metadata: run_metadata: 10 rows where experiment.library_selection = "unspecified" and technology = "10x"

10 rows where experiment.library_selection = "unspecified" and technology = "10x"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	sample.title	sample.alias	sample.attributes	experiment.title	experiment.alias	experiment.library_name	experiment.design_description	experiment.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	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.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	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
54188	54188	SRR10095964	SRX6828145	SRS5370320	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.		5b	strain:Tgolig2:GFPvu12\|age:5 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:5b\|BioSampleModel:Model organism or animal	scRNA seq of whole zebrafish embryos	5b	5b	10X v2 chromium cDNA library	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273	loader:latf load	olig2gfp120hb_S5_L001_R1_001.fastq olig2gfp120hb_S5_L001_R2_001.fastq olig2gfp120hb_S5_L002_R1_001.fastq olig2gfp120hb_S5_L002_R2_001.fastq olig2gfp120hb_S5_L003_R1_001.fastq olig2gfp120hb_S5_L003_R2_001.fastq olig2gfp120hb_S5_L004_R1_001.fastq olig2gfp120hb_S5_L004_R2_001.fastq olig2gfp120hb_S5_L005_R1_001.fastq olig2gfp120hb_S5_L005_R2_001.fastq olig2gfp120hb_S5_L006_R1_001.fastq olig2gfp120hb_S5_L006_R2_001.fastq olig2gfp120hb_S5_L007_R1_001.fastq olig2gfp120hb_S5_L007_R2_001.fastq olig2gfp120hb_S5_L008_R1_001.fastq olig2gfp120hb_S5_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	90080193105.0	566542095.0	5b.gz	0:26 1:133	A:25143336916;C:20071432223;G:20537826191;T:24313961041;N:13636734	26	133	25143336916	20071432223	20537826191	24313961041	13636734	SRX6828145	SRS5370320	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.00976	0.95301	0.00215	0.10077	0.97926	0.77851	0.44407	0.5221	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Larval	Larval	Whole Organism	All anatomical structures
54189	54189	SRR10095965	SRX6828144	SRS5370319	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.		5a	strain:Tgolig2:GFPvu12\|age:5 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:5a\|BioSampleModel:Model organism or animal	scRNA seq of whole zebrafish embryos	5a	5a	10X v2 chromium cDNA library	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273	loader:latf load	olig2gfp120ha_S4_L001_R1_001.fastq olig2gfp120ha_S4_L001_R2_001.fastq olig2gfp120ha_S4_L002_R1_001.fastq olig2gfp120ha_S4_L002_R2_001.fastq olig2gfp120ha_S4_L003_R1_001.fastq olig2gfp120ha_S4_L003_R2_001.fastq olig2gfp120ha_S4_L004_R1_001.fastq olig2gfp120ha_S4_L004_R2_001.fastq olig2gfp120ha_S4_L005_R1_001.fastq olig2gfp120ha_S4_L005_R2_001.fastq olig2gfp120ha_S4_L006_R1_001.fastq olig2gfp120ha_S4_L006_R2_001.fastq olig2gfp120ha_S4_L007_R1_001.fastq olig2gfp120ha_S4_L007_R2_001.fastq olig2gfp120ha_S4_L008_R1_001.fastq olig2gfp120ha_S4_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	106640540616.0	670695224.0	5a.gz	0:26 1:133	A:29532468637;C:23968826821;G:24791831474;T:28331248539;N:16165145	26	133	29532468637	23968826821	24791831474	28331248539	16165145	SRX6828144	SRS5370319	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01014	0.95016	0.00222	0.09527	0.97855	0.78212	0.41929	0.50263	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Larval	Larval	Whole Organism	All anatomical structures
