metadata: run_metadata: 79 rows where experiment.library_strategy = "RNA-Seq", tissue_curation = "Thymus" and tissue_curation

79 rows where experiment.library_strategy = "RNA-Seq", tissue_curation = "Thymus" and tissue_curation_coarse = "Hematopoietic System"

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.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
33158	33158	SRR29791088	SRX25290435	SRS21969151	SRP519440	PRJNA1134759	Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]	GSE272064	Transcriptome Analysis	The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver …		Dr thymus foxn1 / rep3	GSM8392364	source name:thymus\|tissue:thymus\|cell type:thymus cells\|genotype:foxn1 / \|geo loc name:missing\|collection date:missing	Dr thymus foxn1 / rep3	Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample	thymus	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		tissue:thymus\|cell type:thymus cells\|genotype:foxn1 /	GSM8392364	GSM8392364: Dr thymus foxn1 / rep3; Danio rerio; RNA Seq	GSM8392364 r1	GSM8392364	1	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP519440		BK6_R1.fastq.gz BK6_R2.fastq.gz	fastq fastq	40416715568.0	133830184.0	GSM8392364 r1	0:151 1:151	A:11536946706;C:8490306261;G:9295609599;T:11092005423;N:1847579	151	151		11536946706	8490306261	9295609599	11092005423	1847579	SRX25290435	SRS21969151	SRA1922343	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	2	0.89276	0.89283	0.11419	0.11482	0.73306	0.73409	0.46305	0.46571	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	Germany	2024-07-11	Undetermined	Undetermined	Thymus	Hematopoietic System
33159	33159	SRR29791089	SRX25290434	SRS21969152	SRP519440	PRJNA1134759	Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]	GSE272064	Transcriptome Analysis	The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver …		Dr thymus foxn1 / rep2	GSM8392363	source name:thymus\|tissue:thymus\|cell type:thymus cells\|genotype:foxn1 / \|geo loc name:missing\|collection date:missing	Dr thymus foxn1 / rep2	Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample	thymus	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		tissue:thymus\|cell type:thymus cells\|genotype:foxn1 /	GSM8392363	GSM8392363: Dr thymus foxn1 / rep2; Danio rerio; RNA Seq	GSM8392363 r1	GSM8392363	1	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP519440		BK5_R1.fastq.gz BK5_R2.fastq.gz	fastq fastq	41734368446.0	138193273.0	GSM8392363 r1	0:151 1:151	A:12015023285;C:8850050726;G:9485443497;T:11381944831;N:1906107	151	151		12015023285	8850050726	9485443497	11381944831	1906107	SRX25290434	SRS21969152	SRA1922343	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	2	0.88856	0.88918	0.11978	0.11946	0.73003	0.732	0.44244	0.43125	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	Germany	2024-07-11	Undetermined	Undetermined	Thymus	Hematopoietic System
33160	33160	SRR29791090	SRX25290433	SRS21969150	SRP519440	PRJNA1134759	Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]	GSE272064	Transcriptome Analysis	The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver …		Dr thymus foxn1 / rep1	GSM8392362	source name:thymus\|tissue:thymus\|cell type:thymus cells\|genotype:foxn1 / \|geo loc name:missing\|collection date:missing	Dr thymus foxn1 / rep1	Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample	thymus	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		tissue:thymus\|cell type:thymus cells\|genotype:foxn1 /	GSM8392362	GSM8392362: Dr thymus foxn1 / rep1; Danio rerio; RNA Seq	GSM8392362 r1	GSM8392362	1	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP519440		BK4_R2.fastq.gz BK4_R1.fastq.gz	fastq fastq	39302001858.0	130139079.0	GSM8392362 r1	0:151 1:151	A:11220466966;C:8305776940;G:9105878447;T:10668104948;N:1774557	151	151		11220466966	8305776940	9105878447	10668104948	1774557	SRX25290433	SRS21969150	SRA1922343	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	2	0.89299	0.89318	0.11306	0.1139	0.74123	0.74345	0.45102	0.46093	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	Germany	2024-07-11	Undetermined	Undetermined	Thymus	Hematopoietic System
