status: PUBLIC

tag: attribute

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Clostridium_difficile_strain_BI_4-sc-2010-05-07-349

characteristic: Submitter Id

characteristic: collection date

text: USA: MN

characteristic: geographic location (country and/or sea)

text: Peptoclostridium difficile

characteristic: organism

characteristic: pubmed id

text: Peptoclostridium difficile

text: Homo sapiens

characteristic: specific host

text: cdiff BI-4

characteristic: strain


text: SC

text: public

text: Clostridium_difficile_strain_BI_1-sc-2010-05-07-359

text: USA: MN

text: Peptoclostridium difficile

text: Peptoclostridium difficile

text: Homo sapiens

text: cdiff BI-1


text: SC

text: public

text: Clostridium_difficile_strain_BI_2-sc-2010-05-07-348

text: Peptoclostridium difficile

text: Peptoclostridium difficile


text: SC

text: public

text: Clostridium_difficile_strain_BI_15-sc-2010-05-07-357

text: USA: NJ

text: Peptoclostridium difficile

text: Peptoclostridium difficile

text: Homo sapiens

text: cdiff BI-15


text: CEES

text: public

text: Gadus morhua 'NEAC'

text: Gadus morhua 'NEAC'

text: NEAC 001

type: has member


text: Salmonella enterica subsp. enterica serovar Typhimurium

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: GA3844RB-sc-2011-06-02T08:48:33Z-1155745


characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: MEXSALMIPUS03_21-sc-2011-06-02T08:48:38Z-1155753


text: SC

text: public


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: Wellcome Sanger Institute

text: public

tag: Namespace:Wellcome Sanger Institute

text: ArrayExpress

characteristic: broker name

text: M

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

text: Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke’s Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing. Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min. Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min. Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7). For single-cell RNA-seq using the plate-based SS2 protocol, we created overlapping gates that comprehensively and evenly sampled all immune cell population in the decidua. B cells (CD19+ /or CD20+) cells were excluded from our analysis, due to its absence in decidua. Single cells were sorted into 96-well full-skirted Eppendorf plated chilled to 4C, prepared with lysis buffer consisting of 10 ul of TCL buffer (Qiagen) supplemented with 1% b-mercaptoethanol. Single-cell lysates were sealed, vortexed, spin down at 300g at 4C for 1 min, immediately placed on dry ice, and transferred for storage at -80C. The SS2 protocol was performed on single-cells as described previously, with some modifications. Libraries were sequenced aiming at an average depth of 1 million reads/cell, on an Illumina HiSeq 2000 with v4 chemistry (paired-end 75-bp reads). RNA was extracted, cDNA created and amplified, as part of the smart-seq 2 protocol. Libraries were made using Nextera XT

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Wellcome Sanger Institute

text: public

text: ArrayExpress

characteristic: broker name

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

text: adult

text: normal

text: not available

text: Homo sapiens

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


text: Wellcome Sanger Institute

text: public

text: ArrayExpress

text: T

characteristic: cell gating

text: 6 to 12 weeks gestation

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: NK

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: SGSC1430-sc-2011-06-02T08:48:45Z-1155767

characteristic: Submitter Id

characteristic: organism

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public


characteristic: ENA-CHECKLIST

text: Wellcome Sanger Institute

text: public

text: ArrayExpress

characteristic: broker name

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


text: Campylobacter jejuni

characteristic: ArrayExpress-Species

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: collection date

text: United Kingdom

characteristic: geographic location (country and/or sea)

text: not known

characteristic: host health state

text: faeces

characteristic: isolation source

text: Campylobacter jejuni

text: Campylobacter jejuni

text: not known

characteristic: serovar

text: human

characteristic: specific host

text: Campylobacter jejuni; Campylobacter jejuni

characteristic: title


text: Campylobacter jejuni

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: United Kingdom

text: not known

text: faeces

text: Campylobacter coli

characteristic: organism

text: Campylobacter coli

text: not known

text: human

characteristic: strain

text: Campylobacter coli; Campylobacter coli


characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis


text: SC

text: public

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: Gurung 256


text: SC

text: public

text: Neisseria meningitidis

text: Neisseria meningitidis


text: SC

text: public

characteristic: anonymized name

characteristic: collection date

text: Actinomyces viscosus

characteristic: common name

characteristic: culture collection

text: not available: to be reported later

characteristic: host status

text: not available: to be reported later

text: Actinomyces viscosus

text: Actinomyces viscosus

text: not available: to be reported later

text: Hamster


characteristic: ENA-CHECKLIST

text: SC

text: public

text: Porphyromonas macacae

text: not available: to be reported later

text: not available: to be reported later

characteristic: isolation source

text: Porphyromonas macacae

text: Porphyromonas macacae

text: not available: to be reported later

characteristic: serovar

text: Cat

characteristic: specific host

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Oligella ureolytica

text: not available: to be reported later

text: Urine

text: Oligella ureolytica

text: Oligella ureolytica

text: not available: to be reported later

text: Human


characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: Janthinobacterium lividum

