiSM

text: phi SM

text: Uncultured virus

text: phiSM

text: Generic sample from Cellulophaga phage phiSM


PRJNA47441.CAR 9

text: Broad Institute

text: live

text: Generic

text: Caroline Island site 9

text: DNA:ds Viral DNA

text: marine metagenome

characteristic: organism

text: CAR 9

text: Uncultured virus

text: Caroline Island site 9

text: Generic sample from marine metagenome


PRJNA47441.CAR wreck

text: Broad Institute

text: live

text: Generic

text: Caroline Island wreck

text: DNA:ds Viral DNA

text: marine metagenome

text: CAR wreck

text: Uncultured virus

text: Caroline Island wreck

characteristic: strain

text: Generic sample from marine metagenome


PRJNA47441.CAR 12

text: Broad Institute

text: live

text: Generic

text: Caroline Island site 12

text: DNA:ds Viral DNA

text: marine metagenome

text: CAR 12

text: Uncultured virus

text: Caroline Island site 12

text: Generic sample from marine metagenome

characteristic: title


text: Broad Institute

text: live

text: Generic

text: Gulf of Mexico

text: DNA:ds Viral DNA

text: marine metagenome

text: Uncultured virus

text: GOMss Achan-JL2

text: Generic sample from marine metagenome


text: Broad Institute

text: live

text: Generic

text: Saanich Inlet

text: DNA:ds Viral DNA

text: marine metagenome

text: Uncultured virus

text: Saanich Achan-JL3

text: Generic sample from marine metagenome


PRJNA47443.shark Caroline

text: Broad Institute

text: live

text: Generic

text: shark skin Caroline Island

text: DNA:ds Viral DNA

text: gut metagenome

text: shark Caroline

text: Uncultured virus

text: shark skin Caroline Island

text: Generic sample from gut metagenome


PRJNA47443.shark Malden

text: Broad Institute

text: live

text: Generic

text: shark skin Malden Island

text: DNA:ds Viral DNA

text: gut metagenome

text: shark Malden

text: Uncultured virus

text: shark skin Malden Island

text: Generic sample from gut metagenome


text: Broad Institute

text: live

text: Generic

text: Estuary

text: DNA:ds Viral DNA

text: marine metagenome

text: Uncultured virus

text: Generic sample from marine metagenome


text: Broad Institute

text: live

text: Generic

text: Canada

text: unspecified

text: Colwellia phage 9A

text: unknown Unknown Species

text: Generic sample from Colwellia phage 9A


text: Broad Institute

text: live

text: Generic

text: HSV1 (grown on vero cells)

text: Human alphaherpesvirus 1 strain KOS

text: Generic sample from Human herpesvirus 1 strain KOS


PRJNA47563.cyanophage S-CBP4

text: Broad Institute

text: live

text: Generic

text: Chesapeake Bay

text: DNA:ds Viral DNA

text: Synechococcus phage S-CBP4

text: cyanophage S-CBP4

text: Uncultured virus

text: Generic sample from Synechococcus phage S-CBP4


text: Broad Institute

text: live

text: Generic

text: Pacific

text: DNA:ds Viral DNA

text: Vibrio phage SIO-2

text: Uncultured virus

text: Generic sample from Vibrio phage SIO-2


PRJNA39215.12A4 A1

text: Broad Institute

text: live

text: Generic

text: Atlantic:Ipswich Bay

text: Vibrio phage douglas 12A4

text: 12A4 A1

text: Generic sample from Vibrio phage douglas 12A4


PRJNA39217.12B3 A1

text: Broad Institute

text: live

text: Generic

text: Atlantic:Ipswich Bay

text: Vibrio phage helene 12B3

text: 12B3 A1

text: Generic sample from Vibrio phage helene 12B3


PRJNA40641.12B8 A1

text: Broad Institute

text: live

text: Generic

text: Atlantic:Ipswich Bay

text: Vibrio phage henriette 12B8

text: 12B8 A1

text: Generic sample from Vibrio phage henriette 12B8


PRJNA53545.12G5 C1

text: Broad Institute

text: live

text: Generic

text: Atlantic:Ipswich Bay

text: Vibrio phage jenny 12G5

text: 12G5 C1

text: Generic sample from Vibrio phage jenny 12G5


PRJNA39219.12B12 A2

text: Broad Institute

text: live

text: Generic

text: Atlantic:Ipswich Bay

text: Vibrio phage martha 12B12

text: 12B12 A2

text: Generic sample from Vibrio phage martha 12B12


text: head

characteristic: BODYSITES

text: adult

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

text: live

text: Generic

text: Dendroctonus frontalis heads, normalized

characteristic: description

text: females and males emerged from brood tree and unfed; females fed in host tree 24-48 h; fed alone in new host tree, followed by pairing with a mate for an additional 24 h. Males fed with mates for 24 h

characteristic: in vivo conditions

text: normalized

characteristic: library description

text: normalized

characteristic: library type

text: Dendroctonus frontalis

text: pooled

characteristic: sex

text: Generic sample from Dendroctonus frontalis


text: whole bodies

text: larvae and pupae

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC secondary accession

text: live

text: Generic

characteristic: SRA accession

text: Dendroctonus frontalis larvae and pupae, normalized

text: normalized

text: normalized

text: Dendroctonus frontalis

text: pooled


text: whole bodies

text: teneral (pre-emerged) adults

characteristic: INSDC first public

characteristic: INSDC last update

text: live

text: Generic

text: Dendroctonus frontalis teneral adults, normalized

text: normalized

text: normalized

text: Dendroctonus frontalis

text: pooled


text: thorax

text: adult

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

text: Dendroctonus frontalis thoraces, normalized

text: unfed (emerged from brood tree), females fed alone (24 h), or with males (24 h; 48 h total feeding time); males fed with females (24 h)

text: normalized

text: normalized

text: Dendroctonus frontalis

text: pooled


text: abdomen

text: adult

text: live

text: Generic

characteristic: NCBI submission package

text: Dendroctonus frontalis abdomens, normalized

text: normalized

text: normalized

text: Dendroctonus frontalis

characteristic: organism

text: pooled


text: University of Calgary

text: live

text: Generic

text: Water samples from different oil and gas company sites were sampled and sent with the objective of microbial community analysis using 16S pyrotag sequencing.

text: hydrocarbon metagenome

text: Microbial diversity analysis of water samples from various hydrocarbon resource environments using next-generation 16S pyrosequencing

characteristic: title


text: University of Calgary

text: live

text: Generic

text: The energy industry is becoming increasingly aware that microorganisms present in the source water in a SWIS facility can influence the overall quality of the seawater treated in the facility and affect other downstream processes. An oil and gas industry's seawater injection treatment facilities at the Alaska site, regularly transports seawater from the Arctic Ocean through their seawater treatment plants. The overall chemistry of the water flowing through the pipeline is similar to that of the untreated seawater. As a part of a routine baseline quality analysis of the seawater flowing through this SWIS, seawater samples were collected, DNA extracted using Marmur's method and pyrosequenced for 16S rDNA. Successful pyrosequencing generated 48,681 good reads that were taxonomically assigned to phylum, class and genus level of classification of the identified microorganism from the seawater samples. Based on the pyrosequencing results, overall microbial community composition within the seawater treatment facility was similar to that of the microbial communities commonly found in marine and seawater environment. In addition, a higher percentage of SRB Desulfovibrio was observed in the pipeline associated biofilm samples from seawater passing through the pigging facilities.

