characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-09-17T17:01:36Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-09-07T14:18:46Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104286480
characteristics.characteristic: External Id
characteristics.text: Developmental Biology Unit, European Molecular Biology Laboratory (EMBL)
characteristics.characteristic: INSDC center name
characteristics.text: 2017-09-17T17:01:36Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-09-07T14:18:46Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1911458
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5953:CN61x3101
characteristics.characteristic: Submitter Id
characteristics.text: 48
characteristics.unit: hour
characteristics.characteristic: age
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: Dumeril's clam worm
characteristics.characteristic: common name
characteristics.text: Protocols: Cell capture, lysis, reverse transcription and cDNA amplification was performed on the C1 IFC for mRNA-seq, 10-17 μm, Fluidigm cat # 100-5760 or C1 IFC for mRNA-seq for 5-10 um cells, Fluidigm cat # 100-5759) 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 μl 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)). Wild-type P. dumerilii adults were spawned and larvae were incubated in filtered natural seawater, at 18°C, for 47 hours, to reach the desired stage. For cell dissociation, ca 500 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, animals were rinsed in 1xPBS, and incubated for 1 minute in 150 ug/ml Liberase (Roche, cat # 05401119001) in 1xPBS. After this, partially dissociated tissue was rinsed 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, or C1 IFC for mRNA-seq for 5-10 um cells, Fluidigm cat # 100-5759). The cDNA libraries were prepared using the Illumina Nextera XT DNA library preparation kit (Illumina # FC-131-1096) and dual barcoding with Nextera XT Index Kit (Illumina # FC-121-1012).
characteristics.characteristic: description
characteristics.text: larval stage
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000069
characteristics.characteristic: developmental stage
characteristics.text: wild type genotype
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0005168
characteristics.characteristic: genotype
characteristics.text: undifferentiated cell
characteristics.characteristic: inferred cell type
characteristics.text: Platynereis dumerilii
characteristics.characteristic: organism
characteristics.text: Platynereis dumerilii
characteristics.characteristic: organism
characteristics.text: whole organism
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/UBERON_0000468
characteristics.characteristic: organism part
characteristics.text: Platynereis dumerilii
characteristics.characteristic: scientific_name
characteristics.text: single cell
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009899
characteristics.characteristic: single cell well quality
characteristics.text: CN61x3101
characteristics.characteristic: title