{"database": "metadata", "table": "run_metadata", "rows": [[56341, "SRR10948891", "SRX7615949", "SRS6049208", "SRP243873", "PRJNA602610", "Global promoter usage in the differentfractions of the cell during early zebrafish development", "GSE144040", "Other", "We employed transcriptomics methods to examine differences in promoter usage in the nuclear and cytosolic fractions of zebrafish embryonic cells at different stages of development. The analysis of the CAGE seq data revealed differences in promoter width within the same stage Post MZT in different compartments of the embryonic cell proposing a spatial and temporal regulation of gene expression. Overall design: Promoter organisation in the nuclear and cytosolic fractions of zebrafish embryonic cells in the 64 Cell  256 Cell  1000 Cell  Dome   Shield and Prim 5 stages of development.", null, "pubmed:33795334", null, "Prim5 Cyt CAGE", "GSM4278497", null, "source name:24hpf stage embryo|tissue:zebrafish embryos|Stage:24hpf|fraction:Cytosolic|molecule type:capped RNAs", "Prim5 Cyt CAGE", "Library strategy: LQ CAGE sequencing The raw tags from CAGE sequencing were mapped using STAR aligner and the resulting BAM files were used in the bioconductor package CAGEr for further downstream analysis. CAGEr starts from mapped reads and does quality filtering  normalization  removal of the additional 5\u2019 end G nucleotide added during the CAGE protocol and the frequency of the usage of start sites Haberle et al.  2015. Genome build: Zv9 Supplementary files format and content: CTSS files in bedGraph format", "24hpf stage embryo", "Dechorionated embryos were then washed twice with 1 X PBS Phosphate buffer solution  ThermoFisher. RLN buffer was added to the tube containing embryos and the yolk sac disrupted releasing the cells in the buffer. This was then incubated on ice for 5 mins and centrifuged. The resulting supernatant was collected and labelled as the cytosolic fraction. The pellet was washed twice with 200 \u00b5L of RLN buffer and finally  collected and labelled as the nuclear fraction.", "RNA was extracted using the Rneasy mini kit The conventional method used for 5\u2019 cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the 5\u2019 end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.", "Wild type male and female zebrafish AB strain were set up in breeding tanks overnight and the eggs were collected the next day as soon as 10 min they were laid important to get synchronised embryos. About 100 500 depending upon the stage embryos were collected for each developmental stage 64 cell  256 cell  1000 cell  shield  24hpf  50hpf. The embryos were treated with Pronase protease from Streptomyces griseus  Sigma Aldrich to remove the chorion  1mL of Pronase working solution 1mg/mL was added to 2 3 ml of fish water containing embryos.", "tissue:zebrafish embryos|Stage:24hpf|fraction:Cytosolic|molecule type:capped RNAs", "GSM4278497", "GSM4278497: Prim5 Cyt CAGE; Danio rerio; OTHER", "GSM4278497", null, "1", "RNA was extracted using the Rneasy mini kit The conventional method used for five prime cap analysis  also called cap trapping method Carninci et al.  1996  targets all capped mRNAs by chemical modification of the five prime end cap followed by its biotinylation and then a pulldown using streptavidin coated beads. We used a modified version of cap trapping called Low Quantity CAGE or LQ CAGE for our CAGE library preparation. This method allowed use of limited quantities of RNAs as is generally obtained in early stages of development.", "GEO Accession:GSM4278497", "OTHER", "TRANSCRIPTOMIC", "other", "PAIRED", "ILLUMINA", "Illumina HiSeq 2500", null, "SRP243873", null, null, "Prim5_Cyt_L006_R1_001.fastq.gz Prim5_Cyt_L006_R2_001.fastq.gz", "fastq fastq", 11647548055.0, 122605769.0, "GSM4278497 r1", "0:51 1:44", "A:2440692679;C:3082646191;G:3382532043;T:2741423146;N:253996", 51, 44, null, null, 2440692679, 3082646191, 3382532043, 2741423146, 253996, "SRX7615949", "SRS6049208", "SRA1029879", "GEO", "School of Biosciences, University of Birmingham", 2, 0.98284, 0.34054, 0.34811, 0.12661, 0.90753, 0.95018, 0.67956, 0.71841, 51, 44, "B", "T", "mate2 technical by mapping diff", "illumina", "hiseq_era", "5prime", "other", "unknown", "bulk", "unknown", "unknown", null, "United Kingdom", "2020-01-22", "Pharyngula", "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": ["56341"], "units": {}, "query_ms": 7.063402998028323}