{"database": "metadata", "table": "run_metadata", "rows": [[62850, "SRR13402904", "SRX9821929", "SRS8004722", "SRP301260", "PRJNA691237", "Smad4 controls signaling robustness and morphogenesis by differentially contributing to the Nodal and BMP pathways", "GSE164574", "Other", "The goal of this scRNA seq study was to characterize the pseudo spatial distribution of Nodal and BMP effectors SMADs expression prior to the onset of gastrulation Overall design: scRNA seq was performed on Zebrafish embryos at sphere stage", null, "pubmed:34737283", null, "Zsphere scRNA", "GSM5014336", null, "tissue:Zebrafish embryos|Stage:sphere", "Zsphere scRNA", "We used cell ranger version 2.1.1 to deconvolve  align and quantify the per cell transcriptomes. Reads were aligned to version GRCz10 of the zebrafish genome with annotation release 89 from Ensembl software available from 10x genomics. From these alignments we were able to identify 2 644 high quality cells with a mean reads per cell value of 59 754 and a median genes per cell count of 3 807. \u00a0All other QC metrics were within thresholds set by 10x Genomics Genome build: GRCz10 release 89 from Ensembl Supplementary files format and content: tar file containing 10x counts matrix  features and barcode data", "Zebrafish embryos", null, "At high stage  embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage  the embryo media was sequentially replaced with Dulbecco Modified Eagle\u2019s Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100\u00b5l of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200\u00b5l of ice cold PBS+0.04% BSA to which 800\u00b5l of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to  20\u00b0C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4\u00b0C. Cells were resuspended in 100\u00b5l ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3\u2032 Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing  the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime", "Zebrafish embryos were grown in embryo media  for dissection of the blastula cup  embryos were transferred in DMEM F12 media", "Stage:sphere", "GSM5014336", "GSM5014336: Zsphere scRNA; Danio rerio; RNA Seq", "GSM5014336", null, "1", "At high stage  embryos were transferred in agar coated 6 cm petri dish and manually dechorionated in embryo media. At sphere stage  the embryo media was sequentially replaced with Dulbecco Modified Eagle's Medium DMEM F 12 with 0.04% BSA and the blastula cups were dissected away from 25 embryos and transferred to an Eppendorf tube containing 100\u00b5l of DMEM F12 +0.04% BSA. The cell suspension was pelleted at 400 rcf for 30sec. The media was then removed and cells were suspended in 200\u00b5l of ice cold PBS+0.04% BSA to which 800\u00b5l of MeOH were added dropwise. Samples were kept in ice for 15 minutes and finally transferred to  20\u00b0C until use. For rehydration samples were kept in ice for 15 min and cells were pelleted at 1000rcf for 5 min at 4\u00b0C. Cells were resuspended in 100\u00b5l ice cold PBS + 0.04% BSA and the cell suspension was loaded into 10X Genomics Single Cell 3\u2032 Chip The quality and concentration of the cell suspension was measured using an automatic cell counter. For sequencing  the ample was diluted to a concentration of 1000 cells/ul and approximately 10 000 cells were loaded into a Chromium Chip for use in the 10X Chromium Controller. The library was sequenced on a HiSeq 4000. 10x Chromium Single Cell three prime", "GEO Accession:GSM5014336", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 4000", null, "SRP301260", null, "loader:fastq load.py|options:  platform=Illumina   readTypes=TTB   read1PairFiles=GUG739A4 S2 L003 I1 001.fastq.gz   read2PairFiles=GUG739A4 S2 L003 R1 001.fastq.gz   read3PairFiles=GUG739A4 S2 L003 R2 001.fastq.gz", "GUG739A4_S2_L003_I1_001.fastq.gz GUG739A4_S2_L003_R1_001.fastq.gz GUG739A4_S2_L003_R2_001.fastq.gz", "fastq fastq fastq", 5572550130.0, 26535953.0, "GSM5014336 r3", "0:8 1:101 2:101", "A:1249457035;C:994601699;G:1005584984;T:2322470542;N:435870", 8, 101, 101, null, 1249457035, 994601699, 1005584984, 2322470542, 435870, "SRX9821929", "SRS8004722", "SRA1182478", "GEO", "Bioinformatics, Bioinformatics, The Francis Crick Institute", 1, 0.90814, null, 0.11693, null, 0.78565, null, 0.57928, null, 101, null, "B", null, "usable mapping rate", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_droplet", "10x", null, "United Kingdom", "2021-01-11", "Blastula", "Embryo", "Embryo Imprecise", "All anatomical structures"]], "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": ["62850"], "units": {}, "query_ms": 6.440039000153774}