text: hydrocarbon metagenome


text: University of Calgary

text: live

text: Generic

text: Samples from a oil and gas company's seawater Injection system were sent with the objective of 16S pyrosequencing. Six seawater samples were filtered on-site and the filter paper was fixed with particular fixative and dried. Similarly, three seawater samples from crude pipeline were also filtered on-site, filter paper fixed with fixative and dried. Each of the nine fixed filter papers were transferred in a 2 ml Eppendorf tube immersed in 1.5 ml filtrate and sent for 16S pyrosequencing. Samples # 1, 2, 3, 4, 5 and 6 were seawater samples, while samples # 7A, 7B and 8 were seawater samples from crude pipeline (as mentioned with the document included with the samples). On receiving the samples, the Eppendorf tubes were strongly vortexed to get all the biomass into the solution (seawater filtrate). This was repeated 2-3 times to be sure that all the biomass could be recovered from the fixed filter paper. Next, the tubes were centrifuged at 17,000 x g for 10 minutes. The supernatant was discarded and the cell pellet was frozen at -70* till DNA extraction.

text: hydrocarbon metagenome

text: Microbial diversity analysis of seawater samples from SWIS environments using next-generation 16S pyrosequencing


text: University of Calgary

text: live

text: Generic

text: Samples from a oil and gas company's seawater Injection system were sent with the objective of 16S pyrosequencing. Six seawater samples were filtered on-site and the filter paper was fixed with particular fixative and dried. Similarly, three seawater samples from crude pipeline were also filtered on-site, filter paper fixed with fixative and dried. Each of the nine fixed filter papers were transferred in a 2 ml Eppendorf tube immersed in 1.5 ml filtrate and sent for 16S pyrosequencing. Samples # 1, 2, 3, 4, 5 and 6 were seawater samples, while samples # 7A, 7B and 8 were seawater samples from crude pipeline (as mentioned with the document included with the samples). On receiving the samples, the Eppendorf tubes were strongly vortexed to get all the biomass into the solution (seawater filtrate). This was repeated 2-3 times to be sure that all the biomass could be recovered from the fixed filter paper. Next, the tubes were centrifuged at 17,000 x g for 10 minutes. The supernatant was discarded and the cell pellet was frozen at -70° till DNA extraction.

text: hydrocarbon metagenome


text: University of Calgary

text: live

text: Generic

text: Pipelines at a Foster Creek site, transporting water from the Grand Rapids and the McMurray formation to the steam-generating facility, are subject to frequent corrosion failures. In the current experiment, the microbial community composition, determined with state-of-the-art DNA sequencing technology, is determined for transported water samples, collected mainly prior to the SBS injection point, and for pipe-associated solids (PAS) scraped from the walls of pipe cutouts and collected upstream , and downstream of the SBS injection point. Genomic DNA was isolated using a procedure modified from that of Marmur method. Some water samples were processed without bead-beating , while all the other samples were processed with bead-beating . The transported water had a large fraction of Pseudomonas (46%), not found in the pipe samples, demonstrating that the planktonic (=water) and sessile (=PAS) populations were distinct. Methanogens and acetogens ranked 2nd and 3rd in the planktonic population at 10.5 and 1.4%, respectively. SRB were relatively rare. Upstream PAS had methanogens as the main community component (54%), followed by Desulfuromonas (10.6%) and acetogens (2.4%). The most prevalent SRB was present at 0.1%. The microbial community in downstream PAS was dominated by SRB of the genus Desulfomicrobium (36.3%), Desulfocapsa (24%) and Desulfurivibrio (3.7%). Methanogens and acetogens were at 0.4 and 0.3%, respectively, whereas the community at PAS downstream was once again dominated by methanogens (39%), followed by SRB of the genera Desulfocapsa (33%) and Desulfomicrobium (19%). The results indicate that the pipeline-associated sessile microbial community is strongly influenced by SBS injection, leading to a shift in microbial community from methanogens (upstream PAS) to SRB (downstream PAS).

text: hydrocarbon metagenome

text: Microbial diversity analysis of pipe-associated water (PAW) and pipe-associated solid (PAS) samples from hydrocarbon resource environments using next-generation 16S pyrosequencing


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

text: live

text: Generic

text: Chlamydomonas reinhardtii cc124

text: Chlamydomonas reinhardtii

characteristic: sample number

characteristic: strain

text: Generic sample from Chlamydomonas reinhardtii


text: live

text: Generic

text: Escherichia coli K-12

characteristic: description

text: Generic sample from Escherichia coli str. K-12 substr. MG1655


text: live

text: Generic

text: Mimulus guttatus DUN + IM62

text: Erythranthe guttata

text: DUN + IM62

text: Generic sample from Mimulus guttatus


text: live

text: Generic

text: Escherichia coli K-12

text: Escherichia coli str. K-12 substr. MG1655


text: live

text: Generic

text: Turneriella parva DSM 21527

text: Turneriella parva DSM 21527

text: DSM 21527

text: Generic sample from Turneriella parva DSM 21527


text: live

text: Generic

text: Planctomyces brasiliensis DSM 5305

text: Rubinisphaera brasiliensis DSM 5305

text: DSM 5305

text: Generic sample from Planctomyces brasiliensis DSM 5305


text: live

text: Generic

text: Chlamydomonas reinhardtii

text: Chlamydomonas reinhardtii


text: live

text: Generic

text: Streptomyces sp. MPBF4-2a

text: Streptomyces sp. MPBF4-2a

text: Generic sample from Streptomyces sp. MPBF4-2a


text: live

text: Generic

text: Setaria viridis PI 204625

text: Setaria viridis

text: PI 204625

text: Generic sample from Setaria viridis


text: University of Calgary

text: live

text: Generic

text: The microbial diversity in tailings pond hydrocarbon- and long-chain fatty acid degrading population was assessed using a barcoded 16S amplicon approach. Sample preparation with tailings pond samples were performed using sodium pyrophosphate buffer in certain samples to isolated large-sclae of DNA. DNA was isolated either using FastDNA Soil kit or Marmur's method without bead-beating. Little is known about the syntrophic organisms that initially attack hydrocarbons under methanogenic conditions, so this assessment will identify the key microbial players involved in methanogenic decomposition of hydrocarbons and related hydrocarbon compounds.

text: hydrocarbon metagenome

text: Time-dependent variation in the anaerobic microbial community structure of an Alberta Oil Sands Tailings Pond as determined by 16S pyrosequencing


text: University of Calgary

text: live

text: Generic

text: In the current study, we evaluated the effect of anaerobic storage (90% N2, 10% CO2) on the microbial population from this same active tailings pond. DNA was isolated from selected depths from tailings samples stored under anaerobic conditions for 1.5 years. Analysis of 16S genes by pyrosequencing indicated an increase in fermentative bacteria capable of reducing nitrate (Delftia, Acidovorax, Thauera, Pseudomonas) at most of the depths along with a high abundance of methanogens (Methanosaeta, Methanobacterium, Methanolobus) at a depth of 18 m below the surface. No syntrophs or SRB were detected. UniFrac clustering analysis indicated this community profile to be similar to that of another tailings pond that no longer receives input of fresh tailings. The results indicate that tailings pond microbial communities are dynamic and change rapidly when input of fresh tailings and/or gypsum are stopped.

text: hydrocarbon metagenome


text: live

text: Generic

text: Shewanella baltica OS117

text: Shewanella baltica OS117

text: Generic sample from Shewanella baltica OS117


text: live

text: Generic

text: Streptomyces violaceusniger Tu 4113

text: Streptomyces violaceusniger Tu 4113

text: Tu 4113

text: Generic sample from Streptomyces violaceusniger Tu 4113


text: live

text: Generic

text: Niabella soli DSM 19437

text: Niabella soli DSM 19437

text: DSM 19437

text: Generic sample from Niabella soli DSM 19437


text: University of Calgary

text: live

text: Generic

text: A sediment sample from tailings pond 5A operated by Suncor was collected in July 2009 from a depth of 1.5 ft below the surface. The sample jar was filled to the lid to limit oxygen diffusion. The sample was transported to the University of Calgary and stored under anaerobic conditions without hydrogen (90% N2, 10%CO2) at room temperature. The inoculum that seeded all biofilms was tailings sludge (loosely packed sediments). The tailings sludge sample was diluted 2 fold with sterile double distilled water to serve as the inoculum for all biofilms. Biofilms were grown on the Calgary Biofilm Device (CBD). Wells were replenished with fresh growth medium every 24 and 48 hours for aerobic and anaerobic growth respectively. Anaerobic biofilms were grown under atmospheric conditions of 90%N2 and 10% CO2/H2 mix. Microaerobic biofilms were grown in a candle jar and replenished with fresh growth medium every 72 hours. Total genomic DNA was extracted from 250 mg of the starting sludge inoculum. DNA from biofilms was extracted using 2 biofilm pegs per extraction and an isolation kit optimized for the type of sample. DNA was extracted using MO Bio Power Soil™ DNA isolation kit (Carlsbad CA) for aerobic and microaerobic biofilm samples and the MP Bio Soil DNA Extraction™ kit (Solon, OH) with bead beating step for anaerobic biofilms and the sludge inoculum.