33161	33161	SRR29791091	SRX25290432	SRS21969149	SRP519440	PRJNA1134759	Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]	GSE272064	Transcriptome Analysis	The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver …		Dr thymus foxn1+/+ rep3	GSM8392361	source name:thymus\|tissue:thymus\|cell type:thymus cells\|genotype:foxn1+/+\|geo loc name:missing\|collection date:missing	Dr thymus foxn1+/+ rep3	Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample	thymus	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		tissue:thymus\|cell type:thymus cells\|genotype:foxn1+/+	GSM8392361	GSM8392361: Dr thymus foxn1+/+ rep3; Danio rerio; RNA Seq	GSM8392361 r1	GSM8392361	1	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP519440		BK3_R1.fastq.gz BK3_R2.fastq.gz	fastq fastq	37243022634.0	123321267.0	GSM8392361 r1	0:151 1:151	A:10858514997;C:7805630226;G:8359994769;T:10217208022;N:1674620	151	151		10858514997	7805630226	8359994769	10217208022	1674620	SRX25290432	SRS21969149	SRA1922343	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	2	0.87732	0.87686	0.20353	0.20336	0.73261	0.7343	0.49192	0.4924	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	Germany	2024-07-11	Undetermined	Undetermined	Thymus	Hematopoietic System
33162	33162	SRR29791092	SRX25290431	SRS21969148	SRP519440	PRJNA1134759	Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]	GSE272064	Transcriptome Analysis	The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver …		Dr thymus foxn1+/+ rep2	GSM8392360	source name:thymus\|tissue:thymus\|cell type:thymus cells\|genotype:foxn1+/+\|geo loc name:missing\|collection date:missing	Dr thymus foxn1+/+ rep2	Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample	thymus	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		tissue:thymus\|cell type:thymus cells\|genotype:foxn1+/+	GSM8392360	GSM8392360: Dr thymus foxn1+/+ rep2; Danio rerio; RNA Seq	GSM8392360 r1	GSM8392360	1	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP519440		BK2_R1.fastq.gz BK2_R2.fastq.gz	fastq fastq	34154139756.0	113093178.0	GSM8392360 r1	0:151 1:151	A:9754575779;C:7198913431;G:7834944597;T:9364172876;N:1533073	151	151		9754575779	7198913431	7834944597	9364172876	1533073	SRX25290431	SRS21969148	SRA1922343	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	2	0.87955	0.88145	0.18817	0.18856	0.72707	0.72839	0.49921	0.49737	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	Germany	2024-07-11	Undetermined	Undetermined	Thymus	Hematopoietic System
33163	33163	SRR29791093	SRX25290430	SRS21969147	SRP519440	PRJNA1134759	Developmental trajectory and evolutionary origin of thymic mimetic cells [dataset 2]	GSE272064	Transcriptome Analysis	The generation of self tolerant repertoires of T cells depends on the expression of peripheral self antigens in the thymic epithelium and the presence of small populations of cells mimicking the diverse phenotypes of peripheral tissues. Whereas the molecular underpinnings of self antigen expression have been extensively studied the developmental origins and differentiation pathways of thymic mimetic cells remain to be identified. Moreover the histological identification of myoid and other peripheral cell types as components of the thymic microenvironment of many vertebrate species raises questions as to the evolutionary origin of this unique tolerance mechanism. Here we show that during mouse development mimetic cells appear in the microenvironment in two successive waves. Cells exhibiting transcriptional signatures characteristic of muscle ionocyte goblet and ciliated cells emerge before birth whereas others for instance those mimicking enterohepatic cells and skin keratinocytes appear postnatally. These two groups also respond differently to modulations of TEC progenitor pools caused by deletions of Foxn1 and Ascl1 expression of a hypomorphic Foxn1 transcription factor and overexpression of Bmp4 and Fgf7 signalling molecules. Differences in mimetic cell populations were also observed in thymic microenvironments reconstructed by replacement of mouse Foxn1 with evolutionarily ancient Foxn1/4 gene family members including the Foxn4 gene of the cephalochordate amphioxus and the Foxn4 and Foxn1 genes of a cartilaginous fish. Whereas some cell types such as ciliated cells develop in the thymus in the absence of Foxn1 mimetic cells appearing postnatally such as enterohepatic cells require the activity of the vertebrate specific transcription factor Foxn1. The thymus of cartilaginous fishes and the thymoid of lampreys a representative of jawless vertebrates that exhibit an alternative adaptive immune system also harbour cells expressing genes encoding peripheral tissue components such as the liver …		Dr thymus foxn1+/+ rep1	GSM8392359	source name:thymus\|tissue:thymus\|cell type:thymus cells\|genotype:foxn1+/+\|geo loc name:missing\|collection date:missing	Dr thymus foxn1+/+ rep1	Transcriptomes were analyzed on the Galaxy platform. Adapters were trimmed with TrimGalore! version 0.4.3.1. Reads were aligned to the reference genome with Hisat2 version 2.1.0. Counts were generated with featureCounts version 1.6.1.