run_metadata: 41319
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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| 41319 | SRR4241545 | SRX2162516 | SRS1690572 | SRP089817 | PRJNA342843 | Rapid dynamic activation of Müller glial stem cell responses in zebrafish | GSE86872 | Transcriptome Analysis | Purpose: Zebrafish neurons regenerate from Müller glia following retinal lesions. Genes and signaling pathways important for retinal regeneration in zebrafish have been described but our understanding of how Mu¨ller glial stem cell properties are regulated is incomplete. Mammalian Mu¨ller glia possess a latent neurogenic capacity that might be enhanced in regenerative therapies to treat degenerative retinal diseases. Methods: To identify transcriptional changes associated with stem cell properties in zebrafish Mu¨ller glia we performed a comparative transcriptome analysis from isolated cells at 8 and 16 hours following an acute photic lesion prior to the asymmetric division that produces retinal progenitors. Results: We report a rapid dynamic response of zebrafish Müller glia characterized by activation of pathways related to stress NF kappa B signaling cytokine signaling immunity prostaglandin metabolism circadian rhythm and pluripotency and an initial repression of Wnt signaling. When we compared publicly available transcriptomes of isolated mouse Mu¨ller glia from two retinal degeneration models we found that mouse Müller glia showed evidence of oxidative stress variable responses associated with immune regulation and repression of pathways associated with pluripotency development and proliferation. Conclusions: Categories of biological processes/pathways activated following photoreceptor loss in regeneration competent zebrafish Mu¨ller glia which distinguished them from mouse Mu¨ller glia in retinal degeneration models included: cytokine signaling notably NF kappa B prostaglandin E2 synthesis expression of core clock genes and pathways/metabolic states associated with pluripotency. These regulatory mechanisms are relatively unexplored as potential mediators of stem cell properties likely to be important in Müller glial cells for successful retinal regeneration. Overall design: Transcriptional profiles of 0 8 and 16 hour post lesion zebrafish Müller glia in triplicate were generated by high throughput sequencing in an Illumina GAIIx. | pubmed:27699411 | 16 hpl Replicate 3 | GSM2309786 | source name:Müller glia|line:Tggfap:EGFPmi2002|tissue:neural retina|cell type:Muller glia|age:8 month 11 month|treatment:Light lesion 16 hours post lesion | 16 hpl Replicate 3 | Basecalls and quality scores performed using RTA 1.13.48 and Fastq files generated from reads passing chastity filtering. Trim Galore! v0.2.7 Krueger 2012 was used to trim adapter sequences and poor quality bases below Phred of 20 from the reads while removing any reads that were less than 20 nucleotides long using the default parameters. Trim Galore! makes use of cutadapt v1.4.2 Martin 2011 f fastq e 0.1 q 20 O 1 a AGATCGGAAGAGC file.fq.gz . The quality of the reads was assessed before and post trimming with FastQC v0.10.1 Andrews 2010. Quality trimmed and filtered reads were aligned to release 78 of the Zv9 Ensembl genome build with bowtie2 v2.2.6 Langmead and Salzberg 2012 and gene level quantitation was performed with RSEM v1.2.22 Li and Dewey 2011. This was done using the rsem calculate expression command from RSEM which calls bowtie2 sensitive dpad 0 gbar 99999999 mp 1 1 np 1 score min L 0 0.1 and streams reads into RSEM for quantitation. The gene level counts output from RSEM were filtered to remove noise prior to normalization with trimmed means of M TMM such that only genes with a FPKM fragments per kilobase of exon per million reads mapped value greater than 1 in all replicates of any time point were retained. Counts per million CPM were determined using edgeR v3.10.2 Robinson et al. 2010 genes with a CPM < 1 in all samples were removed and remaining counts were TMM normalized. Multidimensional scaling analysis with edgeR showed that one of the replicates at each of the 8 and 16 hpl timepoints did not cluster with the others. Limma v3.24.15 was used to voom transform the filtered count data by empirically deriving and applying quality weights to the samples Law et al. 2014; Ritchie et al. 2015. These weighted values were used to calculate differential expression using limma. Annotations for each gene were added using biomaRt v2.24.0 Durinck et al. 2005; Kersey et al. 2014 including both the Danio rerio Entrez gene identifiers and the corresponding Mus musculus Entrez orthologous gene identifiers. Genome build: Zv9 Release 78 Supplementary files format and content: Excel file containing differential expression data or tab delimited text files containing count and FPKM data. | Müller glia | Free swimming fish exposed to intense light >120 000 lux for 30 minutes. Retinas harvested at 16 hours post lesion hpl. | Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter. | line:Tggfap:EGFPmi2002|tissue:neural retina|cell type:Muller glia|age:8 month 11 month|treatment:Light lesion 16 hours post lesion | GSM2309786 | GSM2309786: 16 hpl Replicate 3; Danio rerio; RNA Seq | GSM2309786 | 1 | Retinas were removed and dissociated to obtain single cell suspensions. Müller glia were collected with fluorescently actived cell sorting. RNA was isolated with TRIzol LS according to recommenders protocol. RNA quality was checked via BioAnalyzer and samples with an RNA integrity number RIN > 7.0 were used for RNA seq library construction. Stranded RNA seq libraries were constructed using a modification of the Illumina TruSeq mRNA Brooks et al. Meth Mol Biol 2012. Each library was single end sequenced in an independent lane of a GAIIx. Fastq files were generated from reads passing chastity filter. | GEO Accession:GSM2309786 | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina Genome Analyzer IIx | SRP089817 | 16hpl3.fq.gz | fastq | 2321192665.0 | 27308149.0 | GSM2309786 r1 | 0:85 | A:578506517;C:590753476;G:555712960;T:595943815;N:275897 | 85 | 578506517 | 590753476 | 555712960 | 595943815 | 275897 | SRX2162516 | SRS1690572 | SRA470722 | GEO | Raymond Lab, Molecular, Cellular, and Developmental Biology, University of Michigan | 1 | 0.56954 | 0.07699 | 0.7667 | 0.49583 | 85 | B | usable mapping rate | illumina | early_illumina | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | United States | 2016-09-13 | Adult | Adult | Eye | Sensory System |