54190	54190	SRR10095966	SRX6828143	SRS5370318	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.		2b	strain:Tgolig2:GFPvu12\|age:2 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:2b\|BioSampleModel:Model organism or animal	scRNA seq of whole zebrafish embryos	2b	2b	10X v2 chromium cDNA library	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273	loader:latf load	olig2gfp48ha_S3_L003_R2_001.fastq olig2gfp48ha_S3_L004_R1_001.fastq olig2gfp48ha_S3_L004_R2_001.fastq olig2gfp48ha_S3_L005_R1_001.fastq olig2gfp48ha_S3_L005_R2_001.fastq olig2gfp48ha_S3_L006_R1_001.fastq olig2gfp48ha_S3_L006_R2_001.fastq olig2gfp48ha_S3_L007_R1_001.fastq olig2gfp48ha_S3_L007_R2_001.fastq olig2gfp48ha_S3_L008_R1_001.fastq olig2gfp48ha_S3_L008_R2_001.fastq olig2gfp48ha_S3_L003_R1_001.fastq olig2gfp48ha_S3_L002_R2_001.fastq olig2gfp48ha_S3_L002_R1_001.fastq olig2gfp48ha_S3_L001_R2_001.fastq olig2gfp48ha_S3_L001_R1_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	100194025377.0	630151103.0	2b.gz	0:26 1:133	A:27235389395;C:22388810842;G:23041272930;T:27513445748;N:15106462	26	133	27235389395	22388810842	23041272930	27513445748	15106462	SRX6828143	SRS5370318	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.0127	0.95456	0.00215	0.09469	0.97463	0.79308	0.43287	0.50046	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Hatching	Embryo	Whole Organism	All anatomical structures
54191	54191	SRR10095967	SRX6828142	SRS5370317	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.		2a	strain:Tgelavl3:GCaMP6s\|age:2 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:2a\|BioSampleModel:Model organism or animal	scRNA seq of whole zebrafish embryos	2a	2a	10X v2 chromium cDNA library	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	NextSeq 500	SRP221273	loader:latf load	2a elav_gcamp_48h_S1_L001_R1_001.fastq elav_gcamp_48h_S1_L001_R2_001.fastq elav_gcamp_48h_S1_L002_R1_001.fastq elav_gcamp_48h_S1_L002_R2_001.fastq elav_gcamp_48h_S1_L003_R1_001.fastq elav_gcamp_48h_S1_L003_R2_001.fastq elav_gcamp_48h_S1_L004_R1_001.fastq elav_gcamp_48h_S1_L004_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq	30654488793.0	192795527.0	2a.gz	0:26 1:133	A:8922702024;C:6370087682;G:7321183700;T:8019014142;N:21501245	26	133	8922702024	6370087682	7321183700	8019014142	21501245	SRX6828142	SRS5370317	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.00427	0.91705	0.00106	0.08701	0.98999	0.8198	0.35255	0.50555	26	133	T	B	sc-like readlen	illumina	nextseq	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Hatching	Embryo	Whole Organism	All anatomical structures
54192	54192	SRR10095968	SRX6828141	SRS5370316	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.		1b	strain:Tgolig2:GFPvu12\|age:1 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:1b\|BioSampleModel:Model organism or animal	scRNA seq of whole zebrafish embryos	1b	1b	10X v2 chromium cDNA library	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273	loader:latf load	olig2gfp24hb_S2_L001_R1_001.fastq olig2gfp24hb_S2_L001_R2_001.fastq olig2gfp24hb_S2_L002_R1_001.fastq olig2gfp24hb_S2_L002_R2_001.fastq olig2gfp24hb_S2_L003_R1_001.fastq olig2gfp24hb_S2_L003_R2_001.fastq olig2gfp24hb_S2_L004_R1_001.fastq olig2gfp24hb_S2_L004_R2_001.fastq olig2gfp24hb_S2_L005_R1_001.fastq olig2gfp24hb_S2_L005_R2_001.fastq olig2gfp24hb_S2_L006_R1_001.fastq olig2gfp24hb_S2_L006_R2_001.fastq olig2gfp24hb_S2_L007_R1_001.fastq olig2gfp24hb_S2_L007_R2_001.fastq olig2gfp24hb_S2_L008_R1_001.fastq olig2gfp24hb_S2_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	98193351273.0	617568247.0	1b.gz	0:26 1:133	A:27237053473;C:21828277485;G:22951157364;T:26162156154;N:14706797	26	133	27237053473	21828277485	22951157364	26162156154	14706797	SRX6828141	SRS5370316	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01479	0.95138	0.00273	0.12104	0.97327	0.78293	0.39405	0.4998	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
