{"database": "metadata", "table": "run_metadata", "rows": [[71777, "SRR22094621", "SRX18074628", "SRS15579663", "SRP405171", "PRJNA893397", "RNA sequencing of the zebrafish superficial epithelial cells", "PRJNA893397", "Other", "We discovered that the superficial epithelial cells SECs of zebrafish larvae could adapt a unique kind of cell division during rapid growth conditions. We termed it \"asynthetic fission\". We determined that asynthetic fission occurs in the absence of DNA replication  generating progeny cells with reduced genome size. Here  we aim to define the transcriptional landscape of the SECs during asynthetic fission by applying RNA sequencing.", null, null, "replicate", "SEC 2dpf r", "SEC 2dpf r", null, "strain:EK|age:2dpf|dev stage:2dpf|sex:NA|tissue:skin superficial epithelial cell|BioSampleModel:Model organism or animal", null, null, null, null, null, null, null, null, "RNA sequencing of zebrafish:superficial epithelial cells 2dpf replicate", "LTS21 YW01", "LTS21 YW01", "100  150 larvae at 2 dpf  6 dpf  14 dpf  and 21 dpf were first rinsed with 1x DPBS Gibco  14190 144  then digested with collagenase Sigma  C9891 and 0.25% trypsin EDTA Sigma  T4049. Digestion was stopped with DMEM Gibco  11995 065 with 10% NCS and rinsed with 1 x DPBS. Then  cells were suspended in DMEM 10% NCS and filtered with a 35 m cell strainer tube. Dissociated cells were stained with PI 1 g/ml for 106 cells per mL for 5 min in the dark. All EGFP+ and PI  cells were sorted by FACSAria IIIu BD Biosciences. Cells were directly sorted in buffer RLT supplemented with 1%  mercapto ethanol provided in RNeasy Micro kit Qiagen and stored in  80 C until RNA extraction was performed. Total 2 replicates for each timepoint were collected. RNA extraction was carried out using RNeasy Micro kit according to manufacturers instructions. Sequencing was performed by the NGS High Throughput Genomics Core in Biodiversity Research Center  Academia Sinica  Taiwan using Illumina NextSeq2000 with paired end 2 x 150 bp chemistry and a library selection of low input stranded RNA library preparation  Poly A.", null, null, "RNA-Seq", "TRANSCRIPTOMIC", "Oligo-dT", "PAIRED", "ILLUMINA", "NextSeq 2000", null, "SRP405171", null, null, "LTS21_YW01_S3_L001_R1_001.fastq.gz LTS21_YW01_S3_L001_R2_001.fastq.gz", "fastq fastq", 19999530824.0, 66223612.0, "LTS21 YW01 S3 L001 R1 001.fastq.gz", "0:151 1:151", "A:5239226851;C:4832853944;G:4579224440;T:5331222900;N:17002689", 151, 151, null, null, 5239226851, 4832853944, 4579224440, 5331222900, 17002689, "SRX18074628", "SRS15579663", "SRA1530145", "Academia Sinica|Institute of Cellular and Organismic Biology", "Academia Sinica", 2, 0.77399, 0.76874, 0.04763, 0.04655, 0.75035, 0.75087, 0.423, 0.42383, 151, 151, "B", "B", "biological fallback assumption", "illumina", "nextseq_v2", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Taiwan", "2022-10-29", "Hatching", "Embryo", "Skin", "Surface Structure"]], "columns": ["rowid", "run.accession", "experiment.accession", "sample.accession", "study.accession", "bioproject", "study.title", "study.alias", "study.type", "study.abstract", "study.attributes", "study.PMIDs", "sample.description", "sample.title", "sample.alias", "sample.centername", "sample.attributes", "GEOsample.title", "GEOsample.dataprocessing", "GEOsample.source", "GEOsample.treatmentprotocol", "GEOsample.extractprotocol", "GEOsample.growthprotocol", "GEOsample.characteristics", "GEOsample.accession", "experiment.title", "experiment.alias", "experiment.library_name", "experiment.design_description", "experiment.library_construction_protocol", "experiment.attributes", "experiment.library_strategy", "experiment.library_source", "experiment.library_selection", "experiment.library_layout", "experiment.platform", "experiment.instrument_model", "experiment.spot_descriptor", "experiment.study_ref", "run.title", "run.attributes", "run.filename", "run.semantic_name", "run.total_bases", "run.total_spots", "run.alias", "run.read_lengths", "run.base_counts", "run.r1_length", "run.r2_length", "run.r3_length", "run.r4_length", "run.Acount", "run.Ccount", "run.Gcount", "run.Tcount", "run.Ncount", "run.experiment", "run.pool_member", "submission.accession", "submission.srasource", "submission.bioprojectsource", "seqdetective.n_mates", "seqdetective.mapping_rate.mate1", "seqdetective.mapping_rate.mate2", "seqdetective.nofeature_rate.mate1", "seqdetective.nofeature_rate.mate2", "seqdetective.sparsity.mate1", "seqdetective.sparsity.mate2", "seqdetective.pos_strand_rate.mate1", "seqdetective.pos_strand_rate.mate2", "seqdetective.readlen.mate1", "seqdetective.readlen.mate2", "seqdetective.judgement.mate1", "seqdetective.judgement.mate2", "seqdetective.judgement.reason", "platform_family", "instrument_generation", "read_bias", "selection_class", "prep_kit", "sc_or_bulk", "tech_class", "technology", "tech_variant", "submission.bioprojectsource.country", "earliest_date", "devstage_curation", "devstage_curation_coarse", "tissue_curation", "tissue_curation_coarse"], "primary_keys": ["rowid"], "primary_key_values": ["71777"], "units": {}, "query_ms": 16.473195995786227}