text: Larval:Day 4 - ZFS:0000036

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: ZMP_phenotype_121_4dpf_pool11-sc-2190191

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 4dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGCATAGT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


status: PUBLIC

text: Larval:Day 5 - ZFS:0000037

tag: attribute

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

characteristic: ENA-CHECKLIST

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

characteristic: Submitter Id

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGCGATCT) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTCCTGCT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAGTGACT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACAGGAT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCCTCAAT) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTGGTTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAGTCTTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTCCATTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCGAAGTG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAACGCTG) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TTGGTATG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a single wild type zebrafish embryo collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGAACTGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACTTCGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCTCACGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCAGGAGG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TAAGTTCG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCCAGTCG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

characteristic: common name

text: Danio rerio

characteristic: organism

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGTATGCG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCATTGAG) is bases 13 to 20 of read 1 followed by CG and polyT.

characteristic: sample description

text: Danio rerio

text: mixed

characteristic: strain


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: Danio rerio

characteristic: ArrayExpress-Species

text: mixed

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TGGCTCAG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

characteristic: ArrayExpress-DevelopmentalStage

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TATGCCAG) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: ZMP_phenotype_122_5dpf_pool10-sc-2190213

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TCAGATTC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Larval:Day 5 - ZFS:0000037

text: Whole embryo

text: Danio rerio

text: mixed

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: ZMP_phenotype_122_5dpf_pool11-sc-2190214

text: zebrafish

text: Danio rerio

text: 3' end enriched mRNA from a pool of eight wild type zebrafish embryos collected at larval - 5dpf plus ERCC spike mix 1 (Ambion). A 8 base indexing sequence (TACTAGTC) is bases 13 to 20 of read 1 followed by CG and polyT.

text: Danio rerio

text: mixed


text: Plasmodium falciparum

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: malaria parasite P. falciparum

text: Plasmodium falciparum

text: Plasmodium falciparum


text: H9 Human embryonic stem cells

characteristic: ArrayExpress-CellType

text: Normal

characteristic: ArrayExpress-Phenotype

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-TimePoint

text: PHI

characteristic: ArrayExpress-Treatment

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with PHI technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: PHI

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Total RNA from H9 Human ESC treated with PHI technical replicate 2

characteristic: sample description

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

characteristic: ArrayExpress-Species

text: 24 hours

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with G6B technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with G6B technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

characteristic: ArrayExpress-CellType

text: Normal

characteristic: ArrayExpress-Phenotype

text: female

text: Homo sapiens

text: 24 hours

text: SC

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with CD200 technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-TimePoint

characteristic: ArrayExpress-Treatment

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with CD200 technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: FBS

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with FBS technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: FBS

text: SC

text: public

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

characteristic: organism

text: Total RNA from H9 Human ESC treated with FBS technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

characteristic: ArrayExpress-Species

text: 24 hours

characteristic: ENA-CHECKLIST

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with ACVR1B technical replicate 1

characteristic: sample description

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: External Id

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with ACVR1B technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

characteristic: ArrayExpress-CellType

text: Normal

characteristic: ArrayExpress-Phenotype

text: female

text: Homo sapiens

text: 24 hours

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with CD226 technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-TimePoint

text: SC

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with CD226 technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: APOH

characteristic: ArrayExpress-Treatment

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with APOH technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: APOH

text: SC

text: public

characteristic: SRA accession

characteristic: Submitter Id

text: human

characteristic: common name

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with APOH technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

characteristic: ArrayExpress-Species

text: 24 hours

text: FAM

characteristic: ENA-CHECKLIST

text: SC

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Total RNA from H9 Human ESC treated with FAM technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: FAM

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with FAM technical replicate 2

characteristic: sample description

text: Homo sapiens


text: H9 Human embryonic stem cells

characteristic: ArrayExpress-CellType

text: Normal

characteristic: ArrayExpress-Phenotype

text: female

text: Homo sapiens

text: 24 hours

characteristic: External Id

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with EFNB1 technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-TimePoint