text: hydrocarbon metagenome

text: Identification of microbial communities directly from an Alberta oil sands tailings pond using an in vitro mixed species biofilm dvice and pyrosequencing.


text: live

text: Generic

text: Phaseolus vulgaris G19833

text: Phaseolus vulgaris

text: Generic sample from Phaseolus vulgaris


text: live

text: Generic

text: Leptotrichia goodfellowii DSM 19756

text: Pseudoleptotrichia goodfellowii DSM 19756

text: DSM 19756

text: Generic sample from Leptotrichia goodfellowii DSM 19756

text: type strain of Leptotrichia goodfellowii

characteristic: type material


text: DOE-GEBA 2009

characteristic: Funding Program

characteristic: GOLD Stamp ID

text: Prodigal 1.4, GenePRIMP

characteristic: Gene Calling Method

text: Gram-

characteristic: Gram Staining

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

text: live

text: Generic

text: Yes

characteristic: Type Strain

text: free living

characteristic: biotic relationship

text: Rod-shaped

characteristic: cell shape

text: Keywords: GSC:MIGS:2.1

characteristic: investigation type

text: surfaces of algal species from the Antarctic marine coast and sea ice

characteristic: isolation site

text: surfaces of algal species from Antarctic marine coast and sea ice

characteristic: isolation-source

text: Motile

characteristic: motility

text: Cellulophaga algicola DSM 14237

characteristic: ph

text: Cellulophaga algicola IC166, DSM 14237

characteristic: project name

text: DSM 14237, ACAM 630

text: aerobe

text: DSM 14237

text: Mesophile

characteristic: temperature range

text: Cellulophaga algicola DSM 14237, complete genome.

text: chemoheterotroph

text: type strain of Cellulophaga algicola


characteristic: External Id

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: Bacteroides helcogenes P 36-108

text: Bacteroides helcogenes P 36-108

characteristic: organism

characteristic: sample number

text: P 36-108

characteristic: strain

text: Generic sample from Bacteroides helcogenes P 36-108

characteristic: title


text: live

text: Generic

text: Nostoc azollae 0708

characteristic: description

text: 'Nostoc azollae' 0708

text: Generic sample from 'Nostoc azollae' 0708


text: live

text: Generic

text: Oryzias latipes

text: Oryzias latipes

text: Generic sample from Oryzias latipes


text: live

text: Generic

text: Shewanella amazonensis SB2B

text: Shewanella amazonensis SB2B

text: Generic sample from Shewanella amazonensis SB2B


text: live

text: Generic

text: Generic sample from Mesorhizobium ciceri biovar biserrulae WSM1271


text: live

text: Generic

text: Asticcacaulis excentricus CB 48

text: Asticcacaulis excentricus CB 48

text: CB 48

text: Generic sample from Asticcacaulis excentricus CB 48


text: Agricultural Research Organization (Volcani Center)

text: live

text: Generic

text: 454-generated pyrosequencing of barcoded 16S rRNA amplicons of root-associated bacteria of 3-month old greenhouse sweet pepper plants

text: soil metagenome

text: unamended root-associated bacterial community replicate 1


text: live

text: Generic

text: soil metagenome

text: unamended root-associated bacterial community replicate 2


text: live

text: Generic

text: soil metagenome

text: Biochar amended root-associated bacterial community replicate 1


text: live

text: Generic

text: soil metagenome

text: Biochar amended root-associated bacterial community replicate 2


text: live

text: Generic

text: Spirochaeta smaragdinae DSM 11293

text: Sediminispirochaeta smaragdinae DSM 11293

text: DSM 11293

text: Generic sample from Spirochaeta smaragdinae DSM 11293


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

text: live

text: Generic

text: Oryza sativa Kitaake

text: Oryza sativa Japonica Group

text: Kitaake

text: Generic sample from Oryza sativa Japonica Group


Wang Lab WGS E.coli JX3.0-1

text: The Salk Institute for Biological Studies

text: live

text: Generic

text: Escherichia coli O111:H-

text: Reassigning the Amber Stop Codon from Nonsense to Sense in Escherichia coli


Metagenomics of the Amazon

text: Evolutionary Genomics Group, División de Microbiología, Universidad Miguel Hernández, San Juan de Alicante, Spain

text: live

text: Generic

text: The sample was collected at a site nearly 400km upstream from Manaus, Brazil at the end of the dry season (September, average rainfall for the month 50 mm). The sample was collected from a depth of 20 m from the Solimões-Amazon River (3°56'11,08 S, 63°10'14,45 W) with a 10 liter Niskin bottle on 17 September, 2008, at 2:00 pm. River depth and width at this location were 15 m and 2100 m respectively, and the sample was taken 600 m away from the shore. Four liters of water were filtered in 3 independent Sterivex filters. Each sample was sequentially filtered through a AP20 glass fiber filter (142 mm of diameter); 5 µm pore size polycarbonate filter (142 mm of diameter) and 0.22 µm-pore size Sterivex GV filters (Durapore, Millipore) using a peristaltic pump. Sterivex filters (retaining the 0.2-5µm-diameter planktonic cells) were filled up with lysis buffer (40 mM EDTA, 50 mM Tris/ HCl, 0.75 M sucrose) and stored at -20 ºC until DNA extraction. The solution was harvested from the filters and DNA was extracted using the Metagenomic DNA from Environmental Water Samples Kit (EPICENTRE, WI, USA). DNA integrity was checked by agarose gel electrophoresis and quantified spectrophotometrically in a NanoDrop ND 1000 instrument (Thermo Scientific, DE, USA). Five micrograms was used for sequencing in the 454 Sequencing GS FLX Titanium platform (Laboratório Nacional de Computação Científica, Petrópolis, Rio de Janeiro, Brazil).

text: freshwater metagenome

text: Metagenomics of the Amazon


text: Massachusetts Institute of Technology

text: live

text: Generic

text: Surface soil collected from 1-10cm below leaf horizon using a soil corer (Harvard Forest, Sept 2010)