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files containing raw counts for each sample	thymus	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		tissue:thymus\|cell type:thymus cells\|genotype:foxn1+/+	GSM8392359	GSM8392359: Dr thymus foxn1+/+ rep1; Danio rerio; RNA Seq	GSM8392359 r1	GSM8392359	1	Thymus tissue was explanted and placed into TRI reagent Sigma Aldrich. RNA was extracted following standard protocols. Each library consists of a pool of RNA from 3 animals. Libraries were constructed with the NEBNext Low Input RNA Library Preparation kit. Library preparation was carried out by the Deep Sequencing core facility at the Max Planck Institute for Immunobiology and Epigenetics according to their standard protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP519440		BK1_R2.fastq.gz BK1_R1.fastq.gz	fastq fastq	48045652026.0	159091563.0	GSM8392359 r1	0:151 1:151	A:13986882382;C:9969611893;G:10712447624;T:13374538759;N:2171368	151	151		13986882382	9969611893	10712447624	13374538759	2171368	SRX25290430	SRS21969147	SRA1922343	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	Boehm, Developmental Immunology, Max Planck Institute for Immunobiology and Epigenetics	2	0.87379	0.87656	0.21786	0.2191	0.73815	0.73975	0.49869	0.49808	151	151	B	B	biological fallback assumption	illumina	novaseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk	Germany	2024-07-11	Undetermined	Undetermined	Thymus	Hematopoietic System
59515	59515	SRR11926689	SRX8472335	SRS6772936	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	WT5	GSM4591370	tissue:Healthy sorted thymus\|cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	WT5	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy sorted thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	GSM4591370	GSM4591370: WT5; Danio rerio; RNA Seq	GSM4591370		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591370	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		FWTsample_5.fastq.gz FWTsample_5_R2.fastq.gz	fastq fastq	4633582858.0	22938529.0	GSM4591370 r1	0:101 1:101	A:1263929939;C:1047240206;G:1052800791;T:1263574247;N:6037675	101	101		1263929939	1047240206	1052800791	1263574247	6037675	SRX8472335	SRS6772936	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.91347	0.91728	0.27187	0.27409	0.76585	0.76859	0.45662	0.48071	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59516	59516	SRR11926688	SRX8472334	SRS6772935	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	WT4	GSM4591369	tissue:Healthy sorted thymus\|cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	WT4	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy sorted thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	GSM4591369	GSM4591369: WT4; Danio rerio; RNA Seq	GSM4591369		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591369	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		FWTsample_4.fastq.gz FWTsample_4_R2.fastq.gz	fastq fastq	4113149600.0	20565748.0	GSM4591369 r1	0:100 1:100	A:1084628064;C:963840734;G:985823964;T:1078691018;N:165820	100	100		1084628064	963840734	985823964	1078691018	165820	SRX8472334	SRS6772935	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.9336	0.93539	0.11919	0.11989	0.76368	0.76757	0.4904	0.47498	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59517	59517	SRR11926687	SRX8472333	SRS6772934	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	WT3	GSM4591368	tissue:Healthy sorted thymus\|cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	WT3	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy sorted thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	GSM4591368	GSM4591368: WT3; Danio rerio; RNA Seq	GSM4591368		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591368	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		FWTsample_3_R2.fastq.gz FWTsample_3.fastq.gz	fastq fastq	3966667200.0	19833336.0	GSM4591368 r1	0:100 1:100	A:1125938234;C:857622800;G:856236104;T:1122434590;N:4435472	100	100		1125938234	857622800	856236104	1122434590	4435472	SRX8472333	SRS6772934	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.93918	0.92495	0.16292	0.15907	0.75866	0.76883	0.51794	0.51278	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59518	59518	SRR11926686	SRX8472332	SRS6772933	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	WT2	GSM4591367	tissue:Healthy sorted thymus\|cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	WT2	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy sorted thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	GSM4591367	GSM4591367: WT2; Danio rerio; RNA Seq	GSM4591367		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591367	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		FWTsample_2_R2.fastq.gz FWTsample_2.fastq.gz	fastq fastq	3598961400.0	17994807.0	GSM4591367 r1	0:100 1:100	A:982353707;C:818188790;G:810911943;T:983465623;N:4041337	