text: BOKU

text: public

text: A. Seidl et al.

text: 51.45718 37.888532

text: Astragalus austriacus

text: Astragalus austriacus

text: WHB 73153

text: Astragalus GBS


status: PUBLIC

tag: attribute

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: BOKU

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: A. Seidl et al.

text: GBS data of silica gel dried leaf material

characteristic: description

text: 51.5696° N, 36.0890° E

text: Astragalus agrestis

characteristic: organism

text: Astragalus agrestis

text: WHB 73209

text: Astragalus GBS

characteristic: title


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 47.23481 39.65665

text: Astragalus austriacus

text: Astragalus austriacus

text: WHB 74128-74131

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 47.23481 39.65665

text: Astragalus austriacus

text: Astragalus austriacus

text: WHB 74128-74131

text: Astragalus GBS repetition


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 47.87949 40.2121

text: Astragalus austriacus

text: Astragalus austriacus

text: WHB 74135

text: Astragalus GBS


text: BOKU

text: public

text: K.-G. Bernhardt et al.

text: 44.3378° N, 78.8398° E

text: Astragalus danicus

text: Astragalus danicus

text: WBH 76476

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 51.68706 73.4376

text: Astragalus austriacus

text: Astragalus austriacus

text: WHB 74881

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 53.5715° N, 62.4608° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74891

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 53.5715° N, 62.4608° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74891

text: Astragalus GBS repetition


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 55.2683° N, 67.2877° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74887

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 54.9690° N, 72.5628° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74894

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 54.9896° N, 74.2275° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74895

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 55.2723° N, 78.2852° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74896

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 54.3851° N, 80.6662° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74899

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 53.3401° N, 80.9572° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: WHB 74902

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 50.39749 46.85141

text: Astragalus austriacus

text: Astragalus austriacus

text: no voucher

text: Astragalus GBS


text: BOKU

text: public

text: S. Pfanzelt et al.

text: 52.6674° N, 50.0354° E

text: Astragalus sulcatus

text: Astragalus sulcatus

text: no voucher

text: Astragalus GBS


E-MTAB-11478:Diploid rep1_1

text: public

text: E-MTAB-11478:Diploid rep1_1

tag: Namespace:The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

characteristic: common name

text: Protocols: Cells were washed with PBS and trypsinized gSYNC DNA extraction kit (Geneaid) The DNA was digested with MspI (NEB), Subsequently, bisulfite treatment was conducted using the ZYMO EZ DNA Methylation-Gold Kit. The converted DNAs are then amplified by twelve cycles of PCR, using 25 μl KAPA HiFi HotStart Uracil+ ReadyMix

text: Homo sapiens

text: Homo sapiens

text: embryo

characteristic: organism part

characteristic: ploidy

text: Homo sapiens

text: Diploid rep1_1


E-MTAB-11478:Diploid rep1_2

characteristic: ENA-CHECKLIST

text: The Azrieli Center for Stem Cells and Genetic Research, Department of Genetics, Silberman Institute of Life Sciences, The Hebrew University