text: marine metagenome

text: Harvard Forest soil surface layer


pig 26-14

text: USDA-ARS

text: live

text: Generic

text: Treated pig, 14 days

text: gut metagenome

text: Antibiotic effects on the swine intestinal microbiome


pig 31-14

text: USDA-ARS

text: live

text: Generic

text: control pig 14 days

text: gut metagenome


pig 32-14

text: USDA-ARS

text: live

text: Generic

text: control pig 14 days

text: gut metagenome


pig 34-14

text: USDA-ARS

text: live

text: Generic

text: control pig 14 days

text: gut metagenome


pig 35-14

text: USDA-ARS

text: live

text: Generic

text: treated pig 14 days

text: gut metagenome


pig 37-14

text: USDA-ARS

text: live

text: Generic

text: treated pig 14 days

text: gut metagenome


pig 26-0

text: USDA-ARS

text: live

text: Generic

text: Treated animal, 0 day

text: gut metagenome


pig 35-0

text: USDA-ARS

text: live

text: Generic

text: Treated animal, 0 day

text: gut metagenome


pig 37-0

text: USDA-ARS

text: live

text: Generic

text: Treated animal, 0 day

text: gut metagenome


pig 31-0

text: USDA-ARS

text: live

text: Generic

text: Control animal, 0 day

text: gut metagenome


pig 32-0

text: USDA-ARS

text: live

text: Generic

text: Control animal, 0 day

text: gut metagenome


pig 34-0

text: USDA-ARS

text: live

text: Generic

text: Control animal, 0 day

text: gut metagenome


Brain

text: UNC Chapel Hill

text: live

text: Generic

text: Mus musculus

text: Brain


Kidney

text: UNC Chapel Hill

text: live

text: Generic

text: Mus musculus

text: Kidney


Heart

text: UNC Chapel Hill

text: live

text: Generic

text: Mus musculus

text: Heart


text: UNC Chapel Hill

text: live

text: Generic

text: Mus musculus


P19 undiff

text: UNC Chapel Hill

text: live

text: Generic

text: Mus musculus

text: P19 undiff


P19 4day

text: UNC Chapel Hill

text: live

text: Generic

text: Mus musculus

text: P19 4day


P19 10day

text: UNC Chapel Hill

text: live

text: Generic

text: Mus musculus

text: P19 10day


text: live

text: Generic

text: Ceriporiopsis subvermispora homokaryon B on ball milled aspen day5

text: standard

characteristic: library description

text: standard

characteristic: library type

text: Gelatoporia subvermispora B

text: B

text: Generic sample from Ceriporiopsis subvermispora B


text: live

text: Generic

text: Ceriporiopsis subvermispora homokaryon B on avicel day5

text: standard

text: standard

text: Gelatoporia subvermispora B

text: B


PRJNA60381.129Sv/Jae mouse #1

text: Broad Institute

text: live

text: Generic

text: Female

characteristic: host sex

text: carcass

characteristic: isolation source

text: Mus musculus

text: 129Sv/Jae mouse #1

characteristic: sample name

text: Generic sample from Mus musculus


characteristic: External Id

text: Comav upv

characteristic: INSDC center name

characteristic: INSDC first public

text: live

text: Generic

text: Cucurbita pepo belongs to the Cucurbitaceae family, whose economic importance is second only to the Solanaceae. It is a highly variable species. The “summer squash” types (including zucchini) rank among the highest-valued vegetables worldwide, and the “winter squash” types of C. pepo and related Cucurbita spp., are food staples and rich sources of fat and vitamins in developing countries.

text: Cucurbita pepo

text: Comav Cucurbita


Bulk soil

text: INRA

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: Bulk soil from core 1 used to extract gDNA and perform 454 pyrosequencing. Publihsed in: Uroz, S., Bu*e, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing highlights the contrasted bacterial diversity in forest soil. Environmental Microbiology Reports. 2: 281-288.

text: soil metagenome

text: sample C1 BS


Bulk soil C2BS

text: INRA

text: live

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: Bulk soil from core 2 used to extract gDNA and perform 454 pyrosequencing. Publihsed in: Uroz, S., Bu*e, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing highlights the contrasted bacterial diversity in forest soil. Environmental Microbiology Reports. 2: 281-288.

text: soil metagenome


bulk soil C3BS

text: INRA

text: live

text: Generic

text: Bulk soil from core 3 used to extract gDNA and perform 454 pyrosequencing. Publihsed in: Uroz, S., Bu*e, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing highlights the contrasted bacterial diversity in forest soil. Environmental Microbiology Reports. 2: 281-288.

text: soil metagenome

characteristic: organism


rhizosphere C1R

text: INRA

text: live

text: Generic

text: Rhizospheric soil from core 1 used to extract gDNA and perform 454 pyrosequencing. Publihsed in: Uroz, S., Bu*e, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing highlights the contrasted bacterial diversity in forest soil. Environmental Microbiology Reports. 2: 281-288.

text: soil metagenome

characteristic: title


rhizosphere C2R

text: INRA

text: live

text: Generic

text: Rhizospheric soil from core 2 used to extract gDNA and perform 454 pyrosequencing. Publihsed in: Uroz, S., Bu*e, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing highlights the contrasted bacterial diversity in forest soil. Environmental Microbiology Reports. 2: 281-288.

characteristic: description

text: soil metagenome


rhizosphere C3R

text: INRA

text: live

text: Generic

text: Rhizospheric soil from core 3 used to extract gDNA and perform 454 pyrosequencing. Publihsed in: Uroz, S., Bu*e, M., Murat, C., Frey-Klett, P. and Martin, F. (2010) Pyrosequencing highlights the contrasted bacterial diversity in forest soil. Environmental Microbiology Reports. 2: 281-288.

text: soil metagenome


gooseRRL

text: Wageningen University

text: live

text: Generic

text: Pooled Genomic DNA of 16 European wild Barnacle Geese was pooled and digested with RsaI or HhaI. Both libraries were pooled after purification and sequenced on an Illumina Genome Analyzer II.

text: Branta leucopsis

text: The development of a SNP set for the Barnacle goose Branta leucopsis


AMCEpooled-sample

text: Universite Laval

text: live

text: Generic

text: marine metagenome

text: Pooled sample of 10 Arctic marine surface water samples from 2003-2009 plus 2010


GossypiumHerbaceumLtranscriptome

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum

text: Gene networks controlling drought traits in Gossypium herbaceum L.


name: EYT1BW 404-4089-B-Guj-cot 21 root (drought tolerant)

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum


name: EYT27PB01-4090 -C- RAHS-IPS-87- leaf(drought sensitive)

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum


name: EYT1BW 401-4086-A- Vagad leaf(drought tolerant )

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum


text: Vanderbilt University

text: live

text: Generic

text: SYTSSX2-expressing C2C12 myoblasts

characteristic: cell type

text: IgG antibody (Abcam)

characteristic: chip antibody

text: Mus musculus


text: Vanderbilt University

text: live

text: Generic

text: SYTSSX2-expressing C2C12 myoblasts

text: anti-FLAG antibody (Sigma)

text: Mus musculus


text: Lymphocyte Cell Biology Section, NIAMS, National Institutes of Health

text: live

text: Generic

text: in vitro polarized T helper17 cells

text: 5 ug of STAT3 (14-6727: eBioScience) per IP

text: wild type

characteristic: genotype/variation

text: Mus musculus

text: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th17 condition and restimulated with IL-6 for 30 minutes

characteristic: passages

text: primary CD4+ T cells from spleen and lymph nodes

characteristic: strain

text: WTTh17STAT3 (ChIP-Seq)


characteristic: External Id

text: live

text: Generic

text: in vitro polarized T helper17 cells

text: mixture of STAT5a (PA-ST5A: R&D) and STAT5b (PA-ST5B: R&D) antibodies, 2 ul each per IP

text: wild type

text: Mus musculus

text: FACS sorted naive CD4+T cells cultured in vitro for 3 days under Th17 condition and restimulated with IL-2 for 30 minutes

text: WTTh17STAT5 (ChIP-Seq)


text: Molecular Medicine, Medical Sciences, Uppsala University

characteristic: INSDC center name

text: live

text: Generic

text: B-cell precursor (BCP) ALL

characteristic: all lineage

characteristic: bcp all subtype

text: acute lymphoblastic leukemia (ALL)

characteristic: disease state

text: Homo sapiens

text: Bone marrow

text: Bone marrow

characteristic: tissue


characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

text: B-cell precursor (BCP) ALL

text: High Hyperploidy (HeH)

text: acute lymphoblastic leukemia (ALL)

text: Homo sapiens

text: Bone marrow

text: Bone marrow


text: live

text: Generic

characteristic: NCBI submission package

characteristic: SRA accession

text: B-cell precursor (BCP) ALL

text: t(12;21) ETV6-RUNX1

text: acute lymphoblastic leukemia (ALL)

text: Homo sapiens

characteristic: organism

text: Bone marrow

text: Bone marrow

characteristic: title


text: live

text: Generic

text: B-cell precursor (BCP) ALL

text: t(9;22) BCR-ABL1

text: acute lymphoblastic leukemia (ALL)

text: Homo sapiens

text: Bone marrow

text: Bone marrow


text: live

text: Generic

text: T-cell lineage ALL (T-ALL)

text: acute lymphoblastic leukemia (ALL)

text: Homo sapiens

text: Bone marrow

text: Bone marrow


text: live

text: Generic

text: T-cell lineage ALL (T-ALL)

text: acute lymphoblastic leukemia (ALL)

text: Homo sapiens

text: Peripheral blood

text: Peripheral blood


Rb-1, J2-352-5-R1

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Rainbow vent field along the Mid-Atlantic Ridge. Sample collected at 36* 13.7487'N, 33* 54.1915'W at a depth of 2297 m.