text: USA: Michigan (State)

characteristic: country

text: Soil

text: Janthinobacterium lividum

characteristic: organism

text: Janthinobacterium lividum

text: not available: to be reported later

text: environmental

characteristic: strain


text: Wellcome Sanger Institute

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: M

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female

characteristic: title


text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

text: not available

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


text: SC

text: public

characteristic: anonymized name

characteristic: collection date

text: Aminobacter aminovorans

characteristic: common name

text: Netherlands: Delft

characteristic: country

characteristic: culture collection

text: Soil

characteristic: isolation source

text: Aminobacter aminovorans

text: Aminobacter aminovorans

text: not available: to be reported later

characteristic: serovar

text: environmental

characteristic: specific host

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: T

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: NK

text: 6 to 12 weeks gestation

text: human

characteristic: common name

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: anonymized name

characteristic: collection date

text: Clostridium botulinum

characteristic: culture collection

text: not available: to be reported later

characteristic: host status

text: not available: to be reported later

characteristic: isolation source

text: Clostridium botulinum

text: Clostridium botulinum

text: not available: to be reported later

characteristic: serovar

text: not available: to be reported later

characteristic: specific host

characteristic: strain


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Clostridium ventriculi

characteristic: common name

text: not available: to be reported later

text: not available: to be reported later

text: Clostridium ventriculi

text: Clostridium ventriculi

text: not available: to be reported later

text: not available: to be reported later


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Clostridium carnis

text: Clostridium carnis

characteristic: organism

text: Clostridium carnis

text: not available

characteristic: title


characteristic: External Id

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: anonymized name

characteristic: collection date

text: Dermatophilus congolensis

text: not available: to be reported later

text: Hoof

text: Dermatophilus congolensis

text: Dermatophilus congolensis

text: not available: to be reported later

text: Sheep


text: SC

text: public

text: Streptomyces griseus

text: United Kingdom: London

characteristic: country

characteristic: culture collection

text: Plate contaminant

characteristic: isolation source

text: Streptomyces griseus

text: Streptomyces griseus

text: not available: to be reported later

characteristic: serovar

text: environmental

characteristic: specific host


text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Corynebacterium xerosis

text: Dried ampoule

text: Corynebacterium xerosis

text: Corynebacterium xerosis

text: not available: to be reported later

text: environmental

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: uncultured Avibacterium sp.

characteristic: common name

text: not available

characteristic: host status

text: not available

text: uncultured Avibacterium sp.

characteristic: organism

text: uncultured Avibacterium sp.

text: not available


characteristic: External Id

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: anonymized name

characteristic: collection date

text: Clostridium cochlearium

text: not available: to be reported later

text: not available: to be reported later

text: Clostridium cochlearium

text: Clostridium cochlearium

text: not available: to be reported later

text: not available: to be reported later

characteristic: title


text: SC

characteristic: INSDC center name

text: public

text: Bordetella bronchiseptica

characteristic: culture collection

text: not available: to be reported later

text: not available: to be reported later

characteristic: isolation source

text: Bordetella bronchiseptica

text: Bordetella bronchiseptica

text: not available: to be reported later

characteristic: serovar

text: not available: to be reported later

characteristic: specific host


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Serratia plymuthica

text: Canal water

text: Serratia plymuthica

text: Serratia plymuthica

text: not available: to be reported later

text: environmental

characteristic: strain


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: Mycobacterium xenopi

characteristic: common name

text: not available: to be reported later

characteristic: host status

text: not available: to be reported later

text: Mycobacterium xenopi

characteristic: organism

text: Mycobacterium xenopi

text: not available: to be reported later

text: Amphibian : African clawed toad


characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: M

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

text: Homo sapiens

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: 6 to 12 weeks gestation

text: human

characteristic: common name

text: adult

text: normal

text: not available

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


text: SC

text: public

characteristic: collection date

text: Nocardia farcinica

characteristic: culture collection

text: not available

characteristic: host status

text: not available

characteristic: isolation source

text: Nocardia farcinica

text: Nocardia farcinica

text: not available

characteristic: serovar

text: not available

characteristic: specific host

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: T

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: NK

text: 6 to 12 weeks gestation

text: human

characteristic: common name

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: anonymized name

characteristic: collection date

text: Pediococcus pentosaceus

characteristic: culture collection

text: not available: to be reported later

characteristic: host status

text: not available: to be reported later

characteristic: isolation source

text: Pediococcus pentosaceus

text: Pediococcus pentosaceus

text: not available: to be reported later

characteristic: serovar

text: not available: to be reported later

characteristic: specific host

characteristic: strain


text: Neisseria meningitidis

characteristic: ArrayExpress-Species

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: H1100_87-sc-2011-08-17T10:28:09Z-1258983