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with EFNB1 technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: SELP

characteristic: ArrayExpress-Treatment

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with SELP technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: SELP

text: SC

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with SELP technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

characteristic: ArrayExpress-Species

text: 24 hours

characteristic: ENA-CHECKLIST

text: SC

text: public

text: human

characteristic: common name

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with SERPINE1 technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Total RNA from H9 Human ESC treated with SERPINE1 technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

characteristic: ArrayExpress-CellType

text: Normal

characteristic: ArrayExpress-Phenotype

text: female

text: Homo sapiens

text: 24 hours

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with ITIH4 technical replicate 1

characteristic: sample description

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-TimePoint

characteristic: External Id

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with ITIH4 technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-Treatment

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with QSOX1 technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with QSOX1 technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

characteristic: ArrayExpress-Species

text: 24 hours

text: GSN

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with GSN technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: GSN

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: human

characteristic: common name

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with GSN technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

characteristic: ArrayExpress-CellType

text: Normal

characteristic: ArrayExpress-Phenotype

text: female

text: Homo sapiens

text: 24 hours

text: SRGN

text: SC

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Total RNA from H9 Human ESC treated with SRGN technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-TimePoint

text: SRGN

text: SC

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with SRGN technical replicate 2

characteristic: sample description

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-Treatment

characteristic: External Id

text: SC

characteristic: INSDC center name

text: public

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with F2R technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

text: SC

characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with F2R technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

characteristic: ArrayExpress-Species

text: 24 hours

characteristic: ENA-CHECKLIST

text: SC

text: public

characteristic: SRA accession

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with FCER1A technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

text: Homo sapiens

text: 24 hours

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

characteristic: Submitter Id

text: human

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with FCER1A technical replicate 2

text: Homo sapiens


text: H9 Human embryonic stem cells

characteristic: ArrayExpress-CellType

text: Normal

characteristic: ArrayExpress-Phenotype

text: female

text: Homo sapiens

text: 24 hours

text: SC

text: public

text: human

characteristic: common name

text: Homo sapiens

text: Total RNA from H9 Human ESC treated with SERPINE2 technical replicate 1

text: Homo sapiens


text: H9 Human embryonic stem cells

text: Normal

text: female

characteristic: ArrayExpress-Sex

text: Homo sapiens

text: 24 hours

characteristic: ArrayExpress-TimePoint

text: SC

text: public

text: human

text: Homo sapiens

characteristic: organism

text: Total RNA from H9 Human ESC treated with SERPINE2 technical replicate 2

text: Homo sapiens


characteristic: External Id

text: MMRI

text: public

text: human

text: Homo sapiens

text: Homo sapiens

characteristic: title

type: has member


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL/6N / C57BL/6N

characteristic: ArrayExpress-Genotype

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: male

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 21 somite mouse embryo, with heterozygous Cpsf3 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus

characteristic: strain


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: male

text: Mus musculus

characteristic: ArrayExpress-Species

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: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 21 somite mouse embryo, with heterozygous Srsf7 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: External Id

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Total RNA from a single wildtype sibling female E9.5 21 somite mouse embryo, with heterozygous Srsf7 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL/6N / C57BL/6N

characteristic: ArrayExpress-Genotype

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: female

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 21 somite mouse embryo, with heterozygous Pitrm1 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: male

text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 22 somite mouse embryo, with heterozygous Cpsf3 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus

characteristic: strain


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 22 somite mouse embryo, with heterozygous Cpsf3 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

text: Mus musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 22 somite mouse embryo, with heterozygous Srsf7 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: male

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: External Id

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Total RNA from a single wildtype sibling male E9.5 22 somite mouse embryo, with heterozygous Fdft1 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL/6N / C57BL/6N

characteristic: ArrayExpress-Genotype

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: male

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 23 somite mouse embryo, with heterozygous Cpsf3 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 23 somite mouse embryo, with heterozygous Fdft1 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus

characteristic: strain


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 23 somite mouse embryo, with heterozygous Pitrm1 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: male

text: Mus musculus

text: SC

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

characteristic: Submitter Id

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 23 somite mouse embryo, with heterozygous Pitrm1 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

characteristic: ArrayExpress-Sex

text: Mus musculus

characteristic: External Id

text: SC

text: public

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Total RNA from a single wildtype sibling female E9.5 24 somite mouse embryo, with heterozygous Cpsf3 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


