run_metadata: 58389
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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| 58389 | SRR11486781 | SRX8062812 | SRS6431234 | SRP252754 | PRJNA612515 | Tissue Regeneration Enhancer Element Discovery by Chromatin Accessibility Profiling of Regenerating Zebrafish Fins | GSE146960 | Other | Mammalian genomes likely encode all gene products required to regenerate an amputated limb yet they lack the correct instructions for strategically modulating those gene products to accomplish limb regeneration. Zebrafish and many other non mammalian vertebrates possess these instructions which exist as gene cis regulatory elements. Here to identify candidate tissue regeneration enhancer elements TREEs important for zebrafish fin regeneration we performed ATAC seq from bulk tissue or purified fibroblasts of uninjured and regenerating caudal fins. We identified thousands of DNA regions from each tissue type with dynamic accessibility during regeneration and assigned these regions to proximal genes with corresponding changes in RNA levels. To determine whether these profiles revealed bona fide TREEs we tested the sufficiency of several sequences in stable transgenic and mutant lines. These experiments identified new regulatory sequences near several induced and/or required genes including fgf20a cx43 and mdka with unique expression domains for each confirmed TREE. Deletion of TREE sequences from the zebrafish genome revealed requirements and redundancies surrounding cis regulatory regions. Our study generates a novel resource for dissecting the regulatory mechanisms of appendage regeneration. Overall design: Samples were enzymatically dissociated with Liberase and collected in biological triplicates for RNA and ATAC library preparation. Corresponding sample pools include: whole fin 0 dpa and whole fin 4 dpa whole fin 0 dpa and whole fin 1 dpa and fibroblast 0 dpa and fibroblast 4 dpa. | pubmed:32665240 | RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1 | GSM4455083 | source name:whole fin|date:2 dpa|tissue:whole fin | RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1 | RNA Seq reads were trimmed by Trim Galore 0.6.4 with q 15 and then mapped with TopHat v 2.1.1 with parameters b2 very sensitive no coverage search and supplying the UCSC danRer10 refSeq gene annotation. Gene level read counts were obtained using the htseq count v1.6.1 by the reads with MAPQ greater than 30. Genome build: danRer10 Supplementary files format and content: raw counts of sequencing reads for the features of interest for RNAseq | whole fin | For fibroblast libraries triplicate Tgtph1b:creER;ubi:switch caudal fins were clipped and treated at 2dpa for 12 hours in 4uM Tamoxifen Sigma Aldritch Tornini et al. 2016. Fins were allowed to regenerate fully for two months and 75 fish fin samples were pooled for each biological replicate pool. | For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. | D. rerio from the outbred Ekkwill EK strain ranging from 4 month to 12 month were used for whole fin library preparations Tgtph1b:mCherry NTR;ubi:switch fish were used for fibroblast library preparation Tornini et al 2016. Water temperature was maintained at 27.5°C and fish were kept on a 14/10 light/dark cycle. Fish were anesthetized in 0.75% v/v 2 phenoxyethanol Sigma Aldrich in fish water. Work with D. rerio was performed in accordance with Duke University guidelines. | date:2 dpa|tissue:whole fin | GSM4455083 | GSM4455083: RNAseq; LEN deletion; 2dpa; injured; batch 3; rep1; Danio rerio; RNA Seq | GSM4455083 | 1 | For RNA seq biological triplicate D. rerio caudal fin clip pools were collected at 0 dpa 1 dpa or 4 dpa time points via razor blade VWR from 15 fish aged between 3 month 12 month. Fin tissue was collected in Tri Reagent Sigma and isolated by ethanol precipitation. RNA was further purified with the RNA Clean & Concentrator Kit 5 Zymo. RNA seq libraries were prepared using a Stranded mRNA seq Kit KAPA. | GEO Accession:GSM4455083 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina HiSeq 4000 | SRP252754 | JK-S8_S75_L008_R1_001.fastq.gz | fastq | 2464411341.0 | 48321791.0 | GSM4455083 r1 | 0:51 1:0 | A:620643336;C:590840801;G:549905028;T:702758180;N:263996 | 51 | 0 | 620643336 | 590840801 | 549905028 | 702758180 | 263996 | SRX8062812 | SRS6431234 | SRA1054723 | GEO | Poss, Cell Biology, Duke University | 1 | 0.91677 | 0.09917 | 0.71981 | 0.46761 | 51 | B | usable mapping rate | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | United States | 2020-04-06 | Multi-stage | Multi-stage | Fin | Surface Structure |