run_metadata
4 rows where experiment.library_layout = "PAIRED", experiment.library_selection = "unspecified" and technology = "10x"
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| Link | 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 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 25302 | 25302 | SRR25793493 | SRX21515745 | SRS18742910 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | Single cell Pr1phros ADULT miR 144 mutant Danio rerio | miR 144 | isolate:miR 144 mutant|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal | Single cell Pr1phros ADULT miR 144 mutant Danio rerio | CD 144 1 | CD 144 1 | Single cell library cloning was done with 10X Genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | unspecified | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_144_1_S3_R1.fastq CD_144_1_S3_R2.fastq | fastq fastq | 12899093774.0 | 108395746.0 | CD 144 1 S3 R1.fastq | 0:28 1:91 | A:3225260764;C:3211986177;G:3151471558;T:3308055659;N:2319616 | 28 | 91 | 3225260764 | 3211986177 | 3151471558 | 3308055659 | 2319616 | SRX21515745 | SRS18742910 | SRA1701829 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.00483 | 0.97382 | 0.00157 | 0.05913 | 0.99439 | 0.86815 | 0.46634 | 0.45907 | 28 | 91 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-08-30 | Adult | Adult | Blood | Hematopoietic System | ||||||||||||||||||||
| 25303 | 25303 | SRR25793494 | SRX21515744 | SRS18742909 | SRP457465 | PRJNA1010662 | The miR 144/Hmgn2 regulatory axis orchestrates chromatin organization during erythropoiesis. | PRJNA1010662 | Other | Differentiation of stem and progenitor cells is a highly regulated process that involves the coordinated action of multiple layers of regulation. Here we show how the post transcriptional regulatory layer instructs the chromatin regulation level via miR 144 and its targets to orchestrate chromatin condensation during erythropoiesis. The loss of miR 144 leads to impaired chromatin condensation during erythrocyte maturation. | Single cell Pr1phros ADULT Wild type Danio rerio | WT | isolate:Wildtype|age:Adult|collection date:N/A|geo loc name:N/A|sex:mixed|tissue:blood|BioSampleModel:Model organism or animal | Single cell Pr1phros ADULT Wild type Danio rerio | CD wt 1 | CD wt 1 | Single cell library cloning was done with 10X Genomics | RNA-Seq | TRANSCRIPTOMIC SINGLE CELL | unspecified | PAIRED | ILLUMINA | NextSeq 2000 | SRP457465 | CD_wt_1_S2_R1.fastq CD_wt_1_S2_R2.fastq | fastq fastq | 12715533299.0 | 106853221.0 | CD wt 1 S2 R1.fastq | 0:28 1:91 | A:3324705878;C:3042843364;G:3105568183;T:3240105528;N:2310346 | 28 | 91 | 3324705878 | 3042843364 | 3105568183 | 3240105528 | 2310346 | SRX21515744 | SRS18742909 | SRA1701829 | University of East Anglia|Biological Sciences | University of East Anglia | 2 | 0.00593 | 0.93177 | 0.00191 | 0.09596 | 0.99257 | 0.84394 | 0.42447 | 0.4869 | 28 | 91 | T | B | sc-like readlen | illumina | nextseq_v2 | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United Kingdom | 2023-08-30 | Adult | Adult | Blood | Hematopoietic System | ||||||||||||||||||||
| 74615 | 74615 | SRR24037111 | SRX19839674 | SRS17198396 | 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 Wild type linc mipep siblings scRNA seq [10x BAM] | linc mipep scMultiome 6d brains WT scRNA AGN002631 [10x BAM] | strain:TU/AB|age:144|dev stage:Day 6|sex:pooled male and female|tissue:brain|genotype:+/+|strain maternal:linc mipep WT|strain paternal:linc mipep WT|molecule:RNA|sample ref:AGS002041|replicate ref:AGN002631|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:WT RNA|replicate label short:WT scRNA|filetype:bam|BioSampleModel:Model organism or animal | linc mipep scMultiome 6d brains Wild type linc mipep siblings scRNA seq [10x BAM] | AGR003365 AGR003384 | AGR003365 AGR003384 | RNA | OTHER | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP427499 | assembly:GRCz11 | linc_mipep_scMultiome_6d_brains_WT_AGN002631_gex_possorted_bam.bam | 10X Genomics bam file | 17819875800.0 | 197998620.0 | linc mipep scMultiome 6d brains WT AGN002631 gex possorted bam.bam | 0:90 | A:5656585750;C:3315807167;G:3546967171;T:5300024689;N:491023 | 90 | 5656585750 | 3315807167 | 3546967171 | 5300024689 | 491023 | SRX19839674 | SRS17198396 | SRA1614141 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.87958 | 0.45053 | 0.7709 | 0.50096 | 90 | B | usable mapping rate | illumina | novaseq_era | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-31 | Larval | Larval | Brain | Nervous System | ||||||||||||||||||||||||||
| 74616 | 74616 | SRR24037113 | SRX19839672 | SRS17198394 | 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 [10x BAM] | linc mipep scMultiome 6d brains linc mipepMut scRNA AGN002629 [10x BAM] | 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|filetype:bam|BioSampleModel:Model organism or animal | linc mipep scMultiome 6d brains linc mipep mutant scRNA seq [10x BAM] | AGR003363 AGR003382 | AGR003363 AGR003382 | RNA | OTHER | TRANSCRIPTOMIC | unspecified | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP427499 | assembly:GRCz11 | linc_mipep_scMultiome_6d_brains_Mut_AGN002629_gex_possorted_bam.bam | 10X Genomics bam file | 18530138610.0 | 205890429.0 | linc mipep scMultiome 6d brains Mut AGN002629 gex possorted bam.bam | 0:90 | A:5801406623;C:3514275581;G:3726649190;T:5487294607;N:512609 | 90 | 5801406623 | 3514275581 | 3726649190 | 5487294607 | 512609 | SRX19839672 | SRS17198394 | SRA1614141 | Yale_Giraldez|Genetics | Yale_Giraldez_Group | 1 | 0.89012 | 0.4464 | 0.76867 | 0.52212 | 90 | B | usable mapping rate | illumina | novaseq_era | unknown | unknown | unknown | sc | single_cell_droplet | 10x | United States | 2023-03-31 | Larval | Larval | Brain | Nervous System |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;