metadata: run_metadata: 17 rows where technology = "10x" and tissue

17 rows where technology = "10x" and tissue_curation = "Thymus"

descending

Link	rowid ▼	run.accession	experiment.accession	sample.accession	study.accession	bioproject	study.title	study.alias	study.type	study.abstract	study.PMIDs	sample.title	sample.alias	sample.attributes	GEOsample.title	GEOsample.dataprocessing	GEOsample.source	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.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.r3_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.nofeature_rate.mate1	seqdetective.sparsity.mate1	seqdetective.pos_strand_rate.mate1	seqdetective.readlen.mate1	seqdetective.judgement.mate1	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
67584	67584	SRR17218121	SRX13397710	SRS11300870	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 4	GSM5732082	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 4	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732082	GSM5732082: Juvenile Thymus 4; Danio rerio; RNA Seq	GSM5732082		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732082	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_6_S4_L001_I1_001.fastq.gz 4wpfThymus_6_S4_L001_R1_001.fastq.gz 4wpfThymus_6_S4_L001_R2_001.fastq.gz	fastq fastq fastq	14767492309.0	116279467.0	GSM5732082 r1	0:8 1:28 2:91	A:3176407665;C:2147673056;G:2551453338;T:2705740495;N:156943	8	28	91	3176407665	2147673056	2551453338	2705740495	156943	SRX13397710	SRS11300870	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.87149	0.22037	0.84049	0.53423	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67585	67585	SRR17218122	SRX13397710	SRS11300870	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 4	GSM5732082	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 4	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732082	GSM5732082: Juvenile Thymus 4; Danio rerio; RNA Seq	GSM5732082		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732082	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_6_S4_L002_I1_001.fastq.gz 4wpfThymus_6_S4_L002_R1_001.fastq.gz 4wpfThymus_6_S4_L002_R2_001.fastq.gz	fastq fastq fastq	14660763541.0	115439083.0	GSM5732082 r2	0:8 1:28 2:91	A:3154820274;C:2128697452;G:2532561232;T:2688755742;N:121853	8	28	91	3154820274	2128697452	2532561232	2688755742	121853	SRX13397710	SRS11300870	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.87166	0.22046	0.8407	0.5334	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67586	67586	SRR17218119	SRX13397709	SRS11300871	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 3	GSM5732081	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 3	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732081	GSM5732081: Juvenile Thymus 3; Danio rerio; RNA Seq	GSM5732081		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732081	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_5_S3_L001_I1_001.fastq.gz 4wpfThymus_5_S3_L001_R1_001.fastq.gz 4wpfThymus_5_S3_L001_R2_001.fastq.gz	fastq fastq fastq	14488701909.0	114084267.0	GSM5732081 r1	0:8 1:28 2:91	A:3107408243;C:2119850736;G:2503503910;T:2650750983;N:154425	8	28	91	3107408243	2119850736	2503503910	2650750983	154425	SRX13397709	SRS11300871	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.85944	0.20997	0.84064	0.53634	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67587	67587	SRR17218120	SRX13397709	SRS11300871	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 3	GSM5732081	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 3	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732081	GSM5732081: Juvenile Thymus 3; Danio rerio; RNA Seq	GSM5732081		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732081	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_5_S3_L002_I1_001.fastq.gz 4wpfThymus_5_S3_L002_R1_001.fastq.gz 4wpfThymus_5_S3_L002_R2_001.fastq.gz	fastq fastq fastq	14352524508.0	113012004.0	GSM5732081 r2	0:8 1:28 2:91	A:3079316058;C:2096769810;G:2479668921;T:2628218918;N:118657	8	28	91	3079316058	2096769810	2479668921	2628218918	118657	SRX13397709	SRS11300871	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.85981	0.21085	0.8393	0.52667	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67588	