text: public

text: E-MTAB-11478:Diploid rep1_2

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Diploid rep1_2


E-MTAB-11478:Diploid rep2_1

characteristic: ENA-FIRST-PUBLIC

text: public

text: E-MTAB-11478:Diploid rep2_1

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Diploid rep2_1


E-MTAB-11478:Diploid rep2_2

characteristic: ENA-LAST-UPDATE

text: public

text: E-MTAB-11478:Diploid rep2_2

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Diploid rep2_2


E-MTAB-11478:Diploid Xi_1

characteristic: External Id

text: public

text: E-MTAB-11478:Diploid Xi_1

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Diploid Xi_1


E-MTAB-11478:Diploid Xi_2

characteristic: INSDC center name

text: public

text: E-MTAB-11478:Diploid Xi_2

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Diploid Xi_2


E-MTAB-11478:Haploid rep1_1

characteristic: INSDC first public

text: public

text: E-MTAB-11478:Haploid rep1_1

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Haploid rep1_1


E-MTAB-11478:Haploid rep1_2

characteristic: INSDC last update

text: public

text: E-MTAB-11478:Haploid rep1_2

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Haploid rep1_2


E-MTAB-11478:Haploid rep2_1

text: public

characteristic: INSDC status

text: E-MTAB-11478:Haploid rep2_1

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Haploid rep2_1


E-MTAB-11478:Haploid rep2_2

text: public

characteristic: SRA accession

text: E-MTAB-11478:Haploid rep2_2

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Haploid rep2_2


E-MTAB-11478:Triploid clone H_1

text: public

text: E-MTAB-11478:Triploid clone H_1

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Triploid clone H_1


E-MTAB-11478:Triploid clone H_2

text: public

text: E-MTAB-11478:Triploid clone H_2

text: ArrayExpress

text: embryonic stem cell

text: human

characteristic: description

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Triploid clone H_2


E-MTAB-11478:Triploid clone K_1

text: public

text: E-MTAB-11478:Triploid clone K_1

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Triploid clone K_1


E-MTAB-11478:Triploid clone K_2

text: public

text: E-MTAB-11478:Triploid clone K_2

text: ArrayExpress

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Triploid clone K_2

characteristic: title


E-MTAB-11478:Triploid clone L_1

text: public

text: E-MTAB-11478:Triploid clone L_1

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: human

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Triploid clone L_1


E-MTAB-11478:Triploid clone L_2

text: public

text: E-MTAB-11478:Triploid clone L_2

text: ArrayExpress

text: embryonic stem cell

text: human

characteristic: common name

text: Homo sapiens

text: Homo sapiens

text: embryo

text: Homo sapiens

text: Triploid clone L_2


text: public

tag: Namespace:Division of Rheumatology, Department of Medicine/Solna, Karolinska Institutet

text: ArrayExpress

text: osteoclast

text: human

text: Protocols: Collection of adherent cells from osteoclast cultures Peripheral blood monocytes (5X10^5/ml) cultured in DMEM+10% FBS in the presence of 25ng/ml M-CSF for 3 days. 50% of the medium was replaced by then and 15ng/ml M-CSF and 1ng/ml RANK-L were added. The cells were cultured for 3 more days. Human monoclonal antibodies 146+:01G07 or 1362:01E02 were added to the cultures in the last 3 days in 5microgram/ml concentration or the cells were left without antibody treatment. RNEeasy PLUS from Qiagen Oligo-dT

text: donor 1

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: blood

characteristic: organism part

text: monocyte

characteristic: progenitor cell type

text: Homo sapiens


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: Division of Rheumatology, Department of Medicine/Solna, Karolinska Institutet

text: public

text: ArrayExpress

text: osteoclast

text: human

text: donor 2

text: Homo sapiens

text: Homo sapiens

text: blood

text: monocyte

text: Homo sapiens


characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: public

text: ArrayExpress

text: osteoclast

text: human

text: donor 3

text: Homo sapiens

text: Homo sapiens

text: blood

text: monocyte

text: Homo sapiens


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: osteoclast

text: human

text: donor 4

text: Homo sapiens

text: Homo sapiens

text: blood

text: monocyte

text: Homo sapiens


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: osteoclast

text: human

text: donor 5

text: Homo sapiens

text: Homo sapiens

text: blood

text: monocyte

text: Homo sapiens


text: public

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: osteoclast

text: human

text: donor 1

text: Homo sapiens

text: Homo sapiens

text: blood

text: monocyte

text: Homo sapiens


SAMIN0000079-TRAINING SAMPLE

text: KLE TEch

text: public

text: SAMIN0000079-TRAINING SAMPLE

tag: Namespace:KLE TEch

text: IBDC

characteristic: collecting institution

text: Collector 1

characteristic: collector name

text: DESCRIPTION FOR TRAINING SAMPLE

characteristic: description

text: India

characteristic: geographic location (country and/or sea)

text: yes

characteristic: hospitalisation

text: Human

characteristic: host common name

text: recovered

characteristic: host disease outcome

text: not collected

characteristic: host health state

text: Homo sapiens

characteristic: host scientific name

text: male

characteristic: host sex

characteristic: host subject id

characteristic: isolate

text: Severe acute respiratory syndrome coronavirus 2

characteristic: organism

characteristic: receipt date

text: active surveillance in response to outbreak

characteristic: sample capture status

text: TRAINING SAMPLE


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany

unit: week

characteristic: age

text: ArrayExpress

characteristic: broker name

text: unestrus

characteristic: clinical information

text: house mouse

characteristic: common name

text: Protocols: To generate single cell suspensions, freshly isolated whole tissues including ovary, oviduct and tissue pieces from uterus, cervix, vagina and spleen were treated by enzymatic digestion. All tissues were initially incubated separately in 2 ml Eppendorf tubes containing 0,25% trypsin in PBS and digested for 30min at 37°C with gentle rocking. A second digestion buffer containing 25 mg/ml Collagenase I, 25 mg/ml Collagenase II, 50mg/ml Collagenase IV, and 25 mg/ml Dispase II in PBS was added, and tissues further dissociated for 2.5 hours at 37 °C with gentle rocking. Enzymatic digestion was quenched by addition of 10% FCS in PBS on ice. The cell suspensions were passaged through a 40µm cell strainer (Greiner Bio One) to remove cell debris and buffer residue. Cell suspensions were gently centrifuged at 350g for 7 min at 4°C. Cells were resuspended in PBS containing 0,04% FCS, 2 mM EDTA and propidium iodide (PI) was added to final concentration of 1 µg/ml prior to FACS sorting. 10x 3'-scRNA-seq ver. 3.0 and 3.1 (10X Genomics® User guide Rev.C and D) 10x 3'-scRNA-seq ver. 3.0 and 3.1 (10X Genomics® User guide Rev.C and D)