characteristic: description

text: hydrothermal vent metagenome

text: Rainbow-1, Archaea


Rb-1B, J2-352-5-R1

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Rainbow-1, Bacteria


text: LMI, NHLBI, NIH

text: live

text: Generic

text: Anti-CTCF

characteristic: antibody

text: CD34 WT

characteristic: condition

text: Homo sapiens

text: Upstate

characteristic: vendor


characteristic: External Id

text: LMI, NHLBI, NIH

characteristic: INSDC center name

text: live

text: Generic

text: Anti-CTCF

text: BRG1 KD shLuc control

text: Homo sapiens

text: Upstate


text: LMI, NHLBI, NIH

text: live

text: Generic

text: Anti-CTCF

text: BRG1 RNAi KD

text: Homo sapiens

text: Upstate


text: LMI, NHLBI, NIH

text: live

text: Generic

text: BRG1 RNAi KD

text: Homo sapiens

text: Santa cruz biotechnology


text: LMI, NHLBI, NIH

text: live

text: Generic

text: BRG1 KD shLuc control

text: Homo sapiens

text: Santa cruz biotechnology


text: LMI, NHLBI, NIH

text: live

text: Generic

text: BRG1 RNAi KD

text: Homo sapiens

text: Abcam


text: LMI, NHLBI, NIH

text: live

text: Generic

text: BRG1 KD shLuc control

text: Homo sapiens

text: Abcam


text: LMI, NHLBI, NIH

text: live

text: Generic

text: CD34 WT

text: Homo sapiens


text: LMI, NHLBI, NIH

text: live

text: Generic

text: BRG1 KD shLuc control

text: Homo sapiens


text: LMI, NHLBI, NIH

text: live

text: Generic

text: BRG1 RNAi KD

text: Homo sapiens


text: LMI, NHLBI, NIH

text: live

text: Generic

text: CD36 WT

text: Homo sapiens


text: LMI, NHLBI, NIH

text: live

text: Generic

text: Anti-Brg1 (Khavari, P. A., et al., 1993, Nature, 366:170-174)

text: CD34 WT

text: Homo sapiens


text: LMI, NHLBI, NIH

text: live

text: Generic

text: CD36 WT

text: Homo sapiens


Rb-2A, J2-353-5-R2

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Rainbow vent field along the Mid-Atlantic Ridge. Sample collected at 36* 13.7688'N, 33* 54.1796'W at a depth of 2292m.

text: hydrothermal vent metagenome

text: Rainbow-2, Archaea


Rb-2B, J2-353-5-R2

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Rainbow vent field along the Mid-Atlantic Ridge. Sample collected at 36* 13.7688'N, 33* 54.1796'W at a depth of 2292 m.

text: hydrothermal vent metagenome

text: Rainbow-2, Bacteria


Rb-3A, J2-353-5-R2

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Rainbow vent field along the Mid-Atlantic Ridge. Sample collected from interior of chimney at 36* 13.7688'N, 33* 54.1796'W at a depth of 2292 m.

text: hydrothermal vent metagenome

text: Rainbow-3, Archaea


Rb-3B, J2-353-5-R2

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Rainbow-3, Bacteria


Rb-4A, J2-354-2-R1

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Rainbow vent field along the Mid-Atlantic Ridge. Sample collected at 36* 13.7661'N, 33* 54.1664'W at a depth of 2293 m.

text: hydrothermal vent metagenome

text: Rainbow-4, Archaea


Rb-4B, J2-354-2-R1

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Rainbow-4, Bacteria


Rb-5A, J2-355-1-R2

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Rainbow vent field along the Mid-Atlantic Ridge. Sample collected at 36* 13.7672'N, 33* 54.1714'W at a depth of 2293 m.

text: hydrothermal vent metagenome

text: Rainbow-5, Archaea


text: Colorado School of Mines

text: live

text: Generic

text: hot spring biofilm streamer

characteristic: bromide

characteristic: calcium

characteristic: chloride

text: pink streamer

text: hot spring

characteristic: env biome

text: spring

characteristic: env feature

text: biofilm

characteristic: env matter

characteristic: latitude

characteristic: longitude

characteristic: nitrate

text: human skin metagenome

characteristic: ph

characteristic: potassium

characteristic: sample name

characteristic: sulfate

characteristic: temp

text: hot spring biofilm streamer


text: Colorado School of Mines

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: hot spring biofilm streamer

text: pink streamer

characteristic: description

text: hot spring

text: spring

text: biofilm

text: human skin metagenome

characteristic: organism

text: hot spring biofilm streamer

characteristic: title


characteristic: External Id

text: Colorado School of Mines

characteristic: INSDC center name

text: live

text: Generic

text: hot spring biofilm

text: yellow biofilm

text: hot spring

characteristic: env biome

text: spring

characteristic: env feature

text: biofilm

characteristic: env matter

characteristic: latitude

characteristic: longitude

text: human skin metagenome

text: hot spring biofilm


text: Colorado School of Mines

characteristic: INSDC first public

text: live

text: Generic

text: hot spring microbial mat

text: orange mat â low temperature

text: hot spring

text: spring

text: biofilm

text: human skin metagenome

characteristic: sample name

text: hot spring microbial mat


text: Colorado School of Mines

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: hot spring biofilm streamer