67588	SRR17218117	SRX13397708	SRS11300869	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 2	GSM5732080	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732080	GSM5732080: Juvenile Thymus 2; Danio rerio; RNA Seq	GSM5732080		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732080	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_3_S2_L001_I1_001.fastq.gz 4wpfThymus_3_S2_L001_R1_001.fastq.gz 4wpfThymus_3_S2_L001_R2_001.fastq.gz	fastq fastq fastq	17459416821.0	137475723.0	GSM5732080 r1	0:8 1:28 2:91	A:3740652508;C:2562291967;G:3023715848;T:3183446304;N:184166	8	28	91	3740652508	2562291967	3023715848	3183446304	184166	SRX13397708	SRS11300869	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.84416	0.21191	0.83897	0.53108	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67589	67589	SRR17218118	SRX13397708	SRS11300869	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 2	GSM5732080	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732080	GSM5732080: Juvenile Thymus 2; Danio rerio; RNA Seq	GSM5732080		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732080	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_3_S2_L002_I1_001.fastq.gz 4wpfThymus_3_S2_L002_R1_001.fastq.gz 4wpfThymus_3_S2_L002_R2_001.fastq.gz	fastq fastq fastq	17241251014.0	135757882.0	GSM5732080 r2	0:8 1:28 2:91	A:3695117374;C:2526230853;G:2985988000;T:3146489343;N:141692	8	28	91	3695117374	2526230853	2985988000	3146489343	141692	SRX13397708	SRS11300869	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.84569	0.21301	0.83899	0.53404	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67590	67590	SRR17218115	SRX13397707	SRS11300868	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 1	GSM5732079	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 1	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732079	GSM5732079: Juvenile Thymus 1; Danio rerio; RNA Seq	GSM5732079		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732079	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_1_S1_L001_I1_001.fastq.gz 4wpfThymus_1_S1_L001_R1_001.fastq.gz 4wpfThymus_1_S1_L001_R2_001.fastq.gz	fastq fastq fastq	16221392627.0	127727501.0	GSM5732079 r1	0:8 1:28 2:91	A:3503038095;C:2359078159;G:2792714907;T:2968200161;N:171269	8	28	91	3503038095	2359078159	2792714907	2968200161	171269	SRX13397707	SRS11300868	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.84501	0.21705	0.8379	0.53566	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67591	67591	SRR17218116	SRX13397707	SRS11300868	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Juvenile Thymus 1	GSM5732079	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Juvenile Thymus 1	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Juvenile\|age:4 wpf bleed:no\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732079	GSM5732079: Juvenile Thymus 1; Danio rerio; RNA Seq	GSM5732079		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732079	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	4wpfThymus_1_S1_L002_I1_001.fastq.gz 4wpfThymus_1_S1_L002_R1_001.fastq.gz 4wpfThymus_1_S1_L002_R2_001.fastq.gz	fastq fastq fastq	16074886951.0	126573913.0	GSM5732079 r2	0:8 1:28 2:91	A:3472769520;C:2334135014;G:2767323491;T:2943866297;N:131761	8	28	91	3472769520	2334135014	2767323491	2943866297	131761	SRX13397707	SRS11300868	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.84624	0.21812	0.83918	0.52823	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Multi-stage	Multi-stage	Thymus	Hematopoietic System
67592	67592	SRR17218113	SRX13397706	SRS11300867	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 2	GSM5732078	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732078	GSM5732078: Adult Thymus 2; Danio rerio; RNA Seq	GSM5732078		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732078	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	lck-eGFP_Thymus_2__S4_L001_I1_001.fastq.gz lck-eGFP_Thymus_2__S4_L001_R1_001.fastq.gz lck-eGFP_Thymus_2__S4_L001_R2_001.fastq.gz	fastq fastq fastq	13928486651.0	110400658.0	GSM5732078 r1	0:8 1:27.57 2:90.59	A:2982389810;C:2043569636;G:2322019641;T:2652821180;N:252711	8	27	90	2982389810	2043569636	2322019641	2652821180	252711	SRX13397706	SRS11300867	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9102	0.22477	0.80227	0.51027	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
