run_metadata: 69464
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| 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 |
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| 69464 | SRR18710067 | SRX14810875 | SRS12567666 | 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. | 7d CV zebrafish rep2 | GSM6038010 | source name:kidney|strain:AB|tissue:kidney|age:7 dpf type | 7d CV 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 | 30 CV and GF zebrafish at 5 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Then the tricane media were replaced with RNAlater RNA Stabilization Solution Thermo and samples were storaged at 4℃ for more than 24h.Their intestines were collected by tweezers under the microscope and the isolated intestines was then transfered into Trizol.50 CV and GF zebrafish at 7 dpf embryos were collected and anesthetized in 0.4% 4g/L tricane respectively. Their kidneys were collected as previously described as intestines. | Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using 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 autoclaved system water and allowed to mate for no more than 60 min. Fertilized eggs were seperated into two groupsCV group and GF group.The CV embryos were transfered to dishes with embryo media and incubated at 28.5℃. The GF embryos subsequently washed three times with the sterile embryo media SEM and transferred to a petri dish with the filter sterilized embryo medium containing antibiotics ABEM. Healthy embryos were sorted into fresh ABEM per 2 hours less than 200 per dish and incubated for 6 h at 28.5℃. The GF zebrafish embryos were then generated as previously described Pham Kanther et al. 2008. Briefly embryos were then washed at room temperature with 0.1% polyvinylpyrrolidone for 90s followed with three times rinsing with the SEM at room temperature. post soaking in 0.003% sodium hypochlorite for 16 min at room temperature these embryos were then washed for three times with the SEM. Finally the GF embryos were transferred into plastic cell culture flasks with SEM and incubated at 28.5℃. | strain:AB|tissue:kidney|age:7 dpf type | GSM6038010 | GSM6038010: 7d CV zebrafish rep2; Danio rerio; RNA Seq | GSM6038010 r1 | GSM6038010 | 1 | Intestines and kidneys were removed flash frozen on dry ice and RNA was harvested using Trizol reagent. RNA libraries were prepared for sequencing using standard Illumina protocols | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP369366 | 7d_CV_2.fq.gz | fastq | 5661243900.0 | 18870813.0 | GSM6038010 r1 | 0:150 1:150 | A:1461910631;C:1369500371;G:1376299382;T:1453491360;N:42156 | 150 | 150 | 1461910631 | 1369500371 | 1376299382 | 1453491360 | 42156 | SRX14810875 | SRS12567666 | Lili Jing's lab, School of Pharmacy, Shanghai Jiao Tong University | 2 | 0.96148 | 0.95899 | 0.06956 | 0.06718 | 0.7165 | 0.71683 | 0.46433 | 0.44486 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2022-04-11 | Larval | Larval | Kidney | Renal System |