text: pink streamer

text: hot spring

text: spring

text: biofilm

characteristic: magnesium

characteristic: nitrate

text: human skin metagenome

characteristic: ph

characteristic: potassium

characteristic: sulfate

characteristic: temp

text: hot spring biofilm streamer


characteristic: External Id

text: Colorado School of Mines

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: hot spring sediment

characteristic: bromide

characteristic: calcium

characteristic: chloride

text: black sediment

characteristic: description

text: hot spring

text: spring

text: sediment

text: human skin metagenome

characteristic: organism

text: hot spring sediment

characteristic: title


text: Colorado School of Mines

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: hot spring sediment

text: black sediment

text: hot spring

characteristic: env biome

text: spring

characteristic: env feature

text: sediment

characteristic: env matter

characteristic: latitude

characteristic: longitude

characteristic: magnesium

text: human skin metagenome

characteristic: sample name

text: hot spring sediment


characteristic: External Id

text: Colorado School of Mines

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: hot spring biofilm

characteristic: bromide

text: yellow biofilm

text: hot spring

text: spring

text: biofilm

characteristic: nitrate

text: human skin metagenome

characteristic: ph

characteristic: potassium

characteristic: sulfate

characteristic: temp

text: hot spring biofilm


text: Colorado School of Mines

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: hot spring microbial mat

characteristic: calcium

characteristic: chloride

text: orange mat â high temperature

characteristic: description

text: hot spring

characteristic: env biome

text: spring

characteristic: env feature

text: biofilm

text: human skin metagenome

characteristic: organism

text: hot spring microbial mat

characteristic: title


characteristic: External Id

text: Colorado School of Mines

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

characteristic: SRA accession

text: hot spring microbial mat

text: orange mat â high temperature

text: hot spring

text: spring

text: biofilm

characteristic: env matter

characteristic: latitude

characteristic: longitude

text: human skin metagenome

characteristic: sample name

text: hot spring microbial mat


text: Colorado School of Mines

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

text: hot spring microbial mat

characteristic: bromide

text: orange mat â low temperature

text: calcite hot spring

text: spring

text: biofilm

characteristic: magnesium

characteristic: nitrate

text: human skin metagenome

characteristic: ph

characteristic: potassium

characteristic: sulfate

characteristic: temp

text: hot spring microbial mat


characteristic: External Id

text: Colorado School of Mines

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

text: hot spring microbial mat

text: orange mat â low temperature

characteristic: description

text: calcite hot spring

characteristic: env biome

text: spring

characteristic: env feature

text: biofilm

text: human skin metagenome

characteristic: organism

text: hot spring microbial mat

characteristic: title


text: Colorado School of Mines

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

characteristic: SRA accession

text: hot spring biofilm streamer

characteristic: calcium

characteristic: chloride

text: pink streamer

text: calcite hot spring

text: spring

text: biofilm

characteristic: env matter

characteristic: latitude

characteristic: longitude

text: human skin metagenome

characteristic: sample name

text: hot spring biofilm streamer


characteristic: External Id

text: Colorado School of Mines

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

text: hot spring sediment

text: black sediment

text: hot spring

text: spring

text: sediment

text: human skin metagenome

characteristic: temp

text: hot spring sediment


text: Colorado School of Mines

text: live

text: Generic

text: hot spring biofilm streamer

characteristic: bromide

text: pink streamer

characteristic: description

text: hot spring

characteristic: env biome

text: spring

characteristic: env feature

text: biofilm

characteristic: nitrate

text: human skin metagenome

characteristic: organism

characteristic: potassium

characteristic: sulfate

text: hot spring biofilm streamer

characteristic: title


text: Colorado School of Mines

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

text: Generic

characteristic: SRA accession

text: hot spring biofilm streamer

text: pink streamer

text: hot spring

text: spring

text: biofilm

characteristic: env matter

characteristic: latitude

characteristic: magnesium

text: human skin metagenome

characteristic: ph

text: hot spring biofilm streamer


characteristic: External Id

text: Colorado School of Mines

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: NCBI submission package

text: hot spring microbial mat

text: orange mat â low temperature

characteristic: description

text: hot spring

text: spring

text: biofilm

characteristic: longitude

text: human skin metagenome

characteristic: sample name

characteristic: temp

text: hot spring microbial mat


text: Colorado School of Mines

characteristic: INSDC center name

text: live

text: Generic

text: hot spring biofilm streamer

characteristic: bromide

characteristic: calcium

characteristic: chloride

text: pink streamer

text: hot spring

characteristic: env biome

text: spring

characteristic: env feature

text: biofilm

characteristic: nitrate

text: human skin metagenome

characteristic: organism

characteristic: potassium

characteristic: sulfate

text: hot spring biofilm streamer

characteristic: title


characteristic: External Id

text: Colorado School of Mines

characteristic: INSDC first public

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

characteristic: NCBI submission model

characteristic: SRA accession

text: hot spring sediment

text: black sediment

text: hot spring

text: spring

text: sediment

characteristic: env matter

characteristic: latitude

characteristic: magnesium

text: human skin metagenome

characteristic: ph

text: hot spring sediment


Rb-5B, J2-355-1-R2

text: Portland State University

characteristic: INSDC center name

text: live

text: Generic

characteristic: NCBI submission package

characteristic: description

text: hydrothermal vent metagenome

text: Rainbow-5, Bacteria


Rb-6A, J2-355-1-R2

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Rainbow vent field along the Mid-Atlantic Ridge. Sample collected from interior of chimney at 36* 13.7672'N, 33* 54.1714'W at a depth of 2293 m.

text: hydrothermal vent metagenome

characteristic: organism

text: Rainbow-6, Archaea


Rb-6B, J2-355-1-R2

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Rainbow-6, Bacteria


text: Colorado School of Mines

text: live

text: Generic

text: human skin metagenome

text: hot spring YNPLIPID_default


Lake Texoma microbial community

text: The University of Oklahoma

text: live

text: Generic

text: We sampled four environmentally-distinct surface water sites: two near-shore (littoral) stations (Lebanon Pool and Soldier Creek) and two off-shore (pelagic) stations (Red River and Buncombe Creek). We then sequenced 16S rRNA genes of bacterial assemblages using high-throughput sequencing (454/Roche Life Sciences GS-FLX Genome Sequencer). Sequence data were analyzed using mothur, an open-source, platform-independent software package for describing and comparing microbial communities. While no formal taxonomic definitions exist for bacteria based on sequence similarity, operational taxonomic units (OTUs) were defined at 3, 7, and 15% sequence dissimilarity cutoff values as rough approximations of species, genus, and family (18, 26, 27, but see 28) as generated using SILVA.

text: freshwater metagenome

text: The microbial rare biosphere in a subtropical freshwater lake


text: UMDNJ

text: live

text: Generic

text: C2C12 cells

characteristic: cell line

text: Mus musculus

text: anti-BrdU antibody

characteristic: rip antibody

text: Sigma

characteristic: rip antibody vendor

text: C2C12 nascent RNA

text: Nascent RNA sequencing of C2C12 cell


LS-7A, J2-356-2-R1

characteristic: External Id

text: Portland State University

characteristic: INSDC first public

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Lucky Strike vent field along the Mid-Atlantic Ridge. Sample collected at 37* 17.5075'N, 32* 16.6743'W at a depth of 1732 m.

text: hydrothermal vent metagenome

text: Lucky Strike-7, Archaea

characteristic: title


LS-7B, J2-356-2-R1

text: Portland State University

characteristic: INSDC last update

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: hydrothermal vent metagenome

text: Lucky Strike-7 Bacteria


LS-8A, J2-357-6-R1

text: Portland State University

text: live

text: Generic

characteristic: NCBI submission model

characteristic: SRA accession

text: Deep-sea hydrothermal vent chimney collected from the Lucky Strike vent field along the Mid-Atlantic Ridge. Sample collected at 37* 17.4528'N, 32* 16.9161'W at a depth of 1730 m.

text: hydrothermal vent metagenome

text: Lucky Strike-8, Archaea


LS-8B, J2-357-6-R1

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Lucky Strike-8, Bacteria


LS-9A, J2-358-6-R1

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Lucky Strike vent field along the Mid-Atlantic Ridge. Sample collected at 37* 17.6395'N, 32* 16.9329'W at a depth of 1652 m.

text: hydrothermal vent metagenome

text: Lucky Strike-9, Archaea


LS-9B, J2-358-6-R1

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Lucky Strike-9, Bacteria


LS-10A, J2-358-4-R1

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Lucky Strike vent field along the Mid-Atlantic Ridge. Sample collected at 37* 17.5410'N, 32* 16.8795'W at a depth of 1729 m.

text: hydrothermal vent metagenome

text: Lucky Strike-10, Archaea


LS-10B, J2-358-4-R1

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Lucky Strike-10, Bacteria


LS-11A, J2-358-5-R2

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Lucky Strike vent field along the Mid-Atlantic Ridge. Sample collected at 37* 17.6487'N, 32* 16.9046'W at a depth of 1660 m.

text: hydrothermal vent metagenome

text: Lucky Strike-11, Archaea


LS-11B, J2-358-5-R2

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Lucky Strike-11, Bacteria


LS-12A, J2-359-7-R1

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the Lucky Strike vent field along the Mid-Atlantic Ridge. Sample collected at 37* 17.3787'N, 32* 16.6212'W at a depth of 1690 m.

text: hydrothermal vent metagenome

text: Lucky Strike-12, Archaea


LS-12B, J2-359-7-R1

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: Lucky Strike-12, Bacteria


TAG-13A, J2-363-7-R3

text: Portland State University

text: live

text: Generic

text: Deep-sea hydrothermal vent chimney collected from the TAG vent field along the Mid-Atlantic Ridge. Sample collected at 26* 8.2043'N, 44* 49.5283'W at a depth of 3622 m.

