characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2014-12-12T17:01:49Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2018-03-08T22:12:07Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA3175204
characteristics.characteristic: External Id
characteristics.text: European Bioinformatics Institute, European Molecular Biology Laboratory (EMBL-EBI)
characteristics.characteristic: INSDC center name
characteristics.text: 2014-12-12T17:01:49Z
characteristics.characteristic: INSDC first public
characteristics.text: 2018-03-08T22:12:07Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS628381
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-2865_2:C2x10_1Sb
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: nervous system cell
characteristics.characteristic: cell type
characteristics.text: Dumeril's clam worm
characteristics.characteristic: common name
characteristics.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.
characteristics.characteristic: description
characteristics.text: 48 hpf
characteristics.characteristic: developmental stage
characteristics.text: C2x10_1Sb
characteristics.characteristic: individual
characteristics.text: Platynereis dumerilii
characteristics.characteristic: organism
characteristics.text: Platynereis dumerilii
characteristics.characteristic: organism
characteristics.text: episphere
characteristics.characteristic: organism part
characteristics.text: Platynereis dumerilii
characteristics.characteristic: scientific_name
characteristics.text: C2x10_1Sb
characteristics.characteristic: title