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: uterine cervix

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Center (DKFZ), Heidelberg, Germany

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: unestrus

text: house mouse

characteristic: description

text: adult

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: oviduct

text: Mus musculus

text: female


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: unestrus

characteristic: clinical information

text: house mouse

characteristic: common name

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: uterus

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: unestrus

text: house mouse

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: vagina

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: unestrus

text: house mouse

characteristic: description

text: adult

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: uterine cervix

text: Mus musculus

text: female


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: unestrus

characteristic: clinical information

text: house mouse

characteristic: common name

text: adult

text: normal

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: unestrus

text: house mouse

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: ovary

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: house mouse

characteristic: description

text: adult

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: uterus

text: Mus musculus

text: female


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: proestrus

characteristic: clinical information

text: house mouse

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text: adult

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text: wild type genotype

text: Mus musculus

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text: uterine cervix

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: proestrus

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text: Mus musculus

text: Mus musculus

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text: Mus musculus

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characteristic: ENA-CHECKLIST

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text: public

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text: ArrayExpress

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text: adult

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text: Mus musculus

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text: Mus musculus

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text: Mus musculus

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text: public

characteristic: INSDC status

characteristic: SRA accession

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text: ArrayExpress

characteristic: broker name

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text: house mouse

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text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: proestrus

text: house mouse

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text: normal

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characteristic: individual

text: Mus musculus

text: Mus musculus

text: uterus

characteristic: organism part

text: Mus musculus

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characteristic: ENA-CHECKLIST

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characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: proestrus

text: house mouse

characteristic: description

text: adult

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text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

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text: Mus musculus

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text: public

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characteristic: SRA accession

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text: ArrayExpress

characteristic: broker name

text: diestrus

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text: Mus musculus

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text: Mus musculus

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text: public

text: ArrayExpress

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text: Mus musculus

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text: Mus musculus

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characteristic: ENA-CHECKLIST

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characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

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text: adult

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text: Mus musculus

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text: Mus musculus

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text: Mus musculus

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characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: diestrus

characteristic: clinical information

text: house mouse

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text: adult

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text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: diestrus

text: house mouse

text: adult

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text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: uterus

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

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characteristic: ENA-CHECKLIST

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characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: diestrus

text: house mouse

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text: adult

text: normal

text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

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text: Mus musculus

text: female


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: estrus

characteristic: clinical information

text: house mouse

characteristic: common name

text: adult

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text: wild type genotype

text: Mus musculus

text: Mus musculus

text: uterine cervix

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: estrus

text: house mouse

text: adult

characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: ovary

characteristic: organism part

text: Mus musculus

text: female

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characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: Submitter Id

text: ArrayExpress

text: estrus

text: house mouse

characteristic: description

text: adult

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text: wild type genotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: oviduct

text: Mus musculus

text: female


characteristic: INSDC first public

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text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: age

text: ArrayExpress

characteristic: broker name

text: estrus

characteristic: clinical information

text: house mouse

characteristic: common name

text: adult

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text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spleen

text: Mus musculus

text: female


text: public

text: ArrayExpress

text: estrus

text: house mouse

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characteristic: developmental stage

text: normal

characteristic: disease

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: uterus

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

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characteristic: External Id

characteristic: INSDC center name

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characteristic: sample storage buffer

characteristic: sample storage temperature

text: 400 ul

characteristic: sample volume or weight for DNA extraction

text: Danio rerio

text: Miseq

characteristic: sequencing method

text: blank


TYR_extraction shield blank

characteristic: External Id

characteristic: INSDC center name

text: public

characteristic: INSDC status

characteristic: SRA accession

text: TYR_extraction shield blank

text: illumina

text: zebrafish

characteristic: common name

text: No

text: Danio rerio

text: Danio rerio

text: Zymo SHIELD

text: 400 ul

text: Danio rerio

text: Miseq

text: blank

text: extraction shield blank

characteristic: title


characteristic: Batch nr

characteristic: ENA-CHECKLIST

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: illumina

characteristic: adapters

text: zebrafish

text: Yes

text: Danio rerio

text: Danio rerio

text: Zymo SHIELD

text: 400 ul

text: Danio rerio

text: Miseq

text: A(a)