67593	67593	SRR17218114	SRX13397706	SRS11300867	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 2	GSM5732078	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 2	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732078	GSM5732078: Adult Thymus 2; Danio rerio; RNA Seq	GSM5732078		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732078	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	lck-eGFP_Thymus_2__S4_L002_I1_001.fastq.gz lck-eGFP_Thymus_2__S4_L002_R1_001.fastq.gz lck-eGFP_Thymus_2__S4_L002_R2_001.fastq.gz	fastq fastq fastq	13882495233.0	110035762.0	GSM5732078 r2	0:8 1:27.57 2:90.59	A:2973325031;C:2035977607;G:2312724405;T:2645711786;N:286217	8	27	90	2973325031	2035977607	2312724405	2645711786	286217	SRX13397706	SRS11300867	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9095	0.22389	0.80135	0.52051	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
67594	67594	SRR17218111	SRX13397705	SRS11300865	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 1	GSM5732077	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 1	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732077	GSM5732077: Adult Thymus 1; Danio rerio; RNA Seq	GSM5732077		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732077	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	lck-eGFP_Thymus_1__S4_L001_I1_001.fastq.gz lck-eGFP_Thymus_1__S4_L001_R1_001.fastq.gz lck-eGFP_Thymus_1__S4_L001_R2_001.fastq.gz	fastq fastq fastq	13683556018.0	108451992.0	GSM5732077 r1	0:8 1:27.57 2:90.60	A:2970924288;C:1965313899;G:2264518373;T:2624238930;N:636831	8	27	90	2970924288	1965313899	2264518373	2624238930	636831	SRX13397705	SRS11300865	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.91685	0.27522	0.81105	0.52662	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
67595	67595	SRR17218112	SRX13397705	SRS11300865	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 1	GSM5732077	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 1	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:Tglck:eGFP\|developmental stage:Adult\|age:3 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732077	GSM5732077: Adult Thymus 1; Danio rerio; RNA Seq	GSM5732077		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732077	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	lck-eGFP_Thymus_1__S4_L002_I1_001.fastq.gz lck-eGFP_Thymus_1__S4_L002_R1_001.fastq.gz lck-eGFP_Thymus_1__S4_L002_R2_001.fastq.gz	fastq fastq fastq	13739084909.0	108892246.0	GSM5732077 r2	0:8 1:27.57 2:90.60	A:2986926683;C:1971756062;G:2268315286;T:2638089379;N:417199	8	27	90	2986926683	1971756062	2268315286	2638089379	417199	SRX13397705	SRS11300865	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.91881	0.27676	0.81217	0.5208	91	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
67608	67608	SRR17218097	SRX13397698	SRS11300859	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 4	GSM5732070	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 4	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732070	GSM5732070: Adult Thymus 4; Danio rerio; RNA Seq	GSM5732070		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732070	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	Fish_24_Thymus__S3_L001_I1_001.fastq.gz Fish_24_Thymus__S3_L001_R1_001.fastq.gz Fish_24_Thymus__S3_L001_R2_001.fastq.gz	fastq fastq fastq	18278645709.0	144870332.0	GSM5732070 r1	0:8 1:27.57 2:90.60	A:3985081516;C:2643040166;G:3063178524;T:3433439412;N:330251	8	27	90	3985081516	2643040166	3063178524	3433439412	330251	SRX13397698	SRS11300859	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.92193	0.26629	0.81191	0.5476	87	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