text: hydrothermal vent metagenome

text: TAG-13, Archaea


TAG-13B, J2-363-7-R3

text: Portland State University

text: live

text: Generic

text: hydrothermal vent metagenome

text: TAG-13, Bacteria


OARI.AW

text: Baylor College of Medicine

text: live

text: Generic

text: Awassi

characteristic: breed

text: Ovis aries breed Awassi

text: Ovis aries

text: Sample from Ovis aries


text: Institute for Genome Sciences University of MD School of Medicine

text: live

text: Generic

text: Escherichia coli LT-41

characteristic: strain

text: Escherichia coli LT-41


OARI.ME

text: Baylor College of Medicine

characteristic: INSDC center name

text: live

text: Generic

text: Merino

text: Ovis aries breed Merino

text: Ovis aries

text: Sample from Ovis aries


name: kimchi bacterial metagenomes_K1, K7, K8, K9, K10 default

text: Jeju National University

text: live

text: Generic

characteristic: NCBI submission package

text: Weissella koreensis

text: Bacterial community analysis during fermentation of 10 representative kinds of kimchi with barcoded pyrosequencing_K1, K7, K8, K9, K10


name: kimchi bacterial metagenomes_K3, K4, K5, K6, K2 default

text: Jeju National University

text: live

text: Generic

text: Weissella koreensis

text: Bacterial community analysis during fermentation of 10 representative kinds of kimchi with barcoded pyrosequencing_K3, K4, K5, K6, K2


name: A New Resistance Source To Powdery Mildew From Diploid Wild Strawberry

text: Gaziosmanpasa University

text: live

text: Generic

text: Podosphaera aphanis var. aphanis

text: Podosphaera aphanis var aphanis DNA encoding 5.8 rDNA, ITS1 and ITS2


Gossypium herbaceum L

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum

text: Gene networks controlling drought traits in Gossypium herbaceum L


Copepods

text: Karpaga Vinayaga College of Engineering and Technology

text: live

text: Generic

text: Thermocyclops decipiens is a microarthropods and commonly available in freshwater bodies, Tamilnadu. which is used as live feed in aquaculture industry

characteristic: description

text: Cyclopoida

text: Cyclopoids


G.herbaceum 4086

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum

characteristic: organism

text: Transcriptome sequences of leaf from drought tolerant germplasm of G.herbaceum


G.herbaceum 4089

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum

text: Transcriptome sequences of root from drought tolerant germplasm of G.herbaceum


default sample for day 0

text: USDA-ARS

text: live

text: Generic

text: gut metagenome

text: default sample for day 0


G.herbaceum 4090

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum

text: Transcriptome sequences of leaf from drought sensitive germplasm of G.herbaceum


default sample for day 14

text: USDA-ARS

text: live

text: Generic

text: gut metagenome

text: default sample for day 14


G.herbaceum 4091

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum

text: Transcriptome sequences of root from drought sensitive germplasm of G.herbaceum


G.herbaceum 4092

text: National Botanical Research Institute

text: live

text: Generic

text: Gossypium herbaceum


text: live

text: Generic

text: Escherichia coli DEC10E

text: Escherichia coli DEC10E


text: live

text: Generic

text: Escherichia coli DEC10D

text: Escherichia coli DEC10D


text: live

text: Generic

text: Escherichia coli DEC10C

text: Escherichia coli DEC10C


Raw sequencing data for MLL library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the MLL-rearranged precursor B-ALL-representing library. The library was constructed using pooled RNA extracted from 10 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens


text: University of California, Los Angeles

text: live

text: Generic

text: Columbia

characteristic: ecotype

text: wildtype

characteristic: genotype

text: Arabidopsis thaliana

characteristic: ploidy

text: leaves

text: leaf

characteristic: tissue

text: 2C wild-type


characteristic: External Id

text: University of California, Los Angeles

characteristic: INSDC first public

text: live

text: Generic

text: Columbia

text: wildtype

text: Arabidopsis thaliana

text: leaves

text: leaf

text: 4C wild-type


text: University of California, Los Angeles

characteristic: INSDC last update

text: live

text: Generic

text: Columbia

text: wildtype

text: Arabidopsis thaliana

text: leaves

text: leaf

text: 8C wild-type

characteristic: title


text: University of California, Los Angeles

characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: Columbia

text: wildtype

text: Arabidopsis thaliana

text: leaves

text: leaf

text: 16C wild-type


text: University of California, Los Angeles

text: live

text: Generic

characteristic: NCBI submission model

characteristic: SRA accession

text: Columbia

text: atxr5 atxr6

text: Arabidopsis thaliana

text: leaves

text: leaf

text: 2C atxr5 atxr6


text: University of California, Los Angeles

text: live

text: Generic

text: Columbia

text: atxr5 atxr6

text: Arabidopsis thaliana

text: leaves

text: leaf

text: 4C atxr5 atxr6


text: University of California, Los Angeles

text: live

text: Generic

text: Columbia

text: atxr5 atxr6

text: Arabidopsis thaliana

text: leaves

text: leaf

text: 8C atxr5 atxr6


text: University of California, Los Angeles

text: live

text: Generic

text: Columbia

text: atxr5 atxr6

text: Arabidopsis thaliana

text: leaves

text: leaf

text: 16C atxr5 atxr6


text: University of California, Los Angeles

text: live

text: Generic

text: Columbia

text: wildtype

text: Arabidopsis thaliana

text: leaves

text: leaf

text: input wild-type


text: University of California, Los Angeles

text: live

text: Generic

text: Columbia

text: atxr5 atxr6

text: Arabidopsis thaliana

text: leaves

text: leaf

text: input atxr5 atxr6


text: University of California, Los Angeles

text: live

text: Generic

characteristic: chip antibody

text: Upstate

characteristic: chip antibody manufacturer

text: Columbia

text: wildtype

text: Arabidopsis thaliana

text: leaves

text: leaf

text: H3K27me1 ChIP wild-type


text: University of California, Los Angeles

characteristic: INSDC center name

text: live

text: Generic

characteristic: NCBI submission package

text: Abcam

text: Columbia

text: atxr5 atxr6

text: Arabidopsis thaliana

text: leaves

text: leaf

text: H3 ChIP atxr5 atxr6


name: Raw sequencing data for TEL-AML1 library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the TEL-AML1-positive precursor B-ALL-representing library. The library was constructed using pooled RNA extracted from 10 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

characteristic: description

text: Homo sapiens

characteristic: organism

text: Raw sequencing data for the TEL-AML1-positive precursor B-ALL-representing library


Raw sequencing data for BCR-ABL library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the BCR-ABL-positive precursor B-ALL-representing library. The library was constructed using pooled RNA extracted from 10 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: Raw sequencing data for the BCR-ABL- positive precursor B-ALL-representing library


name: Raw sequencing data for E2A-PBX1 library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the E2A-PBX1-positive precursor B-ALL-representing library. The library was constructed using pooled RNA extracted from 10 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: Raw sequencing data for the E2A-PBX1-positive precursor B-ALL-representing library


name: Raw sequencing data for hyperdiploid library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the hyperdiploid-positive precursor B-ALL-representing library. The library was constructed using pooled RNA extracted from 10 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: Raw sequencing data for the hyperdiploid-positive precursor B-ALL-representing library


Raw sequencing data for T-ALL library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the T-ALL-representing library. The library was constructed using pooled RNA extracted from 10 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: Raw sequencing data for the T-ALL-representing library