text: Neisseria meningitidis

text: Neisseria meningitidis


text: Leptospira interogans

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: Submitter Id

text: Leptospira interrogans serovar Autumnalis

characteristic: organism


characteristic: ENA-CHECKLIST

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

characteristic: broker name

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: anonymized name

characteristic: collection date

text: Malawi

characteristic: country

text: Disease

characteristic: host status

text: Blood

characteristic: isolation source

text: Streptococcus pneumoniae

characteristic: organism

text: Streptococcus pneumoniae

characteristic: serovar

text: Human

characteristic: specific host


text: Streptococcus pneumoniae

characteristic: ArrayExpress-Species

text: NIG 545-05

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC last update

text: public

text: NIG545_05-sc-2011-05-13T10:23:26Z-1138797

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: NIG 545-05


text: Streptococcus pneumoniae

text: NIG 265-09

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

text: NIG265_09-sc-2011-05-13T10:23:35Z-1138812

text: Streptococcus pneumoniae

text: Streptococcus pneumoniae

text: NIG 265-09

characteristic: strain


characteristic: ENA-CHECKLIST

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: Submitter Id

characteristic: anonymized name

text: UK

text: disease

text: not recorded

text: Neisseria gonorrhoeae

text: Neisseria gonorrhoeae

text: human

characteristic: title


text: SC

text: public

characteristic: collection date

text: Israel

characteristic: geographic location (country and/or sea)

text: Diseased

characteristic: host health state

text: Faeces

characteristic: isolation source

text: Shigella sonnei

characteristic: organism

text: Shigella sonnei

text: Human


text: 24464101; 33347430; 34414415; 34461978; 31736907; 35780211

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: RUS

text: Mycobacterium

characteristic: genus

text: Russia

text: Homo sapiens

characteristic: host

text: disease

characteristic: isolate

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

text: Mycobacterium tuberculosis

type: AMR curated data - CABBAGE

value: rifampin

value: broth dilution

value: susceptible

value: Mycobacterium tuberculosis

value: amikacin

value: streptomycin

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text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis

characteristic: title


text: 24464101; 31736907; 34414415; 35780211; 34461978

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: RUS

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

characteristic: isolate

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

text: public

text: ArrayExpress

characteristic: broker name

text: M

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


text: 24464101; 34414415; 34461978; 35780211

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RUS

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

characteristic: strain

text: Mycobacterium tuberculosis

characteristic: title


text: 31736907; 35780211

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: RUS

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

characteristic: host health state

text: not known

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: not available

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

characteristic: collection date

text: Russia

characteristic: geographic location (country and/or sea)