67609	67609	SRR17218098	SRX13397698	SRS11300859	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 4	GSM5732070	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 4	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732070	GSM5732070: Adult Thymus 4; Danio rerio; RNA Seq	GSM5732070		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732070	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	Fish_24_Thymus__S3_L002_I1_001.fastq.gz Fish_24_Thymus__S3_L002_R1_001.fastq.gz Fish_24_Thymus__S3_L002_R2_001.fastq.gz	fastq fastq fastq	18204716552.0	144284032.0	GSM5732070 r2	0:8 1:27.57 2:90.60	A:3970235370;C:2631055170;G:3048647071;T:3421683260;N:373327	8	27	90	3970235370	2631055170	3048647071	3421683260	373327	SRX13397698	SRS11300859	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.9219	0.26619	0.80971	0.54097	90	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
67614	67614	SRR17218091	SRX13397695	SRS11300857	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 3	GSM5732067	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 3	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732067	GSM5732067: Adult Thymus 3; Danio rerio; RNA Seq	GSM5732067		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732067	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	Fish_22_Thymus__S3_L001_I1_001.fastq.gz Fish_22_Thymus__S3_L001_R1_001.fastq.gz Fish_22_Thymus__S3_L001_R2_001.fastq.gz	fastq fastq fastq	15755989697.0	124869852.0	GSM5732067 r1	0:8 1:27.57 2:90.61	A:3460847047;C:2243842372;G:2624369866;T:2984076004;N:733016	8	27	90	3460847047	2243842372	2624369866	2984076004	733016	SRX13397695	SRS11300857	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.91732	0.27669	0.81669	0.55139	90	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
67615	67615	SRR17218092	SRX13397695	SRS11300857	SRP350544	PRJNA788489	Single Cell Analyses Reveal Early Thymic Progenitors and Pre B Cells in the Zebrafish	GSE190794	Transcriptome Analysis	The zebrafish has proven to be a valuable model organism for studying hematopoiesis but relatively little is known about zebrafish immune cell development and functional diversity. Elucidating key aspects of zebrafish lymphocyte development and exploring the breadth of effector functions would provide valuable insight into the evolution of adaptive immunity. We performed single cell RNA sequencing on 70 000 cells from the zebrafish marrow and thymus to establish a gene expression map of zebrafish immune cell development. We uncovered rich cellular diversity in the juvenile and adult zebrafish thymus elucidated B and T cell developmental trajectories and transcriptionally characterized subsets of hematopoietic stem and progenitor cells and early thymic progenitors. Our analysis permitted the identification of two dendritic like cell populations and provided evidence in support of the existence of a pre B cell state. Our results provide critical insights into the landscape of zebrafish immunology and offer a foundation for cellular and genetic studies. Overall design: To analyze the composition of the zebrafish primary hematopoietic organs and to characterize immune cell subpopulations a total of 7 adult zebrafish 3 mpf 5 mpf and 21 juvenile zebrafish 4 wpf were studied. More specifically kidney marrows only were dissected from 3 adult GESTALT zebrafish paired kidney marrows and thymi were dissected from 2 adult GESTALT zebrafish and thymi only were dissected from 2 adult Tglck:eGFP zebrafish. Thymi only were dissected and pooled from 21 juvenile Tglck:eGFP zebrafish. No other pooling as performed. All tissues were subjected to mechanical dissociation filtering and cell sorting on a BD FACSAriaII. Live cells from whole thymi and two fractions of live cells from whole kidney marrow sorted based on FSC and SSC characteristics lymphoid and progenitor fraction; granulocyte fraction were collected in preparation for 10x single cell RNA sequencing. A single 10x lane was used for each adult sample whereas 4 lane…	pubmed:35938989	Adult Thymus 3	GSM5732067	tissue:sorted live thymus cells\|cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	Adult Thymus 3	The libraries were sequenced on NovaSeq platforms. BCL files were analyzed with the Cell Ranger pipeline version 3.1.0. The demultiplexed FASTQ data was aligned to zebrafish Ensembl GRCz11 reference and generated the single cell count matrix. Genome build: Zebrafish Ensembl GRCz11 reference Supplementary files format and content: h5 count matrices from the NovaSeq platforms	sorted live thymus cells	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell 3’ v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	Zebrafish were maintained in accordance with Boston Children’s Hospital Institutional Animal Care and Use Committee protocols and in line with Animal Resources at Children’s Hospital ARCH guidelines.	