characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2019-03-13T17:03:39Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-08-10T11:55:20Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA104208764
characteristics.characteristic: External Id
characteristics.text: Institute of Medical Biology
characteristics.characteristic: INSDC center name
characteristics.text: 2019-03-13T17:03:39Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-08-10T11:55:20Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1867782
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5958:GATA6Het_Day3_rep3.bam
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: H9
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0003045
characteristics.characteristic: cell line
characteristics.text: embryonic stem cell
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0002322
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: hPSCs were routinely cultured in feeder-free conditions on vitronectin-coated (Stemcell Technologies #07180) sterile plates (Corning, Costar) with Essential 8 (E8) media (Life Technologies #A1517001). Subculture was performed every 4-6 days by aspirating the cell culture media, washing the cells once with D-PBS, incubating them in 0.5 mM EDTA (Invitrogen, #15575020) for 5 min at room temperature, aspirating the EDTA and adding appropriate volumes of fresh E8 media (Table 2) to the cells. hPSCs were further physically detached from the plates by gentle pipetting, collected in a 15 ml Falcon tube (BD Falcon) and allowed to settle for 10 min. The supernatant was aspirated and hPSCs were re-suspended in fresh E8 media, and then dissociated into smaller clumps by gentle pipetting. The cells were split at a split ratio of 1:6 and plated onto fresh vitronectin-coated plates containing appropriate volumes of media. Cells were maintained by refreshing E8 media on a daily basis. Cells were grown in 12 well plates for total RNA isolation. 3 wells were harvested per sample to obtain technical triplicates. RNeasy Mini Kit together with the Qiacube (Qiagen) was used for total RNA extraction. Cell culture media was aspirated and the cells were washed once with D-PBS. The D-PBS was completely aspirated and cells were lysed directly in the 12 well plates by adding 350 μl of Buffer RLT. Cell lysates were transferred to 2 ml tubes and were either frozen at -80°C or used immediately with the Qiacube for RNA extraction. Each sample was treated with RNase-Free DNase (Qiagen) to avoid DNA contamination. RNA was eluted in a volume of 30 μl. RNA was either frozen at -80°C or immediately taken to the next step of first strand cDNA synthesis. If RNA samples were frozen, they were thawed on ice to prevent degradation. Library preparations were made manually using the Illumina TruSeq™ RNA Sample Preparation Kit with no major deviations from this protocol.
characteristics.characteristic: description
characteristics.text: c.618_619insTGCA/+
characteristics.characteristic: genotype
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: definitive endoderm cell
characteristics.characteristic: phenotype
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: GATA6Het_Day3_rep3.bam
characteristics.characteristic: title