characteristic: ArrayExpress-DevelopmentalStage

text: C57BL/6N / C57BL/6N

characteristic: ArrayExpress-Genotype

text: Whole embryo

characteristic: ArrayExpress-OrganismPart

text: male

text: Mus musculus

characteristic: ArrayExpress-StrainOrLine

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 24 somite mouse embryo, with heterozygous Cpsf3 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: male

text: Mus musculus

text: SC

characteristic: INSDC center name

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling male E9.5 24 somite mouse embryo, with heterozygous Srsf7 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

characteristic: sample description

text: Mus musculus

characteristic: strain


text: C57BL/6N / C57BL/6N

text: Whole embryo

text: female

text: Mus musculus

characteristic: ArrayExpress-Species

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: SC

text: public

text: house mouse

text: Mus musculus

text: Total RNA from a single wildtype sibling female E9.5 24 somite mouse embryo, with heterozygous Pitrm1 / C57BL/6N parents. This study forms part of the Deciphering the Mechanisms of Developmental Disorders (DMDD) project.

text: Mus musculus


text: University of Manchester

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

tag: Namespace:University of Manchester

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: house mouse

text: Protocols: Palatal shelves from 5 embryos were dissected from E13.5 mouse embryos and pooled for RNA extraction. The same was done for E14.5 mouse embryos. All mice were housed with free access to food and water under specific pathogen free conditions at the University of Manchester. Temperature 20-22 °C, Humidity 40-60%, Specified mouse pathogen free conditions, 12 hours light/dark cycle. Nutrients Rat and Mouse Standard Diet no.1 expanded (Ban Kingman). All experiments were performed under regulations of The UK Home Office Scientific Procedures Act (1986). BALB/c mouse strain (Charles River Ltd, UK) were used for the experiment. Embryos were obtained after matings, the morning of the vaginal plug being considered embryonic day (E) 0.5. RNA was isolated mouse palatal shelves using the Qiagen RNeasy kit. SOLiDTM Total RNA-Seq Kit (PN 4445374)

characteristic: description

text: embryonic day 13.5

characteristic: developmental stage

text: Mus musculus

text: Mus musculus

text: palate

characteristic: organism part

text: Mus musculus

characteristic: title


characteristic: External Id

text: University of Manchester

characteristic: INSDC center name

text: public

text: ArrayExpress

text: house mouse

characteristic: common name

text: embryonic day 14.5

text: Mus musculus

characteristic: organism

text: Mus musculus

text: palate

text: Mus musculus


text: Mouse

characteristic: ArrayExpress-Phenotype

text: Mus musculus

characteristic: ArrayExpress-Species

text: SC

characteristic: INSDC first public

text: public

text: house mouse

text: Mus musculus

text: Mus musculus


E-MTAB-3156:Ring1aKO H3K4me1 rep2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: London Research Institute CRUK

text: public

text: E-MTAB-3156:Ring1aKO H3K4me1 rep2

tag: Namespace:London Research Institute CRUK

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: house mouse

text: Protocols: Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Ring1A-KO and Ring1A/B-dKO mESCs (2 x 108) were fixed in ChIP fix buffer (1% formaldehyde, 5 μM EGTA, 10 μM EDTA, 1 mM NaCl, and 0.5 mM HEPES in PBS) for 10 min at RT. Fixation was stopped by glycine (final concentration 125 mM). Cells were washed with PBS, buffer A (10 mM Hepes pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100) and buffer B (10 mM Hepes pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). Cell extracts were lysed in lysis buffer (25 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.1% Triton X-100, 1% SDS, 0.5% deoxycholate complete protease inhibitor (Roche)) for 30 min on ice. Sonication was performed using a BioRupter sonicator (Diagenode) to obtain an average DNA fragment size of 300 bp. Chromatin was diluted with ChIP dilution buffer (25 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.5% deoxycolate complete protease inhibitor (Roche)). Dynabeads® Protein G beads were blocked for 1 hr at 4°C with 1 mg/ml BSA and 1 mg/ml yeast tRNA (AM7119 Life Technologies,). For each IP 150 µg of chromatin and 5 µg of antibodies H3K4me1 (ab8895 Abcam) and H3K27ac (ab4729 Abcam) were used, for input samples the chromatin was directly taken to the DNA purification step. Chromatin was pre-cleared with blocked beads for 1 hr at 4°C. Chromatin was incubated with antibodies overnight at 4°C with rotation. Protein-antibody complexes were immuno-precipitated by addition of beads for 2 hr. Complexes were washed twice with wash buffer A (50 mM Tris pH 8.0, 150 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP40, 1 mM EDTA), once with wash buffer B (50 mM Tris pH8.0, 500 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP40, 1 mM EDTA), once with wash buffer C (50 mM Tris pH8.0, 250 mM LiCl, 0.5% deoxycholate, 1% NP40, 1 mM EDTA) and once with TE. Samples were treated with RNase A and Proteinase K and cross-links were reversed overnight. DNA was purified using a ChIP DNA clean and concentrator column (Zymo Research). Libraries were prepared using NEB Next Fast DNA Fragmentation and library preperation set for Ion Torrent kit (E6285S) following manufacturer’s instructions. Briefly, 40 ng of ChIP or input DNA was used for library generation. Libraries were size-selected for 250 bp fragments using 2% E-gel Size Select agarose gel (Life Technologies) and were amplified with 5 PCR cycles.

