{"database": "metadata", "table": "run_metadata", "rows": [[69455, "SRR21377196", "SRX17382861", "SRS14941973", "SRP369366", "PRJNA825466", "The transcriptome profiling analysis of intestines and kidneys in conventionally raised CV and germ free GF wild type zebrafish embryos", "GSE200577", "Transcriptome Analysis", "To investigate how the zebrafish embryos respond to the absence of the microbiota  the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. 32 948 cDNAs of the zebrafish genome assembly were annotated post reads mapping for further analysis. For the 5 dpf intestinal tissue samples  948 genes 4% of the total number of genes were differentially expressed  371 genes were up regulated and 577 genes were down regulated in the GF group . For the 7 dpf kidney tissue samples  697 genes 3% of the total number of genes were differentially expressed  341 genes were up regulated and 356 genes were down regulated in the GF group. The enrichment analysis showed that the immune and cytokine related pathways were affected by the GF treatment in the wildtype embryos both in intestines at 5 dpf and in kidneys at 7 dpf. To investigate how the transcriptome changes in the chd8 /  zebrafish embryos  the intestinal tissue associated and the kidney tissue associated gene expressions were examined at 5 dpf and 7 dpf respectively. Overall design: Intestinal mRNA profiles of conventionally raisedCV and germ freeGF embryos at 5 dpf and renal the location of their hematopoietic tissue mRNA profiles of CV and GF embryos at 7 dpf. Analysis of  mRNA profiles of intestines at 5 dpf and renal the location of their hematopoietic tissue at 7 dpf in chd8 /  embryos  and comparing the data with those from the wildtype embryos.", null, null, null, "7d chd8 /  zebrafish rep2", "GSM6532688", null, "source name:kidney|strain:AB|tissue:kidney|age:7 dpf / ", "7d chd8 /  zebrafish rep2", "Sequenced raw datas have been qualitifed by fastqc version 0.11.9 and trimmed by trim galore version 0.6.7 for subsequent analysis with parameters   phred33  q 20   length 15   stringency 3   fastqc   max n 3 The processed datas have been mapped to Danio rerio.GRCz11 whole genome using STAR version 2.7.9a  then applied subread version 2.0.1 to get raw gene conunts for every sample with parameters featureCounts  T 6  t exon  g gene id Assembly: GRCz11 Supplementary files format and content: Table with raw gene counts for every gene and every sample", "kidney", "40 chd8 /  zebrafish embryos at 5 dpf were collected and anesthetized in 0.4% 4g/L tricane. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo  and samples were storaged at 4\u2103 for more than 24h. The intestines were removed and collected by tweezers under the microscope  and the isolated tissue was then transfered into Trizol. About 70 chd8 /  zebrafish embryos at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane.  Then the media were replaced with RNAlater RNA Solution  and samples were storaged at 4\u2103 for more than 24h. Their kidneys were removed by tweezers under the microscope. Then the tissues were immersed in Trizol  and the RNA of them were extracted as previously described for intestine tissues.", "Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately  flash frozen in  80\u2103  and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", "The parent adult zebrafish are placed in pair mating tanks with dividers separating males and females the postnoon or evening prior to mating Day  1. At the start of the light cycle the following morning day x  the parents were transferred to new clean pair mating tanks with fish feeding circulation system water and allowed to mate for no more than 1 hour. Fertilized eggs were transfered into petri dishes less than 100 embryos per dish with embryo media. Then all of the embryos are incubated at 28.5\u2103 until the 5 dpf or 7 dpf.  Embryo media:1L ddH2O with 10 ml stock solution A  1 mL stock solution B  10 mL stock solution C  10 mL stock solution D and 10 mL stock solution E  adjust pH to 7.2 with 1 M HCl.A: 250 mL RO H2O  20 g NaCl  1 g KCl;B: 100 mL RO H2O  0.358 g Na2HPO4 anhydrous  0.6 g KH2PO4 monobasic;C: 250 mL RO H2O  4.68 g CaCl2 dihydrate;D: 250 mL RO H2O  6.15 g MgSO4\u00b77H2O;E: 250 mL RO H2O  8.75 g NaHCO3.  System water:purified water with sea salt and NaHCO3\uff0cconductivity 450 500 \u03bcs/cm\uff0cpH 7.0\u00b10.2.", "strain:AB|tissue:kidney|age:7 dpf / ", "GSM6532688", "GSM6532688: 7d chd8 /  zebrafish rep2; Danio rerio; RNA Seq", "GSM6532688 r1", "GSM6532688", "1", "Intestines and kidneys were removed immerse the tissues in Trizol reagent immediately  flash frozen in  80\u2103  and RNA was harvested following the manual of the Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "SINGLE", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP369366", null, null, "7d_chd8_2.fq.gz", "fastq", 5791321500.0, 19304405.0, "GSM6532688 r1", "0:150 1:150", "A:1504780584;C:1391586880;G:1405013206;T:1489820370;N:120460", 150, 150, null, null, 1504780584, 1391586880, 1405013206, 1489820370, 120460, "SRX17382861", "SRS14941973", null, null, "Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University", 2, 0.95947, 0.95202, 0.07494, 0.07307, 0.71074, 0.71163, 0.45745, 0.44001, 150, 150, "B", "B", "biological fallback assumption", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "bulk", "unknown", "unknown", null, "China", "2022-08-31", "Larval", "Larval", "Kidney", "Renal System"]], "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": ["69455"], "units": {}, "query_ms": 9.551165989250876}