run_metadata: 68837
This data as json
| 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 68837 | SRR18192320 | SRX14338851 | SRS12152780 | SRP362184 | PRJNA812001 | scRNA seq of roof and floor endothelial cells at 21 hpf and 28 hpf in zebrafish | GSE197757 | Transcriptome Analysis | In order to obtain the transcriptomic information about roof/dorsal and floor/ventral endothelial cells ECs of the dorsal aorta DA in zebrafish we isolated single ECs from the DA roof and the floor respectively using the Tgflk1:eGFP;flk1:NLS Eos zebrafish post photoconversion and then performed scRNA sequencing. These single ECs were isolated at two different time points 21 hpf and 28 hpf when the lumen of the DA is established and the EHT begins respectively. Overall design: Spatial photoconversion DA roof versus DA floor cell dissociation and mannual picking of photoconverted ECs | pubmed:35333649 | dorsal EC 21hpf 1 | GSM5929570 | source name:Trunk DA endothelium|strain:Tgflk1:eGFP; Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs | dorsal EC 21hpf 1 | Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence using TrimGalore with parameters trim galore q 20 phred33 stringency 5 length 20 e 0.1 paired Trimed reads were mapped to GRCz11.94 danRer11 genome using STAR Mapped reads Bam were quantified using Rsubred package Genome build: GRCz11.94 danRer11 Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample | Trunk DA endothelium | Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq | strain:Tgflk1:eGFP;Tgflk1:NLS Eos|developmental stage:21 hpf|tissue:dorsal aorta DA|tissue region:DA roof|cell type:endothelial cells ECs | GSM5929570 | GSM5929570: dorsal EC 21hpf 1; Danio rerio; RNA Seq | GSM5929570 r1 | GSM5929570 | 1 | Single Red Eos+ cell was manually picked with micromanipulator system NT 88 V3; Nikon under fluorescence microscope then washed with 2% BSA/PBS and finally transferred into 4.4ul lysis buffer. The smart seq2 protocol was used for whole transcriptome amplification. Smart seq2 oligodT captured cDNA libraries were prepared for sequencing using standard Illumina protocols 150bp paired end RNA seq | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2000 | SRP362184 | loader:fastq load.py | zsz_RNAseq-Dorsal_1_FKDL190751240-1a-N701-N501_1.fq.gz zsz_RNAseq-Dorsal_1_FKDL190751240-1a-N701-N501_2.fq.gz | fastq fastq | 1591674900.0 | 5305583.0 | GSM5929570 r1 | 0:150 1:150 | A:445156133;C:336201938;G:359744664;T:450558818;N:13347 | 150 | 150 | 445156133 | 336201938 | 359744664 | 450558818 | 13347 | SRX14338851 | SRS12152780 | Wen's lab, LIFS, HKUST | 2 | 0.85257 | 0.85794 | 0.14033 | 0.14535 | 0.86371 | 0.86135 | 0.55057 | 0.55035 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | poly_a | unknown | sc | single_cell_plate | smartseq | China | 2022-03-02 | Segmentation | Embryo | Heart | Cardiovascular System |