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Ring1a knockout

characteristic: phenotype

text: Mus musculus

characteristic: strain

text: Ring1aKO H3K4me1 rep2


E-MTAB-3156:Ring1a/b dKO H3K4me1 rep1

text: London Research Institute CRUK

characteristic: INSDC last update

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3156:Ring1a/b dKO H3K4me1 rep1

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: house mouse

text: Protocols: Ring1A−/−;Ring1Bfl/fl;Rosa26::CreERT2 mESCs (Ring1A-KO) were cultured as described previously in Endoh et al. Dishes were coated with 0.1 % gelatine and irradiated mouse embryonic fibroblasts (MEFs). For harvesting, ESCs were trypsinized and pre-plated twice for 30 min to remove contaminating feeder cells. Conditional deletion of Ring1B in Ring1A-KO cells was carried out by addition of 800 nM tamoxifen for 48 h as previously described in Endoh et al. Ring1A-KO and Ring1A/B-dKO mESCs (2 x 108) were fixed in ChIP fix buffer (1% formaldehyde, 5 μM EGTA, 10 μM EDTA, 1 mM NaCl, and 0.5 mM HEPES in PBS) for 10 min at RT. Fixation was stopped by glycine (final concentration 125 mM). Cells were washed with PBS, buffer A (10 mM Hepes pH 7.5, 10 mM EDTA, 0.5 mM EGTA, 0.75% Triton X-100) and buffer B (10 mM Hepes pH 7.5, 200 mM NaCl, 1 mM EDTA, 0.5 mM EGTA). Cell extracts were lysed in lysis buffer (25 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 0.1% Triton X-100, 1% SDS, 0.5% deoxycholate complete protease inhibitor (Roche)) for 30 min on ice. Sonication was performed using a BioRupter sonicator (Diagenode) to obtain an average DNA fragment size of 300 bp. Chromatin was diluted with ChIP dilution buffer (25 mM Tris pH 7.5, 150 mM NaCl, 5 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.5% deoxycolate complete protease inhibitor (Roche)). Dynabeads® Protein G beads were blocked for 1 hr at 4°C with 1 mg/ml BSA and 1 mg/ml yeast tRNA (AM7119 Life Technologies,). For each IP 150 µg of chromatin and 5 µg of antibodies H3K4me1 (ab8895 Abcam) and H3K27ac (ab4729 Abcam) were used, for input samples the chromatin was directly taken to the DNA purification step. Chromatin was pre-cleared with blocked beads for 1 hr at 4°C. Chromatin was incubated with antibodies overnight at 4°C with rotation. Protein-antibody complexes were immuno-precipitated by addition of beads for 2 hr. Complexes were washed twice with wash buffer A (50 mM Tris pH 8.0, 150 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP40, 1 mM EDTA), once with wash buffer B (50 mM Tris pH8.0, 500 mM NaCl, 0.1% SDS, 0.5% deoxycholate, 1% NP40, 1 mM EDTA), once with wash buffer C (50 mM Tris pH8.0, 250 mM LiCl, 0.5% deoxycholate, 1% NP40, 1 mM EDTA) and once with TE. Samples were treated with RNase A and Proteinase K and cross-links were reversed overnight. DNA was purified using a ChIP DNA clean and concentrator column (Zymo Research). Libraries were prepared using NEB Next Fast DNA Fragmentation and library preperation set for Ion Torrent kit (E6285S) following manufacturer’s instructions. Briefly, 40 ng of ChIP or input DNA was used for library generation. Libraries were size-selected for 250 bp fragments using 2% E-gel Size Select agarose gel (Life Technologies) and were amplified with 5 PCR cycles.