text: disease

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

characteristic: strain

text: Mycobacterium tuberculosis

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: T

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RUS

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

characteristic: isolate

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

characteristic: strain

text: Mycobacterium tuberculosis

characteristic: title


text: 24464101; 34414415; 34461978; 35780211

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: RUS

characteristic: SRA accession

characteristic: Submitter Id

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RUS

characteristic: collection date

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

text: SC

text: public

text: RUS

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

characteristic: isolate

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

text: Mycobacterium tuberculosis


text: 31736907; 35780211

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: RUS

characteristic: SRA accession

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: strain

text: Mycobacterium tuberculosis

characteristic: title


characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: NK

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

text: RUS

characteristic: SRA accession

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

characteristic: isolate

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

characteristic: strain

text: Mycobacterium tuberculosis

characteristic: title


text: 24464101; 34414415; 34461978; 35780211; 31736907

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: RUS

characteristic: Submitter Id

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

characteristic: INSDC status

text: RUS

characteristic: SRA accession

characteristic: collection date

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

text: SC

text: public

text: RUS

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

characteristic: isolate

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: M

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

text: Protocols: Placental and decidual tissue for immunohistochemistry were obtained from elective terminations of normal pregnancies at Addenbrooke’s Hospital between 6 and 12 weeks gestation. Decidual and placental tissue were washed in HAMS F12 medium, macroscopically separated and then washed for at least 10 mins in RPMI or HAMS F12 medium respectively before processing. Decidual tissues were chopped using scalpels into approximately 0.2 mm3 cubes and enzymatically digested in 15ml 0.4mg/mL collagenase V (Sigma, C-9263) solution in RPMI 1640 medium (ThermoFisher Scientific, 21875-034)/10% FCS (Biosfera, FB-1001) at 37°C for 45 min. The supernatant was diluted with medium and passed through 100um cell sieve (Corning, 431752) and then 40um cell sieve (Corning, 431750). The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min. Each first trimester placenta was placed in a petri dish and the placental villi were scraped from the chorionic membrane using a scalpel. The stripped membrane was discarded and the resultant villous tissue was enzymatically digested in 70 ml 0.2% trypsin 250 (Pan Biotech P10-025100P)/0.02% EDTA (Sigma E9884) in PBS with stirring at 37°c for 9 min. The disaggregated cell suspension was passed through sterile muslin gauze (Winware food grade) and washed through with Hams F12 medium (Biosera SM-H0096) containing 20% FBS (Biosera FB-1001). Cells were pelleted from the filtrate by centrifugation and re-suspended in Hams F12. The undigested, gelatinous tissue remnant was retrieved from the gauze and further digested with 10-15 ml collagenase V at 1.0mg/ml (Sigma C9263) in Hams F12 medium/10% FBS with gentle shaking at 37°C for 10 min. The disaggregated cell suspension from collagenase digestion was passed through sterile muslin gauze and the cells pelleted from the filtrate as before. Cells obtained from both enzyme digests were pooled together and passed through 100um cell sieve (Corning, 431752) and washed in Hams F12. The flow-through was centrifuged and resuspended in 5ml of red blood cell lysis buffer (Invitrogen, 00-4300) for 10min. Decidual and blood cells were incubated at 4°C with 2.5ul of antibodies in 1% FBS in DPBS without Calcium and Magnesium (ThermoFisher Scientific, 14190136). DAPI was used for live/dead discrimination. We used an antibody panel designed to enrich for certain population for single-cell sorting and single-cell RNA sequencing (scRNA-seq). Cells were sorted using a Becton Dickinson (BD) FACS Aria Fusion with 5 excitation lasers (355nm, 405nm, 488nm, 561nm and 635nm Red), and 18 fluorescent detectors plus forward and side scatter. The sorter was controlled using BD FACS DIVA software (version 7). For single-cell RNA-seq using the plate-based SS2 protocol, we created overlapping gates that comprehensively and evenly sampled all immune cell population in the decidua. B cells (CD19+ /or CD20+) cells were excluded from our analysis, due to its absence in decidua. Single cells were sorted into 96-well full-skirted Eppendorf plated chilled to 4C, prepared with lysis buffer consisting of 10 ul of TCL buffer (Qiagen) supplemented with 1% b-mercaptoethanol. Single-cell lysates were sealed, vortexed, spin down at 300g at 4C for 1 min, immediately placed on dry ice, and transferred for storage at -80C. The SS2 protocol was performed on single-cells as described previously, with some modifications. Libraries were sequenced aiming at an average depth of 1 million reads/cell, on an Illumina HiSeq 2000 with v4 chemistry (paired-end 75-bp reads). RNA was extracted, cDNA created and amplified, as part of the smart-seq 2 protocol. Libraries were made using Nextera XT