cell type:sorted live thymus cells\|strain:GESTALT\|developmental stage:Adult\|age:4 mpf bleed:yes\|dissection buffer:0.5% BSA in HBSS no Ca2+ or Mg2+\|dissection temperature:room temperature	GSM5732067	GSM5732067: Adult Thymus 3; Danio rerio; RNA Seq	GSM5732067		1	Adult and juvenile zebrafish were euthanized by rapid chilling and confirmed deceased prior to dissecting thymi and/or kidney marrows. Live cells were sorted 85 um nozzle on a BD FACSAriaII into 300 μL of 0.5% BSA in DPBS and kept on ice following the sort. Between 50 000 and 100 000 cells were sorted per sample assessed by Trypan blue staining and then pelleted by centrifugation at 400g x 5 minutes and resuspended to a final concentration of 1000 cells/uL. Transcriptome profiling was performed using the Chromium Next GEM Single Cell three prime v3.1 Reagent Kits 10x Genomics Inc.. A targeted recovery of 6 000 cells was set for loading the Chromium Controller in all assays and steps were performed as described in the Chromium Next GEM Single Cell three prime Reagent Kits v3.1 User Guide Rev D. The final transcriptome libraries were pooled in sets of 4 or 5 and sequenced at the Harvard University Bauer Core https://bauercore.fas.harvard.edu/ on an Illumina NovaSeq 6000 using an SP flow cell Read 1: 28 cycles i7 index: 8 cycles i5 index: 0 cycles Read 2: 91 cycles. scRNA Seq	GEO Accession:GSM5732067	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP350544	loader:fastq load.py	Fish_22_Thymus__S3_L002_I1_001.fastq.gz Fish_22_Thymus__S3_L002_R1_001.fastq.gz Fish_22_Thymus__S3_L002_R2_001.fastq.gz	fastq fastq fastq	15822948086.0	125400460.0	GSM5732067 r2	0:8 1:27.57 2:90.61	A:3480626521;C:2251532188;G:2629092513;T:3000199704;N:484646	8	27	90	3480626521	2251532188	2629092513	3000199704	484646	SRX13397695	SRS11300857	SRA1342645	GEO	Oncology/Hematology, Boston Children's Hospital	1	0.91806	0.27586	0.81588	0.5457	90	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2021-12-13	Adult	Adult	Thymus	Hematopoietic System
76726	76726	SRR25288288	SRX21031897	SRS18304343	SRP449631	PRJNA994919	Diverse Epithelial Lymphocytes in Zebrafish Revealed Using a Novel Scale Biopsy Method	GSE237417	Transcriptome Analysis	Zebrafish Danio rerio are a compelling model to study lymphocytes because zebrafish and humans have similar adaptive immune systems including their lymphocytes. Antibodies that recognize zebrafish proteins are sparse so many investigators utilize transgenic lymphocyte specific fluorophore labeled lines. Human and zebrafish lymphocyte types are conserved but many aspects of zebrafish lymphocyte biology remain uninvestigated including lymphocytes in peripheral tissues like epidermis. Here we report the first study focused on zebrafish epidermal lymphocytes using scales. Obtaining zebrafish blood via non lethal methods is difficult; scales represent a source to longitudinally sample live fish. We developed a novel biopsy technique collecting scales to analyze epithelial lymphocytes from several fluorescently labeled lines. We imaged scales via confocal microscopy and demonstrated multiple lymphocyte types in scales/epidermis quantifying them flow cytometrically. We profiled gene expression of scale thymic and marrow lymphocytes from the same animals revealing B and T lineage signatures. Single cell qRT PCR and RNA sequencing scRNA seq show not only canonical B and T cells but also novel lymphocyte populations not described previously. To validate longitudinal scale biopsies we serially sampled scales from fish treated with dexamethasone DXM demonstrating epidermal lymphocyte responses. To analyze cells functionally we employed a bead ingestion assay showing thymic marrow and epidermal lymphocytes have phagocytic activity. In summary we establish a novel non lethal technique to obtain zebrafish lymphocytes providing the first quantification expression