run_metadata: 61955
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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| 61955 | SRR13075147 | SRX9522190 | SRS7729390 | SRP292933 | PRJNA679002 | Role of Il 11 signaling in adult heart and fin regeneration in zebrafish | GSE161647 | Transcriptome Analysis | In adult mammals tissue damage post myocardial infarction induces myofibroblast differentiation and the formation of a permanent functionally inert scar. However the molecular mechanisms that govern myofibroblast differentiation and scarring remain poorly understood. Some vertebrates like zebrafish display a remarkable regenerative potential with only limited and transient fibrosis post tissue damage including in the heart. Here employing comparative expression profiling coupled with loss of function approaches we identified the canonical Interleukin 11/Stat3 signaling axis as a core component of regeneration in zebrafish. Notably animals with loss of Interleukin 11 receptor Il11ra function reach maturity without xxx developmental defects but exhibit strongly impaired cardiac regeneration with increased myofibroblast differentiation and the formation of a permanent collagenous scar similar to what is observed in adult mammals. Using zebrafish fate mapping approaches reporter lines and human primary cell culture methods we provide evidence that Interleukin 11 signaling limits endothelial to myofibroblast transdifferentiation and maintains a pro regenerative niche to promote cardiac regeneration. Altogether our data reveal a vital role for endothelial Interleukin 11/Stat3 signaling in containing injury induced cardiac fibrosis. Overall design: 96 hours post cryoinjury cardiac ventricle samples from adult il11ra mutant vs. wild type were analyzed in duplicates with each replicate derived by pooling 2 ventricles. 24 hours post amputation caudal fin samples from adult il11ra mutant vs. wild type were analyzed in triplicates with each replicate derived from single fins. | pubmed:34516874 | il11ra mutant fin 24 hpa rep1 | GSM4911938 | tissue:Caudal fin|developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa | il11ra mutant fin 24 hpa rep1 | The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was employed to trim reads post a quality drop below a mean of Q20 in a window of 10 nucleotides. Only reads between 30 and 150 nucleotides were cleared for further analyses. Trimmed and filtered reads were aligned versus Ensembl zebrafish genome version danRer11 GRCz11 using STAR 2.7.3a with the parameter “ outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%. The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded. Differentially expressed genes were identified using DESeq2 version 1.26. The Ensemble annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: danRer11 Supplementary files format and content: library size normalized counts | Caudal fin | Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in 80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina | developmental stage:adult|genotype:il11ra mutant|treatment:fin amputation|time point:24 hpa | GSM4911938 | GSM4911938: il11ra mutant fin 24 hpa rep1; Danio rerio; RNA Seq | GSM4911938 | 1 | Ventricle and fin samples were harvested into TRIzol and flash frozen in liqN2. and stored in 80°C until further processing. Tissues were then blended with Bullet blender and RNA was isolated from adult zebrafish ventricles and caudal fin tissues using the miRNeasy micro Kit Qiagen combined with on column DNase digestion DNase Free DNase Set Qiagen to avoid contamination by genomic DNA. 200 500ng of total RNA was used as input for Truseq Stranded mRNA Library preparation following the low sample protocol Illumina | GEO Accession:GSM4911938 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | NextSeq 500 | SRP292933 | Reischauer_Mut1_R1.fastq.gz | fastq | 1531546717.0 | 20622961.0 | GSM4911938 r1 | 0:74.26 1:0 | A:407261383;C:338321295;G:350917574;T:435041628;N:4837 | 74 | 0 | 407261383 | 338321295 | 350917574 | 435041628 | 4837 | SRX9522190 | SRS7729390 | SRA1160354 | GEO | MPI for heart and lung research | 1 | 0.90833 | 0.10892 | 0.77928 | 0.48087 | 75 | B | usable mapping rate | illumina | nextseq | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | Germany | 2020-11-17 | Adult | Adult | Fin | Surface Structure |