characteristic: description

text: Mus musculus

text: Mus musculus

text: tamoxifen-mediated knockout of Ring1b on Ring1a-/- background

text: Mus musculus

text: Ring1a/b dKO H3K4me1 rep1


E-MTAB-3156:Ring1a/b dKO H3K4me1 rep2

characteristic: External Id

text: London Research Institute CRUK

characteristic: INSDC center name

text: public

text: E-MTAB-3156:Ring1a/b dKO H3K4me1 rep2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Ring1a/b dKO H3K4me1 rep2

characteristic: title


E-MTAB-3156:Ring1aKO H3K27ac rep2

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: London Research Institute CRUK

characteristic: INSDC first public

text: public

text: E-MTAB-3156:Ring1aKO H3K27ac rep2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Ring1a knockout

text: Mus musculus

text: Ring1aKO H3K27ac rep2


E-MTAB-3156:Ring1aKO H3K4me1 rep1

characteristic: ENA-LAST-UPDATE

text: London Research Institute CRUK

text: public

text: E-MTAB-3156:Ring1aKO H3K4me1 rep1

text: ArrayExpress

text: embryonic stem cell

characteristic: cell type

text: house mouse

characteristic: genotype

text: Mus musculus

text: Mus musculus

text: Ring1a knockout

text: Mus musculus

text: Ring1aKO H3K4me1 rep1


E-MTAB-3156:Ring1a/b dKO H3K27ac rep2

text: London Research Institute CRUK

characteristic: INSDC last update

text: public

text: E-MTAB-3156:Ring1a/b dKO H3K27ac rep2

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

characteristic: phenotype

text: Mus musculus

characteristic: strain

text: Ring1a/b dKO H3K27ac rep2


E-MTAB-3156:Ring1a/bdKO input

text: London Research Institute CRUK

text: public

characteristic: INSDC status

characteristic: SRA accession

text: E-MTAB-3156:Ring1a/bdKO input

characteristic: Submitter Id

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Mus musculus

text: Ring1a/bdKO input


characteristic: External Id

text: London Research Institute CRUK

text: public

text: ArrayExpress

characteristic: broker name

text: embryonic stem cell

text: house mouse

characteristic: description

text: Mus musculus

text: Mus musculus

text: Ring1a knockout

text: Mus musculus


E-MTAB-3156:Ring1a/b dKO H3K27ac rep1

text: London Research Institute CRUK

characteristic: INSDC center name

text: public

text: E-MTAB-3156:Ring1a/b dKO H3K27ac rep1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

characteristic: common name

text: Mus musculus

characteristic: organism

text: Mus musculus

text: Mus musculus

text: Ring1a/b dKO H3K27ac rep1


E-MTAB-3156:Ring1aKO H3K27ac rep1

characteristic: ENA-CHECKLIST

characteristic: ENA-FIRST-PUBLIC

text: London Research Institute CRUK

text: public

text: E-MTAB-3156:Ring1aKO H3K27ac rep1

text: ArrayExpress

text: embryonic stem cell

text: house mouse

text: Mus musculus

text: Mus musculus

text: Ring1a knockout

text: Mus musculus

text: Ring1aKO H3K27ac rep1

characteristic: title


characteristic: ENA-LAST-UPDATE

text: University of Michigan

characteristic: INSDC first public

text: public

tag: Namespace:University of Michigan

text: ArrayExpress

text: definitive endoderm differentiated from H9 stem cells

characteristic: cell type

text: human

text: Protocols: Definitive endoderm was generated by treating H9 embryonic stem cells with Activin A for 3 days as previously described by Spence, et al. Nature 470: 105-109 (2010) and McCracken, et al. Nature Protocols 6:1920-1928 (2011). RNA was extracted from samples and then prepared for RNAseq using the Illumina TruSeq mRNA method

