run_metadata: 74619
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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| 74619 | SRR24010017 | SRX19812853 | SRS17053323 | SRP427499 | PRJNA945049 | linc mipep and linc wrb encode micropeptides that regulate chromatin accessibility in vertebrate specific neural cells | PRJNA945049 | Other | Thousands of long intergenic non coding RNAs lincRNAs are transcribed throughout the vertebrate genome. A subset of lincRNAs enriched in developing brains have recently been found to contain cryptic open reading frames and are speculated to encode micropeptides. However systematic identification and functional assessment of these transcripts have been hindered by technical challenges caused by their small size. Here we show that two putative lincRNAs linc mipep also called lnc rps25 and linc wrb encode micropeptides with homology to the vertebrate specific chromatin architectural protein Hmgn1 and demonstrate that they are required for development of vertebrate specific brain cell types. Specifically we show that NMDA receptor mediated pathways are dysregulated in zebrafish lacking these micropeptides and that their loss preferentially alters the gene regulatory networks that establish cerebellar cells and oligodendrocytes evolutionarily newer cell types that develop postnatally in humans. These findings reveal a key missing link in the evolution of vertebrate brain cell development and illustrate a genetic basis for how some neural cell types are more susceptible to chromatin disruptions with implications for neurodevelopmental disorders and disease. | linc mipep scMultiome 6d brains linc mipep mutant scRNA seq | linc mipep scMultiome 6d brains linc mipepMut scRNA AGN002629 | strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype: / |strain maternal:linc mipep MUT|strain paternal:linc mipep MUT|molecule:RNA|sample ref:AGS002016|replicate ref:AGN002629|replicate order:1|project label long:linc mipep homozygous mutant vs WT siblings sc Multiome 6dpf brains|project label short:linc mipep scMultiome 6d brains|sample label short:Mut RNA|replicate label short:linc mipepMut scRNA|BioSampleModel:Model organism or animal | linc mipep scMultiome 6d brains linc mipep mutant scRNA seq | AGR003382 | AGR003382 | RNA | OTHER | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP427499 | AGR003382_I1.fastq.gz AGR003382_R1.fastq.gz AGR003382_R2.fastq.gz AGR003382_R3.fastq.gz | fastq fastq fastq fastq | 28412879202.0 | 205890429.0 | AGR003382 I1.fastq.gz | 0:10 1:28 2:10 3:90 | A:5801406623;C:3514275581;G:3726649190;T:5487294607;N:512609 | 10 | 28 | 10 | 90 | 5801406623 | 3514275581 | 3726649190 | 5487294607 | 512609 | SRX19812853 | SRS17053323 | SRA1612740 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.89026 | 0.44521 | 0.76905 | 0.51993 | 90 | B | usable mapping rate | illumina | novaseq_era | unknown | unknown | unknown | sc_generic | single_cell_generic | generic-scrnaseq-only | United States | 2023-03-29 | Larval | Larval | Brain | Nervous System |