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: illumina

text: zebrafish

characteristic: description

text: Yes

text: Danio rerio

characteristic: host scientific name

text: Danio rerio

characteristic: organism

characteristic: project name

text: Zymo SHIELD

text: 400 ul

text: Danio rerio

text: Miseq

text: B(a)


characteristic: External Id

characteristic: INSDC center name

text: public

text: illumina

text: zebrafish

text: Yes

text: Danio rerio

text: Danio rerio

text: Zymo SHIELD

characteristic: sample storage buffer

characteristic: sample storage temperature

text: 400 ul

characteristic: sample volume or weight for DNA extraction

text: Danio rerio

text: Miseq

characteristic: sequencing method

text: C(a)


characteristic: ENA-CHECKLIST

text: NEWCASTLE UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:NEWCASTLE UNIVERSITY

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: Protocols: Samples were collected from the clinic and dissected before storage in hypothermosol over night. Tissues were digested using collagenase type 4 and trypsin before dead cell removal using FACS. Nucleic acids were extracted as part of the 10x Genomics Chromium Single Cell V(D)J protocol. Nucleic acid libraries were constructed as part of the 10x Genomics Chromium Single Cell V(D)J protocol.

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: carnegie stage 16

characteristic: embryo stage

text: section one

characteristic: fraction

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: lower vertebrae

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NEWCASTLE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: embryo stage

text: normal

text: carnegie stage 16

text: section two

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: lower vertebrae; yolk sac stalk

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

text: NEWCASTLE UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: embryo stage

characteristic: developmental stage

text: normal

text: carnegie stage 16

text: section three

text: Homo sapiens

text: Homo sapiens

text: mid-low vertebrae

text: Homo sapiens

text: female


text: NEWCASTLE UNIVERSITY

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

characteristic: disease

text: carnegie stage 16

characteristic: embryo stage

text: section four

characteristic: fraction

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: liver

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: NEWCASTLE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: carnegie stage 16

text: section five

text: Homo sapiens

text: Homo sapiens

text: mid vertebrae

text: Homo sapiens

text: female

characteristic: title


characteristic: ENA-CHECKLIST

text: NEWCASTLE UNIVERSITY

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: Submitter Id

text: ArrayExpress

text: human

characteristic: description

text: embryo stage

text: normal

text: carnegie stage 16

text: section six

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: internal organs

text: Homo sapiens

text: female


text: NEWCASTLE UNIVERSITY

text: public

characteristic: SRA accession

text: ArrayExpress

characteristic: broker name

text: human

characteristic: common name

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: carnegie stage 16

characteristic: embryo stage

text: section seven

text: Homo sapiens

text: Homo sapiens

text: brain; heart; eye

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NEWCASTLE UNIVERSITY

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: carnegie stage 16

text: section eight

characteristic: fraction

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: upper vertebrae

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


characteristic: ENA-CHECKLIST

characteristic: External Id

text: NEWCASTLE UNIVERSITY

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: carnegie stage 16

text: section nine

text: Homo sapiens

text: Homo sapiens

text: internal organs

text: Homo sapiens

text: female

characteristic: title


text: NEWCASTLE UNIVERSITY

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: human

characteristic: description

text: embryo stage

text: normal

text: carnegie stage 16

text: section ten

text: Homo sapiens

characteristic: organism

text: Homo sapiens

text: brain; heart; eye

text: Homo sapiens

text: female


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: NEWCASTLE UNIVERSITY

text: public

text: ArrayExpress

text: human

characteristic: common name

text: embryo stage

characteristic: developmental stage

text: normal

characteristic: disease

text: carnegie stage 16

characteristic: embryo stage

text: section eleven

text: Homo sapiens

text: Homo sapiens

text: brain; stroma

text: Homo sapiens

text: female


characteristic: ENA-CHECKLIST

characteristic: External Id

text: NEWCASTLE UNIVERSITY

text: public

text: ArrayExpress

text: human

text: embryo stage

text: normal

text: carnegie stage 16

text: section twelve

characteristic: fraction

characteristic: individual

text: Homo sapiens

text: Homo sapiens

text: brain; stroma

characteristic: organism part

text: Homo sapiens

text: female

characteristic: sex


Awh smallRNA

text: UNIVERSITY OF OSLO

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Awh smallRNA

tag: Namespace:UNIVERSITY OF OSLO

text: mixed

text: small RNAs from Abeoforma whisleri

text: mixed

text: Abeoforma whisleri

text: Abeoforma whisleri

text: Awh smallRNA

characteristic: title


112912_ 1_A01

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: Evolutionary Biology Centre