profiling and functional data DXM responses and phagocytosis from epidermal lymphocytes in the zebrafish model. Overall design: This experimental study aimed to investigate the gene expression profiles of individual lymphocytes from the zebrafish lck:GFP transgenic line by using single cell RNA sequencing scRNA seq analysis. We performed scRNA …	pubmed:39503619	Thymus S1	GSM7611259	source name:Thymus\|tissue:Thymus\|cell line:NA\|cell type:Lymphocytes\|genotype:lck:GFP\|geo loc name:missing\|collection date:missing	Thymus S1	post conversion to fastq files reads for each sample were processed and aggregated using the 10x Genomics Cell Ranger v.6.0.0 pipeline no normalization default settings and processed in the Seurat R package v.4.3.0. We obtained transcriptomes for 6 359 cells post Cell Ranger processing. SoupX v.1.6.2 was used to model and remove ambient RNA contamination per sample and scDblFinder v.1.12.0 was used to detect potential multiplets default settings per individual tissue type. Additional QC filtering was performed to remove potential dead or dying cells along with cells exhibiting abnormal read/gene counts and high levels of mitochondrial transcripts resulting in 1 890 usable cells for our analysis. Using fastMNN cells were normalized and integrated and then clustered within Seurat Leiden algorithm. Clustering resolution was optimized using the clustree package v.0.5.0. Cluster boundaries were manually examined and fine tuned to optimize biological interpretation. Collective diagnostic gene signatures corresponding to published gene lists and our own sc qRT PCR results were explored using Seurat and UCell v.2.2.0. Preferential gene markers were determined for each distinct population using the FindAllMarkers function within Seurat to aid in cell type assignment p.adj ≤ 0.05 min.pct = 0.25. Assembly: GRCz11 Supplementary files format and content: Tab delimited value files and matrices.	Thymus	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymus kidney marrow and scale samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating tissues using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. Following creation of single cell emulsions uniquely identifiable 1st strand template single cell cDNA libraries were generated from each cell by emulsion PCR. 2nd strand cDNA was generated and ligated to compatible Illumina adapters. Libraries were loaded onto single NovaSeq 6000 lanes and sequenced using read lengths of 28 bp for the first read 120 bp for the second read and 8 base index reads.		tissue:Thymus\|cell line:NA\|cell type:Lymphocytes\|genotype:lck:GFP	GSM7611259	GSM7611259: Thymus S1; Danio rerio; RNA Seq	GSM7611259 r1	GSM7611259	1	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymus kidney marrow and scale samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating tissues using a pestle and passed through 35 um filters. Various fluorescent populations were sorted from the lymphoid and precursor gates using a BD FACSJazz Instrument analysis performed in FlowJo softare. Following creation of single cell emulsions uniquely identifiable 1st strand template single cell cDNA libraries were generated from each cell by emulsion PCR. 2nd strand cDNA was generated and ligated to compatible Illumina adapters. Libraries were loaded onto single NovaSeq 6000 lanes and sequenced using read lengths of 28 bp for the first read 120 bp for the second read and 8 base index reads.		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP449631	loader:fastq load.py	3_Mo_1ck_Thymus_S1_L001_I1_001.fastq.gz 3_Mo_1ck_Thymus_S1_L001_R1_001.fastq.gz 3_Mo_1ck_Thymus_S1_L001_R2_001.fastq.gz	fastq fastq fastq	13930287540.0	89296715.0	GSM7611259 r1	0:8 1:28 2:120	A:3208073091;C:2208968733;G:2525266634;T:2773161165;N:136177	8	28	120	3208073091	2208968733	2525266634	2773161165	136177	SRX21031897	SRS18304343	SRA1673435	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	1	0.92048	0.30227	0.81708	0.53081	120	B	usable mapping rate	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x	United States	2023-07-14	Undetermined	Undetermined	Thymus	Hematopoietic 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");;