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RUS

characteristic: SRA accession

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

characteristic: isolate

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

characteristic: strain

text: Mycobacterium tuberculosis


text: 31736907; 35780211

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: RUS

characteristic: Submitter Id

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis

characteristic: title


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RUS

characteristic: SRA accession

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

text: SC

text: public

text: RUS

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

characteristic: isolate

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RUS

characteristic: SRA accession

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

text: not known

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

characteristic: strain

text: Mycobacterium tuberculosis

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: T

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

text: not available

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


text: 31736907; 35780211

text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: RUS

characteristic: Submitter Id

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

characteristic: strain

text: Mycobacterium tuberculosis

characteristic: title


text: Mycobacterium tuberculosis

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: RUS

characteristic: SRA accession

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

characteristic: isolate

text: not known

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: RUS

characteristic: Submitter Id

text: Mycobacterium

text: Russia

text: Homo sapiens

text: disease

text: not known

text: Mycobacterium tuberculosis

characteristic: organism

text: Mycobacterium tuberculosis

text: human

text: Mycobacterium tuberculosis


text: Mycobacterium tuberculosis

text: SC

text: public

text: RUS

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: Russia

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease

characteristic: host health state

text: not known

characteristic: isolation source

text: Mycobacterium tuberculosis

text: Mycobacterium tuberculosis

text: human

characteristic: specific host

text: Mycobacterium tuberculosis


characteristic: ENA-FIRST-PUBLIC

text: Wellcome Sanger Institute

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

characteristic: broker name

text: NK

characteristic: cell gating

text: 6 to 12 weeks gestation

characteristic: clinical information

text: human

characteristic: common name

characteristic: description

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: decidua

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Wellcome Sanger Institute

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: 6 to 12 weeks gestation

text: human

text: adult

text: normal

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: decidua

text: Homo sapiens

text: female


text: Plasmodium falciparum 3D7

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Plasmodium falciparum 3D7

text: 454 Sequencing

characteristic: sample description

text: Plasmodium falciparum 3D7

characteristic: strain


text: DUKE

text: public

text: ArrayExpress

characteristic: broker name

text: Protocols: In order to establish single spore isolates sporophytes were surface sterilized and their spore content germinated in petri dishes (9 mm diameter) containing full strength Hoaglands medium (14h day/10h night, 40 mmol/m2/sec, 25 oC). After one week ten sporelings were transplanted to new separate Petri dishes in order to establish single spore isolates. Emerging protonemata (appr. 2 weeks old) were transferred to liquid culture (full strength Hoaglands solution) and two weeks later, contents of the liquid cultures were emptied into small pots (5 x 5 cm) filled with soil (1:1 mixture of potting soil and sand). Single spore isolates were kept under these conditions until gametophytes filled the pot (appr. 1.5-2 months). Plants were watered (ddH2O) from below. To generate sufficient material for RNA extraction and to correct for the inherent stochasticity of gene expression the single genetic individual was clonally replicated by dividing the mat into eight equal parts and each was transferred to a new pot. Four pots (referred to as sporophyte pots) were immediately brought to the greenhouse whereas the rest (referred to as gametophyte pots) were kept in a growth chamber and received water just from below to prevent self-fertilization (14h day/10h night, 40 mmol/m2/sec, 25 oC). When the first gametangia and/or young sporophytes appeared in the sporophyte pots (appr. after one month) the gametophyte pots were also brought to the greenhouse. Gametophyte and sporophyte pots were grown next to one other in the greenhouse for at least one month and were watered (ddH2O) for 10 minutes at 120 minute intervals by an automatic misting system. Sporophyte and gametophyte tissues were collected separately from each pot in parallel between 8-10 am. Premeiotic sporophytes with both swollen and unswollen capsules (sporangia) were clipped at their bases. Gametophyte tissues were obtained by clipping the top five millimeters from the gametophores. Tissues collected were immediately immersed into RNAlater solution (Ambion, Woodward, Austin, TX) and stored at -80 oC prior to RNA extraction (for appr. 2-3 weeks).

characteristic: description

text: Funaria hygrometrica

text: Funaria hygrometrica

text: gametophyte

characteristic: organism part

text: Funaria hygrometrica


characteristic: ENA-CHECKLIST

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: anonymized name

text: United Kingdom

characteristic: country

text: not available: not collected

characteristic: host status

text: not available: not collected

characteristic: isolation source

text: Mycobacterium avium subsp. paratuberculosis

text: not available: not collected

characteristic: serovar

text: Lab

characteristic: specific host

characteristic: title


text: Vibrio cholerae

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: Vibrio cholerae

characteristic: organism

text: Vibrio cholerae


text: Vibrio cholerae

characteristic: ENA-LAST-UPDATE

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: Vibrio cholerae

text: Vibrio cholerae


text: Vibrio cholerae

text: SC

text: public

text: N16961M2-sc-2011-08-30T12:20:25Z-1264824

text: Vibrio cholerae

text: Vibrio cholerae


text: 26116186; 26686880; 31736907; 33075053; 34461978; 35780211

text: Mycobacterium tuberculosis

characteristic: ENA-CHECKLIST

text: SC

text: public

text: GBR

characteristic: collection date

text: Mycobacterium

characteristic: genus

text: United Kingdom: Midlands

characteristic: geographic location (country and/or sea)

text: Homo sapiens

characteristic: host

text: disease: tuberculosis

characteristic: host health state

characteristic: isolate

text: not known

text: Mycobacterium tuberculosis

characteristic: pubmed id

text: Mycobacterium tuberculosis

text: human

text: Bir 264

characteristic: strain


text: Mycobacterium tuberculosis

characteristic: ArrayExpress-Species

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-FIRST-PUBLIC

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: GBR

text: Mycobacterium

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