text: public

text: 112912_ 1_A01

tag: Namespace:Evolutionary Biology Centre

characteristic: Submitter Id

text: Acanthoscelides obtectus

characteristic: organism

text: Acanthoscelides obtectus


text: Evolutionary Biology Centre

text: public

text: Acanthoscelides obtectus

text: Acanthoscelides obtectus


151227_ 1_A01

text: Evolutionary Biology Centre

text: public

text: 151227_ 1_A01

text: Acanthoscelides obtectus

text: Acanthoscelides obtectus


151305_ 1_A01

text: Evolutionary Biology Centre

text: public

text: 151305_ 1_A01

text: Acanthoscelides obtectus

text: Acanthoscelides obtectus


113651_ 1_A01

text: Evolutionary Biology Centre

text: public

text: 113651_ 1_A01

text: Acanthoscelides obtectus

text: Acanthoscelides obtectus


text: 1. Plate-forme Technologique Biomics - Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Paris, France 2. Hub de Bioinformatique et Biostatistique - Departement Biologie Computationnelle, Institut Pasteur, 75015 Paris, France

text: public

tag: Namespace:1. Plate-forme Technologique Biomics – Centre de Ressources et Recherches Technologiques (C2RT), Institut Pasteur, Paris, France 2. Hub de Bioinformatique et Biostatistique - Departement Biologie Computationnelle, Institut Pasteur, 75015 Paris, France

text: ArrayExpress

characteristic: broker name

text: Protocols: RNA extraction and RNAseq have been performed in two different batches, corresponding to Ag43 and the nanobodies experiments. Bacteria were grown as described above until OD600 =0.5 and then left for aggregation at 37°C for 3h in separating funnel. Then, by opening the tap of the separating funnel, only the lower part of the culture, corresponding to the aggregated part (in strain forming aggregates), is collected and placed in an eppendorf tube. The aggregated or non aggregated cells were then washed with 2 volumes of RNAprotect (Qiagen) to prevent RNA degradation, and the pellets were kept at -80°C Bacterial strains used in this study are listed in Supplementary table 8 S8. All strains were grown in Miller’s Lysogeny Broth (LB) (Corning) supplemented with chloramphenicol (25µg/mL), kanamycin (50µg/mL) or ampicillin (100µg/mL) when needed. Cultures where incubated at 37°C with 180 rpm shaking during growth phase or put at 37°C in static condition during aggregation phase. Cultures on solid media were done on LB with 1.5% agar supplemented with antibiotics when required. Prior to liquid cultures, bacteria were always streaked on LB agar from glycerol stocks. All media and chemicals were purchased from Sigma-Aldrich unless mentioned otherwise. All experiments and genetic construction were done in E. coli K12 MG1655 (F-,-, rph-1) obtained E. coli genetic stock center CGSC#6300. Ag43 (Flu) was used as a “natural” adhesin since it is the major aggregation factor in E. coli K12. For the Ag43 natural adhesin, we used two sets of couples. The first couple is composed of ∆flu deleted for ag43 and its isogenic opposite, PcLflu, constitutively expressing Ag43 (high level of Ag43). Since Ag43 is a naturally phase variable adhesin we also used a strain in which the Ag43 ON or OFF status is traceable through the use of an operon fusion of ag43 with the lacZ gene. The second couple is therefore composed of cultures of “lacZ blue” Ag43 ON cells and “lacZ white” Ag43 OFF cells. For the synthetic adhesins, we used “chimeric” proteins recently described in (Glass and Riedel-Kruse, 2018). These fusion proteins mainly consist of an anchoring and an adhesin domain. The outer membrane anchor is composed of the intimin N terminus from an enterohemorrhagic E. coli (EHEC O157:H7), including a small N-terminal signal peptide, a LysM domain for peptidoglycan binding, and a β-barrel for transmembrane insertion. The adhesin domain, composed of a nanobody (the variable domains of camelid heavy-chain antibodies) or its corresponding antigen, is then fused to the C-terminus part of the truncated intimin. We introduced the corresponding genetic constructions to replace the ag43 gene, under the control of the constitutive lambda PR promoter PcL. We used four couples of synthetic adhesins: Nb2-Ag2, Nb3-Ag3, Nb3-Ag2 and Nb2-Ag3. 1:1 mixture of cells constitutively expressing Ag2 and Nb2, and Ag3 and Nb3 were used as synthetic adhesins aggregates, while 1:1 mixture of cells constitutively expressing Ag2 and Nb3, and Ag3 and Nb2 were used as synthetic adhesins non-aggregating cells. E. coli MG1655 has the F-,l-, rph-1 genotype. ∆flu = MG1655 deleted of agn43, KmR. MG1655 PcLflu λPr placed in front of agn43, resulting in constitutive expression of the gene, CmR. MG1655 EndfluLacZzeo = lacZ gene is transcriptionally fused at the end of agn43, allowing the tracking of the ON/OFF status of the natural promoter of agn43, ZeoR. All other genotypes mean the synthetic adhesion locus is placed at the agn43 locus site, under the control of the λPr, KmR, CmR. Total RNA was extracted using MP Biomedicals FastRNA ProTM BLUE KIT following provider’s manual and treated with Ambion Turbo DNA-free™ kit to remove possible DNA contamination. Total RNA from 4 independent replicates for each strain/couple were checked on RNA6000 RNA chips on Bioanalyzer (Agilent) for its quality and integrity. The QIAseq Fast Select -5s/16s/23s (QIAGEN) was used for ribosomal RNA depletion according to manufacturer instructions. Libraries were built using a TruSeq Stranded mRNA library Preparation Kit (Illumina, USA) following the manufacturer’s protocol. Quality control was performed on an Agilent BioAnalyzer.