54193	54193	SRR10095969	SRX6828140	SRS5370315	SRP221273	PRJNA564810	A Single Cell Transcriptome Atlas for Zebrafish Development	PRJNA564810	Other	The ability to define cell types and how they change during organogenesis is central to our understanding of animal development and human disease. Despite the crucial nature of this knowledge we have yet to fully characterize all distinct cell types and the gene expression differences that generate cell types during development. To address this knowledge gap we produced an Atlas using single cell RNA sequencing methods to investigate gene expression from the pharyngula to early larval stages in developing zebrafish. Our single cell transcriptome Atlas encompasses transcriptional profiles from 44 102 cells across four days of development using duplicate experiments that confirmed high reproducibility. We annotated 220 identified clusters and highlighted several strategies for interrogating changes in gene expression associated with the development of zebrafish embryos at single cell resolution. Furthermore we highlight the power of this analysis to assign new cell type or developmental stage specific expression information to many genes including those that are currently known only by sequence and/or that lack expression information altogether. The resulting Atlas is a resource of biologists to generate hypotheses for genetic mutant or functional analysis to launch an effort to define the diversity of cell types during zebrafish organogenesis and to examine the transcriptional profiles that produce each cell type over developmental time.		1a	strain:Tgolig2:GFPvu12\|age:1 dpf\|sex:unknown\|tissue:whole embryo\|Replicate name:1a\|BioSampleModel:Model organism or animal	scRNA seq of whole zebrafish embryos	1a	1a	10X v2 chromium cDNA library	RNA-Seq	TRANSCRIPTOMIC	unspecified	SINGLE	ILLUMINA	Illumina HiSeq 4000	SRP221273	loader:latf load	olig2gfp24ha_S1_L001_R1_001.fastq olig2gfp24ha_S1_L001_R2_001.fastq olig2gfp24ha_S1_L002_R1_001.fastq olig2gfp24ha_S1_L002_R2_001.fastq olig2gfp24ha_S1_L003_R1_001.fastq olig2gfp24ha_S1_L003_R2_001.fastq olig2gfp24ha_S1_L004_R1_001.fastq olig2gfp24ha_S1_L004_R2_001.fastq olig2gfp24ha_S1_L005_R1_001.fastq olig2gfp24ha_S1_L005_R2_001.fastq olig2gfp24ha_S1_L006_R1_001.fastq olig2gfp24ha_S1_L006_R2_001.fastq olig2gfp24ha_S1_L007_R1_001.fastq olig2gfp24ha_S1_L007_R2_001.fastq olig2gfp24ha_S1_L008_R1_001.fastq olig2gfp24ha_S1_L008_R2_001.fastq	fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq fastq	99552249225.0	626114775.0	1a.gz	0:26 1:133	A:27540748865;C:22111148705;G:23108024457;T:26777444676;N:14882522	26	133	27540748865	22111148705	23108024457	26777444676	14882522	SRX6828140	SRS5370315	SRA960102	University of Oregon\|Institute of Neuroscience	University of Oregon	2	0.01166	0.95413	0.002	0.08635	0.9779	0.80034	0.44044	0.48046	26	133	T	B	sc-like readlen	illumina	hiseq_era	unknown	unknown	unknown	sc	single_cell_droplet	10x	United States	2019-12-10	Pharyngula	Embryo	Whole Organism	All anatomical structures
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");;