Raw sequencing data for B-other library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the B-other precursor B-ALL-representing library. B-other subtype of precursor B-ALL represents the remaining precursor B-ALL patients negative for hyperdiploidy and MLL-, TEL-AML1-, and E2A-PBX1-translocations. The library was constructed using pooled RNA extracted from 10 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: sequencing data for the B-other precursor B-ALL-representing library


text: Jiming Jiang, UW-Madison

text: live

text: Generic

text: Nipponbare

characteristic: cultivar

text: Oryza sativa Japonica Group

text: Seedling

text: Seedling

text: Rice-DH-seedling


text: Jiming Jiang, UW-Madison

text: live

text: Generic

text: Nipponbare

text: Oryza sativa Japonica Group

text: Callus

text: Callus

text: Rice-DH-callus


Raw sequencing data for CD34 library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the normal CD34 progenitor blood cell-representing library. The library was constructed using pooled RNA extracted from 3 children with healthy bone marrow after G-CSF-stimulation. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: Raw sequencing data for the CD34 progenitor blood cell-representing library


name: Raw sequencing data for normal bone marrow library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the normal bone marrow-representing library. The library was constructed using pooled RNA extracted from 10 children with healthy bone marrow. Only RNA with an RNA Integrity Number of more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: Raw sequencing data for the normal bone marrow-representing library


text: Institute for Genome Sciences University of MD School of Medicine

text: live

text: Generic

text: Escherichia coli DEC10A

characteristic: strain

text: Escherichia coli DEC10A


name: Raw sequencing data for thymocytes library

text: Erasmus MC-Sophia Children's Hospital

text: live

text: Generic

text: File contains the raw RNA sequence data as generated by the deep sequencing method for the normal thymocytes-representing library. The library was constructed using pooled RNA extracted from 6 individual patients. Only RNA with an RNA Integrity Number more than/equal to 7.5 was used (as measured on the 2100 Bioanalyzer of Agilent, Amstelveen, the Netherlands).

text: Homo sapiens

text: Raw sequencing data for the thymocytes-representing library


text: live

text: Generic

text: Escherichia coli DEC10B

text: Escherichia coli DEC10B


text: live

text: Generic

text: Escherichia coli DEC9A

text: Escherichia coli DEC9A


text: live

text: Generic

text: Escherichia coli DEC9B

text: Escherichia coli DEC9B


text: live

text: Generic

text: Escherichia coli DEC8E

text: Escherichia coli DEC8E


text: live

text: Generic

text: Escherichia coli DEC9C

text: Escherichia coli DEC9C


text: live

text: Generic

text: Escherichia coli DEC8D

text: Escherichia coli DEC8D


text: Level 4, Institute of Metabolic Science, University of Cambridge Metabolic Research Laboratories

text: live

text: Generic

text: Mus musculus

text: Liver cells

characteristic: time

text: Liver

characteristic: tissue


characteristic: External Id

characteristic: INSDC first public

text: live

text: Generic

text: Mus musculus

text: Liver cells

text: Liver


characteristic: INSDC last update

text: live

text: Generic

text: Escherichia coli DEC8A

text: Escherichia coli DEC8A

characteristic: title


characteristic: INSDC secondary accession

text: live

characteristic: INSDC status

text: Generic

text: Escherichia coli DEC9D

text: Escherichia coli DEC9D


text: live

text: Generic

characteristic: NCBI submission model

characteristic: SRA accession

text: Escherichia coli DEC7E

text: Escherichia coli DEC7E


text: Reproductive Biology, Biology, Shantou University

text: live

text: Generic

text: Homo sapiens

text: endometrium


text: live

text: Generic

text: Escherichia coli DEC7A

text: Escherichia coli DEC7A


text: live

text: Generic

text: Escherichia coli DEC7B

text: Escherichia coli DEC7B


text: live

text: Generic

text: Escherichia coli DEC6E

text: Escherichia coli DEC6E


text: live

text: Generic

text: Escherichia coli DEC6C

text: Escherichia coli DEC6C


text: live

text: Generic

text: Escherichia coli DEC6D

text: Escherichia coli DEC6D


text: live

text: Generic

text: Escherichia coli DEC6B

text: Escherichia coli DEC6B


text: live

text: Generic

text: Escherichia coli DEC3B

text: Escherichia coli DEC3B


text: live

text: Generic

text: Escherichia coli DEC3C

text: Escherichia coli DEC3C


text: live

text: Generic

text: Escherichia coli DEC3A

text: Escherichia coli DEC3A


text: live

text: Generic

text: Escherichia coli DEC6A

text: Escherichia coli DEC6A


text: live

text: Generic

text: Escherichia coli DEC5D

text: Escherichia coli DEC5D


text: The Holden Arboretum

text: live

text: Generic

text: Metagenome from artificial vernal pool soil that experienced nitrate addition

text: sediment metagenome

text: Nitrate Addition


text: The Holden Arboretum

text: live

text: Generic

text: Metagenome from artificial vernal pool soil that experienced no nutrient addition

text: sediment metagenome

text: Control Metagenome


text: live

text: Generic

text: Escherichia coli DEC5A

text: Escherichia coli DEC5A


text: live

text: Generic

text: Escherichia coli DEC5B

text: Escherichia coli DEC5B


text: live

text: Generic

text: Escherichia coli DEC5C

text: Escherichia coli DEC5C


text: live

text: Generic

text: Escherichia coli DEC3D

text: Escherichia coli DEC3D


text: live

text: Generic

text: Escherichia coli DEC3F

text: Escherichia coli DEC3F


text: live

text: Generic

text: Escherichia coli DEC3E

text: Escherichia coli DEC3E


text: live

text: Generic

text: Escherichia coli DEC4B

text: Escherichia coli DEC4B


text: live

text: Generic

text: Escherichia coli DEC4A

text: Escherichia coli DEC4A


text: live

text: Generic

text: Escherichia coli DEC4C

text: Escherichia coli DEC4C


text: live

text: Generic

text: Escherichia coli DEC1E

text: Escherichia coli DEC1E


text: live

text: Generic

text: Escherichia coli DEC2B

text: Escherichia coli DEC2B


text: live

text: Generic

text: Escherichia coli DEC4D

text: Escherichia coli DEC4D


text: live

text: Generic

text: Escherichia coli DEC4F

text: Escherichia coli DEC4F


text: live

text: Generic

text: Escherichia coli DEC4E

text: Escherichia coli DEC4E


text: live

text: Generic

text: Escherichia coli DEC1D

text: Escherichia coli DEC1D


text: live

text: Generic

text: Escherichia coli DEC1C

text: Escherichia coli DEC1C


text: live

text: Generic

text: Escherichia coli DEC5E

text: Escherichia coli DEC5E


Lane 1

text: UCLA

text: live

text: Generic

text: Random mutagenesis was performed with N’-nitro-N-nitrosoguanidine (NTG), using as a parent strain the E. coli JCL16 (BW25113/F’ [traD36, proAB , lacIq ZDM15]). Brieﬂy, exponential-phase cultures of JCL16 were concentrated two-fold by centrifugation and suspension in 0.1 M citrate buﬀer (pH 5.5) and exposed to N’-nitro-N-nitrosoguanidine(NTG) at ﬁnal concentration of 50 g/ml for 30 minutes at 37C to reach a percentage kill of approximately 50%. The cells were washed twice with 0.1 M phosphate buﬀer (pH 7.0) and grown in LB plus 4% glucose for two hours. The outgrown culture were then challenged in the presence of 14 g/L isobutanol which is highly toxic to the wildtype type strain JCL16, for 12 h and plated on LB agar plates containing 25 g/mL tetracycline. To select isobutanol tolerant mutants, isolated colonies were inoculated in 2 mL deep-96-well plates containing 300 L LB plus 8 g/L isobutanol per well and incubated for 24 h at 30C in a rotary shaker (250 rpm) (VWR). Bacterial growth was then determined by densitometry at 600 nm using a microplate reader (BioTek instruments Inc.)

text: Escherichia coli BW25113

text: JCL16 - BW25113/F′ [traD36, proAB+, lacIq ZΔM15]

text: 32 NTG-derived and screened mutants of parent strain JCL16, sequenced in pooled libraries.