characteristic: description

text: MG1655 ∆flu PcLAg2; PcLNb2

characteristic: genotype

text: LB agar

characteristic: growth condition

text: Escherichia coli O17 str. K12a

text: Escherichia coli O17 str. K12a

text: whole organism

text: Escherichia coli O17 str. K12a

characteristic: strain


characteristic: ENA-CHECKLIST

characteristic: External Id

text: public

text: ArrayExpress

text: MG1655 ∆flu PcLAg2; PcLNb3

text: LB agar

text: Escherichia coli O17 str. K12a

text: Escherichia coli O17 str. K12a

text: whole organism

characteristic: organism part

text: Escherichia coli O17 str. K12a


characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: ArrayExpress

text: MG1655 ∆flu PcLAg3, PcLNb2

text: LB agar

text: Escherichia coli O17 str. K12a

text: Escherichia coli O17 str. K12a

text: whole organism

text: Escherichia coli O17 str. K12a


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: MG1655 ∆flu PcLAg3, PcLNb3

text: LB agar

text: Escherichia coli O17 str. K12a

text: Escherichia coli O17 str. K12a

text: whole organism

text: Escherichia coli O17 str. K12a


text: public

characteristic: SRA accession

text: ArrayExpress

text: MG1655 PcLflu

text: LB agar

text: Escherichia coli O17 str. K12a

text: Escherichia coli O17 str. K12a

text: whole organism

text: Escherichia coli O17 str. K12a

characteristic: title


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: MG1655 ∆flu

text: LB agar

text: Escherichia coli O17 str. K12a

text: Escherichia coli O17 str. K12a

text: whole organism

text: Escherichia coli O17 str. K12a


text: public

characteristic: Submitter Id

text: ArrayExpress

text: MG1655 EndfluLacZzeo - OFF

text: LB agar

text: Escherichia coli O17 str. K12a

characteristic: organism

text: Escherichia coli O17 str. K12a

text: whole organism

text: Escherichia coli O17 str. K12a


text: public

text: ArrayExpress

characteristic: broker name

characteristic: description

text: MG1655 EndfluLacZzeo - ON

text: LB agar

text: Escherichia coli O17 str. K12a

text: Escherichia coli O17 str. K12a

text: whole organism

text: Escherichia coli O17 str. K12a


text: Marine College, Shandong University

text: public

tag: Namespace:Marine College, Shandong University

text: Marine College, Shandong University

characteristic: collection date

text: seawater was pumped into a 500 L sterile sampling bags, brought ashore, subsequently filtered through 0.2 μm - pore-size polycarbonate filters, frozen at -80°C.

text: marine biome [ENVO:00000447]

characteristic: environment (biome)

text: microbial feature [ENVO:00002150]

characteristic: environment (feature)

text: coastal sea water [ENVO:00002150]