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: University of Michigan

characteristic: INSDC last update

text: public

text: ArrayExpress

text: human intestinal organoids derived from H9 stem cells

text: human

text: Protocols: H9 embryonic stem cells were differentiated into definitive endoderm and then treated with FGF4/Chiron (a Wnt agonist) in order to generate intestinal organoids as previously described by Spence, et al. Nature 470: 105-109 (2010) and McCracken, et al. Nature Protocols 6:1920-1928 (2011). RNA was extracted from samples and then prepared for RNAseq using the Illumina TruSeq mRNA method

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: University of Michigan

text: public

text: ArrayExpress

text: Undifferentiated H9 Stem Cells

text: human

text: Protocols: Cells were cultured in mTeSR on matrigel coated plates and collected for RNA when ~70% confluent with no signs of spontaneous differentiation. RNA was extracted from samples and then prepared for RNAseq using the Illumina TruSeq mRNA method

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Introgression line (IL) containing DNA segments of Hordeum bulbosum (Hb) in the genetic background of Hordeum vulgare (Hv)

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Hordeum vulgare introgression donor, barley cv. Emir

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: Emir


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Hordeum vulgare introgression donor, barley cv. Golden Promise

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Hordeum vulgare introgression donor, barley cv. Morex

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: Morex


text: IPK-Gatersleben

text: public

text: domesticated barley

text: Hordeum vulgare introgression donor, barley cv. Vada

text: Hordeum vulgare subsp. vulgare

text: Hordeum vulgare subsp. vulgare

text: Vada


text: public

tag: Namespace:Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan

text: ArrayExpress

characteristic: cell line

text: human

text: Protocols: MCF-7 cells were cultured in RPMI1640 medium (GIBCO/BRL) supplemented with 10% (v/v) fetal bovine serum (GIBCO/BRL), 2.0 g/L sodium bicarbonate, and were incubated in a humidified 37°C incubator with 5% CO2. Immunoprecipitation was performed according to the manufacturer’s protocol (Upstate Biotechnology, Inc., Lake Placid, NY) with slight modifications. MCF-7 cells were fixed for 10 min with 1% of formaldehyde at room temperature, and then quenched with a final of 1M of glycine. The cells were lysed and the chromatin was sonicated to 200-500 bp fragments with a Bioruptor (Diagenode, Sparta, NJ). Chromatin was immunoprecipitated by using anti-HA tag antibody (ab1424; Abcam) and Protein A Agarose beads. The beads were washed once with each washing buffer, including low salt immune complex wash buffer, high salt immune complex wash buffer, and LiCl immune complex wash buffer, and twice with 1X TE buffer. Precipitates were eluted with 1% of SDS and 100 mM of NaHCO3. The samples were heated at 65°C for 6 hr in order to reverse cross-link, extracted with phenol/chloroform, ethanol-precipitated. The sequencing libraries were constructed from immunoprecipitated and input DNA using TruSeq ChIP Sample Preparation Kit (Illumina Inc., USA) according to the manufacturer’s instruction. The fragmented DNA was end repaired following by addition 3’-A to the ends and ligation of adapters. The adapter-ligated DNA library was sized-selected (300-500 bp) on a 2% agarose gel and amplified by PCR for 16 cycles with the use of KAPA HiFi DNA Polymerase (Kapa Biosystems).

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Taipei, Taiwan

text: public

characteristic: INSDC status

text: ArrayExpress

text: human

text: Homo sapiens

text: Homo sapiens

text: Homo sapiens


text: public

characteristic: SRA accession

tag: Namespace:European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI)

text: ArrayExpress

text: Dumeril's clam worm

text: no cell observed Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

characteristic: developmental stage

characteristic: individual

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

characteristic: organism part

text: Platynereis dumerilii


characteristic: External Id

text: European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI)

text: public

characteristic: Submitter Id

text: ArrayExpress

characteristic: broker name

text: nervous system cell

text: Dumeril's clam worm

text: C2x85_1L Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

characteristic: description

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: ENA-CHECKLIST

characteristic: INSDC center name

text: public

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

characteristic: common name

text: C2x92_1Sb Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

characteristic: organism

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

text: ArrayExpress

text: Dumeril's clam worm

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii

characteristic: title


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: nervous system cell

characteristic: cell type

text: Dumeril's clam worm

text: single cell Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


text: public

characteristic: SRA accession

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: C2x71_2 Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

