run_metadata: 52228
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 |
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| 52228 | SRR13912633 | SRX10292190 | SRS8427105 | SRP195753 | PRJNA541476 | Transcriptomic profiling of zebrafish livers with nAtf6 overexpression at collected at 78 hpf and 120 hpf | GSE130800 | Transcriptome Analysis | Activting transcription factor 6 Atf6 is one of three main mediators of the Unfolded Protein Response and it gets cleaved cleaved in the Golgi and its N terminal consisting of the bZip domain translocates into the nucleus to generate a transcriptional response nAtf6. This study carries out RNAseq on an established transgenic overexpression of nAtf6 in zebrafish hepatocytes tgfabp10:nAtf6 cherry; cmlc2:GFP C allele. Samples were collected at 78 hpf and 120 hpf to detect gene expression changes at early and late time points post nAtf6 is overexpressed. Overall design: We used two transgenic lines: Tgfabp10a: CAAX EGFP to use as a marker of the liver for dissction and tgfabp10:nAtf6 cherry; cmlc2:GFP C allele to overexpress nAtf6 specifically in hepatocytes.This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C and tgfabp10a:CAAX EGFP . Using GFP to guide microdissscion of 20 25 livers at 78 hpf and 120 hpf . Total RNA isolated using TRIZOL and treated by DNAse I. Libraries were prepared using RiboZero for 120 hpf samples or polyA selection for 78 hpf samples. Samples from 2 clutches collected at 78 hpf and 3 clutches at 120 hpf. Samples were sequenced on NextSeq550 Illumina | parent bioproject:PRJNA541472 | 78 hpf liver from transgenics overexpressing nAtf6 Clutch 2 | GSM5145709 | tissue:Liver|genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20 | 78 hpf liver from transgenics overexpressing nAtf6 Clutch 2 | Illumina Casava software used for basecalling. Sequencing quality was assessed by using MultiQC v1.7 Alignment by HISTA2 with default parameters only paired reads are aligned and multiple alignments are kept Gene expression is counted in the exon of ensemble gene annotation with HTseq in union mode Test of differential expression of Genes or transposonis was implemented by DESeq2 in Bioconductor V4.0.2 Genome build: GRCz10 Supplementary files format and content: csv files for raw reads count of genes | Liver | At approximately 78 hpf/3 dpf 3 PM and at 120 hpf/ 5 dpf 9 AM plates were treated with 500 uM tricaine Ethyl 3 aminobenzoate methanesulfonate Sigma Aldrich USA and were first sorted for green liver positive as all fish needed to have marked livers to proceed. Next green liver positive fish were spilt between siblings without xxx hearts larvae that don't express nAtf6 Sample name Sibs and with green hearts larvae that express nAtf6 Sample name : Natf6. These fish were dissected in 3% methyl cellulose. | 20 livers were microdissected and immediately placed into 500 uL of TRIzol Thermo Fisher 15596026. RNA from pooled livers was then extracted per standard TRIzol/Chloroform method and concentrated through isopronanol and resuspended in 20 uL of DNase/RNase free water Thermo Fisher Scientifc.RNA was quantified by Qubit flurometer.Thermo Scientific The 120 hpf samples were DNAseI treated for 30 minutes at 37°C followed by RNA purification RapidOut DNA Removal Kit–Thermo Fisher Scientific. | This experiment was conducted by natural spawnings between tg:fabp10:nAtf6 cherry; cmlc2:GFP C and tgfabp10a:CAAX EGFP . Mating tanks were set up at approximately 4:30 PM the night before and embryos were collected at 10:30 AM the following morning. Following collection embryos were divided into 30 mL plates 60 embryos per plate in embryo medium Zebrafish Information Network. Plates were cleaned daily to remove unfertilized or dead embryos. | genotype:Tgfabp10a:CAAX EGFP; Tgfabp10:nAtf6 mcherry; cmlc2:EGFP C|pool:20|rna qbit concentrationng/ul:10 | GSM5145709 | GSM5145709: LIV nAtf6 2; Danio rerio; RNA Seq | GSM5145709 | 1 | TRIzol/Choloform RNA seq libraries treated with polyA were prepared by Mehar | GEO Accession:GSM5145709 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 550 | SRP195753 | Liv_SIBS_2_S1_read1.fastq.gz Liv_SIBS_2_S1_read2.fastq.gz | fastq fastq | 2358265150.0 | 8259166.0 | GSM5145709 r1 | 0:142.48 1:143.06 | A:628232000;C:556398561;G:558335926;T:614539765;N:758898 | 142 | 143 | 628232000 | 556398561 | 558335926 | 614539765 | 758898 | SRX10292190 | SRS8427105 | SRA883585 | GEO | Biology, New York University Abu Dhabi | 2 | 0.79869 | 0.80429 | 0.04449 | 0.04602 | 0.75422 | 0.76355 | 0.569 | 0.56414 | 142 | 142 | B | B | biological fallback assumption | illumina | nextseq | unknown | poly_a | ribozero | bulk | unknown | unknown | United Arab Emirates | 2021-03-09 | Multi-stage | Multi-stage | Liver | Liver and Biliary System |