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

unit: m

characteristic: geographic location (depth)

unit: DD

characteristic: geographic location (latitude)

characteristic: geographic location (longitude)

text: mimarks-survey

characteristic: investigation type

text: uncultured marine microorganism

text: Phycosphere bacterial community of marine macroalgae and bacterial community of surrounding seawater and sediment

characteristic: project name

text: uncultured marine microorganism

text: Illumina Nova-PE250

characteristic: sequencing method

text: water

characteristic: water environmental package


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: Marine College, Shandong University

characteristic: INSDC center name

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: Marine College, Shandong University

text: marine biome [ENVO:00000447]

text: microbial feature [ENVO:00002150]

text: coastal sea water [ENVO:00002150]

text: China

text: mimarks-survey

text: uncultured marine microorganism

text: Phycosphere bacterial community of marine macroalgae and bacterial community of surrounding seawater and sedimenta

text: uncultured marine microorganism

text: Illumina Nova-PE250

characteristic: title

text: water


text: Marine College, Shandong University

text: public

characteristic: Submitter Id

text: Marine College, Shandong University

characteristic: collection date

text: Sediment samples were collected by a surface sediment sampler. Following collection, samples were placed in sterile 50 ml plastic bags, frozen at -80°C.

characteristic: description

text: marine biome [ENVO:00000447]

characteristic: environment (biome)

text: microbial feature [ENVO:01000007]

characteristic: environment (feature)

text: coastal sediment [ENVO:03000034]

characteristic: environment (material)

text: China

characteristic: geographic location (country and/or sea)

characteristic: geographic location (depth)

characteristic: geographic location (elevation)

text: mimarks-survey

text: uncultured marine microorganism

characteristic: organism

text: uncultured marine microorganism

text: sediment

characteristic: sediment environmental package

text: Illumina Nova-PE250


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

tag: Namespace:Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

unit: day

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: Protocols: The microdissected spinal cord central canal region from each mouse was dissociated into a cell suspension (two cell preparations each day, one from a young adult mouse and one from an aged mouse). Cells from each mouse were loaded into a well of the Chromium Next GEM chip (10x Genomics, cat# 1000127) and then into the Chromium Single Cell controller (10x Genomics) to partition cells in GEMs (Gel Beads-in-emulsion). Nuclei acid extraction was performed following the manufacturer's instructions (10x Genomics, as part of the Chromium Single Cell 3' v3.1). Libraries were generated using the Chromium Next GEM Single Cell 3ʹ GEM, Library & Gel Bead Kit v3.1 (cat# 1000092) following the manufacturer's instructions (10x Genomics).

text: adult

characteristic: developmental stage

text: wild type genotype

characteristic: genotype

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

characteristic: strain


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: wild type genotype

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-11563:A2-B001635-ARA-KGS_BB001635_340370-1_S206

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11563:A20-B001633-ARA-KGS_BB001633_339373-1_S56

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-11563:A24-B001634-ARA-KGS_BB001634_35865-1_S14

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-11563:A5-B001635-ARA-KGS_BB001635_340370-1_S209

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-11563:A6-B001636-ARA-KGS_BB001636_340371-1_S294

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F10-B001633-1_S166

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-115631647023036:F10-B001634-1_S250

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F10-B001635-1_S34

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F10-B001636-1_S118

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-115631647023036:F11-B001633-1_S167

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F11-B001634-1_S251

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F11-B001635-1_S35

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-115631647023036:F11-B001636-1_S119