characteristic: developmental stage

characteristic: individual

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: External Id

text: public

characteristic: Submitter Id

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: single cell (dead cell) Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

characteristic: organism part

text: Platynereis dumerilii


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: nervous system cell

text: Dumeril's clam worm

text: C2x74_1M Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

characteristic: description

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: INSDC center name

text: public

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

characteristic: common name

text: C2x95_1Sb Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

characteristic: organism

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

characteristic: INSDC first public

text: public

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: C2x72_1L Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: C2x96_1Sb Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii

characteristic: title


text: public

characteristic: SRA accession

text: ArrayExpress

text: nervous system cell

characteristic: cell type

text: Dumeril's clam worm

text: C2x86_1L Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

characteristic: developmental stage

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: External Id

text: public

characteristic: Submitter Id

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: C2x90_1L Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

characteristic: individual

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: nervous system cell

text: Dumeril's clam worm

text: 2 cells Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

characteristic: organism part

text: Platynereis dumerilii


characteristic: INSDC center name

text: public

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

characteristic: common name

text: C2x67_1S Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

characteristic: description

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: C2x65_1Sb Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

characteristic: organism

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: INSDC first public

characteristic: INSDC last update

text: public

characteristic: INSDC status

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: one cell Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


text: public

characteristic: SRA accession

text: ArrayExpress

text: nervous system cell

characteristic: cell type

text: Dumeril's clam worm

text: 4 cells Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii

characteristic: title


characteristic: External Id

text: European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI)

text: public

characteristic: Submitter Id

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: 5 cells Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

characteristic: developmental stage

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: ENA-CHECKLIST

text: public

text: ArrayExpress

characteristic: broker name

text: nervous system cell

text: Dumeril's clam worm

text: single cell, dead Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

characteristic: individual

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii


characteristic: INSDC center name

text: public

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

characteristic: common name

text: C2x91_1L Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

characteristic: organism part

text: Platynereis dumerilii


characteristic: ENA-FIRST-PUBLIC

characteristic: ENA-LAST-UPDATE

text: public

text: ArrayExpress

text: nervous system cell

text: Dumeril's clam worm

text: C2x58_1S Protocols: Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18oC, for 47 hours, to reach the desired stage. For cell dissociation, ca 100 47hpf P.dumerilii larvae were picked and incubated for 5 minutes in 0.5% Pronase (Roche cat # 10165921001), 1% sodium thioglycolate (Sigma T0632) diluted in calcium- and magnesium-free artificial sea water. After this treatment, the separated brains (epispheres) were picked, rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. Epispheres were rinsed twice in 1xPBS, transferred to a non-stick eppendorf tube and triturated by pipetting. Dissociated cells were washed twice in 200 ul of 1xPBS and concentrated by centrifuging (1 min, 200xg). Cells were resuspended in 20 ul of 1xPBS, of which 5 ul was loaded on the capture chip (C1 IFC for mRNA-seq for 10-17 um cells, Fluidigm cat # 100-5760). Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq (10-17 um, Fluidigm cat # 100-5760) on Fluidigm C1 Single-Cell Auto Prep System. We used SMARTer Ultra Low Input RNA Kit for reverse transcription and the ADVANTAGE-2 PCR kit (Clontech cat # 634832) for PCR. We added 1 ul of 1:4000 dilution of ERCC spike-in RNA (Ambion, cat # 4456740) to the cell lysis mix. Sequencing libraries were prepared using the Nextera XT DNA Sample Preparation kit (Illumina cat # FC-131-1096) ). The samples in this study were derived from altogether 5 IFC-s (termed C1, C2, C3, C4, C5 in the batch information). The samples from IFCs C1 and C2 were pooled into one sequencing library. This library was loaded on 2 lanes on Illumina HiSeq2000, obtaining 2 technical replicates per sample. The samples from IFCs C3 and C4 were pooled into one sequencing library. The samples from IFC C5 were pooled into a separate sequencing library.

characteristic: description

text: 48 hpf

text: Platynereis dumerilii

text: Platynereis dumerilii

text: episphere

text: Platynereis dumerilii