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F12-B001633-1_S168

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F12-B001634-1_S252

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

text: public

text: E-MTAB-115631647023036:F12-B001635-1_S36

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F12-B001636-1_S120

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

text: Protocols: The ependymal cell layer from the thoracic spinal cord of FOXJ1-EGFP mice was microdissected and dissociated it into a cell suspension. GFP-positive DAPI-negative cells were then sorted into 384-well plates containing lysis buffer. GFP-positive DAPI-negative cells were sorted into lysis plates with a BD Influx Cell Sorter using 6 psi pressure and a 130 μm nozzle. Lysis plates were created by dispensing 0.4 μl lysis buffer (0.5 U Recombinant RNase Inhibitor (Takara Bio, 2313B), 0.0625% Triton X-100 (Sigma, 93443-100ML), 3.125 mM dNTP mix (Thermo Fisher, R0193), 3.125 μM Oligo-dT 30 VN (IDT, 5'AAGCAGTGGTATCAACGCAGAGTACT 30 VN-3') and 1:600,000 ERCC RNA spike-in mix (Thermo Fisher, 4456740)) into 384-well hard-shell PCR plates (Biorad HSP3901) using a Tempest liquid handler (Formulatrix). cDNA synthesis was performed using the Smart-seq2 protocol (Picelli et al., 2013, 2014). Briefly, 384-well plates containing single-cell lysates were thawed on ice followed by first strand synthesis. 0.6 μl of reaction mix (16.7 U/μl SMARTScribe TM Reverse Transcriptase (Takara Bio, 639538), 1.67 U/μl Recombinant RNase Inhibitor (Takara Bio, 2313B), 1.67X First-Strand Buffer (Takara Bio, 639538), 1.67 μM TSO (Exiqon, 5'-AAGCAGTGGTATCAACGCAGACTACATrGrG+G-3'), 8.33 mM DTT (Bioworld, 40420001-1), 1.67 M Betaine (Sigma, B0300-5VL), and 10 mM MgCl 2 (Sigma, M1028-10X1ML)) was added to each well using a Tempest liquid handler. Bulk wells received twice the amount of RT mix (1.2 μl). Reverse transcription was carried out by incubating wells on a ProFlex 2x384 thermal-cycler (Thermo Fisher) at 42°C for 90 min and stopped by heating at 70°C for 5 min. Subsequently, 1.6 μl of PCR mix (1.67X KAPA HiFi HotStart ReadyMix (Kapa Biosystems, KK2602), 0.17 μM IS PCR primer (IDT, 5'-AAGCAGTGGTATCAACGCAGAGT-3'), and 0.038U/μl Lambda Exonuclease (NEB, M0262L)) was added to each well with a Tempest liquid handler (Formulatrix). The amplified product was diluted with a ratio of 1 part cDNA to 10 parts 10mM Tris-HCl (Thermo Fisher, 15568025), and concentrations were measured with dye-fluorescence assay (Quant-iT dsDNA High Sensitivity kit; Thermo Fisher, Q33120) on a SpectraMax i3x microplate reader (Molecular Devices). These wells were reformatted to a new 384-well plate at a concentration of 0.3 ng/μl and final volume of 0.4 μl using an Echo 550 acoustic liquid dispenser (Labcyte). If the cell concentration was below 0.3 ng/μl, 0.4 μl of sample was transferred. Illumina sequencing libraries were prepared using the Nextera XT Library Sample Preparation kit (Illumina, FC-131-1096) (Darmanis et al., 2015; Schaum et al., 2018). Each well was mixed with 0.8 μl Nextera tagmentation DNA buffer (Illumina) and 0.4 μl Tn5 enzyme (Illumina), then tagmented at 55°C for 10 min. The reaction was stopped by adding 0.4 μl \Neutralize Tagment Buffer\ (Illumina) and spinning at room temperature (RT) in a centrifuge at 3220 xg for 5 min. Indexing PCR reactions were performed by adding 0.4 μl of 5 μM i5 indexing primer, 0.4 μl of 5 μM i7 indexing primer, and 1.2 μl of Nextera NPM mix (Illumina). PCR amplification was carried out on a ProFlex 2x384 thermal cycler using the following program: 1. 72°C for 3 minutes, 2. 95°C for 30 s, 3. 12 cycles of 95°C for 10 s, 55°C for 30 s, and 72°C for 1 min, and 4. 72°C for 5 min.

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F13-B001633-1_S169

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-115631647023036:F13-B001634-1_S253

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F13-B001635-1_S37

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F13-B001636-1_S121

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-115631647023036:F14-B001633-1_S170

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F14-B001634-1_S254

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F14-B001635-1_S38

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-115631647023036:F14-B001636-1_S122

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F15-B001633-1_S171

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F15-B001634-1_S255

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: public

text: E-MTAB-115631647023036:F15-B001635-1_S39

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F15-B001636-1_S123

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title


characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

characteristic: INSDC center name

text: public

text: E-MTAB-115631647023036:F16-B001633-1_S172

text: ArrayExpress

text: ependymal cell

text: house mouse

text: adult

text: GFP-positive

characteristic: immunophenotype

text: Mus musculus

characteristic: organism

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: single cell well quality


text: Division of Cell and Developmental Biology, School of Life Sciences, University of Dundee

text: public

text: E-MTAB-115631647023036:F16-B001634-1_S256

characteristic: age

text: ArrayExpress

characteristic: broker name

text: ependymal cell

text: house mouse

characteristic: common name

text: adult

characteristic: developmental stage

characteristic: genotype

text: GFP-positive

characteristic: individual

text: Mus musculus

text: Mus musculus

text: spinal cord

characteristic: organism part

text: Mus musculus

text: female

characteristic: sex

text: OK


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-115631647023036:F16-B001635-1_S40

characteristic: Submitter Id

text: ArrayExpress

text: ependymal cell

text: house mouse

characteristic: description

text: adult

text: GFP-positive

text: Mus musculus

text: Mus musculus

text: spinal cord

text: Mus musculus

text: female

text: OK

characteristic: strain

characteristic: title