100	100		982353707	818188790	810911943	983465623	4041337	SRX8472332	SRS6772933	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.93426	0.9195	0.12591	0.12501	0.76763	0.77621	0.49491	0.50063	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59519	59519	SRR11926685	SRX8472331	SRS6772932	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	WT1	GSM4591366	tissue:Healthy sorted thymus\|cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	WT1	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy sorted thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tglck:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Frazer lab	GSM4591366	GSM4591366: WT1; Danio rerio; RNA Seq	GSM4591366		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591366	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		FWTsample_1_R2.fastq.gz FWTsample_1.fastq.gz	fastq fastq	3686706000.0	18433530.0	GSM4591366 r1	0:100 1:100	A:1004954280;C:838347690;G:833756041;T:1005493425;N:4154564	100	100		1004954280	838347690	833756041	1005493425	4154564	SRX8472331	SRS6772932	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.93171	0.91783	0.13677	0.13606	0.76723	0.7752	0.51062	0.50949	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59520	59520	SRR11926684	SRX8472330	SRS6772931	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	SPL002	GSM4591365	tissue:shrek preleukemic thymocytes\|cell type:thymocytes\|genotype:shrek;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	SPL002	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	shrek preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:shrek;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591365	GSM4591365: SPL002; Danio rerio; RNA Seq	GSM4591365		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591365	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_48.fastq.gz Fsample_48_R2.fastq.gz	fastq fastq	23525993582.0	77900641.0	GSM4591365 r1	0:151 1:151	A:6365057472;C:5454588670;G:5620997543;T:6082859005;N:2490892	151	151		6365057472	5454588670	5620997543	6082859005	2490892	SRX8472330	SRS6772931	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.96011	0.96113	0.23076	0.22681	0.80858	0.81221	0.52577	0.51928	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59521	59521	SRR11926683	SRX8472329	SRS6772930	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	SPL001	GSM4591364	tissue:shrek preleukemic thymocytes\|cell type:thymocytes\|genotype:shrek;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	SPL001	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	shrek preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:shrek;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591364	GSM4591364: SPL001; Danio rerio; RNA Seq	GSM4591364		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591364	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_47.fastq.gz Fsample_47_R2.fastq.gz	fastq fastq	26795594770.0	88727135.0	GSM4591364 r1	0:151 1:151	A:7305822132;C:6082789601;G:6442162847;T:6961938191;N:2881999	151	151		7305822132	6082789601	6442162847	6961938191	2881999	SRX8472329	SRS6772930	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.96139	0.96343	0.22215	0.2185	0.81296	0.81647	0.50868	0.51446	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59532	59532	SRR11926672	SRX8472318	SRS6772919	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	OPL4	GSM4591353	tissue:otg preleukemic thymocytes\|cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	OPL4	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	otg preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591353	GSM4591353: OPL4; Danio rerio; RNA Seq	GSM4591353		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591353	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_36.fastq.gz Fsample_36_R2.fastq.gz	fastq fastq	4686865610.0	23202305.0	GSM4591353 r1	0:101 1:101	A:1290395271;C:1046629683;G:1049444449;T:1294288823;N:6107384	101	101		1290395271	1046629683	1049444449	1294288823	6107384	SRX8472318	SRS6772919	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.92236	0.92454	0.31359	0.31617	0.76625	0.76779	0.48273	0.47205	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59533	59533	SRR11926671	SRX8472317	SRS6772918	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	OPL3	GSM4591352	tissue:otg preleukemic thymocytes\|cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	OPL3	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	otg preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591352	GSM4591352: OPL3; Danio rerio; RNA Seq	GSM4591352		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591352	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_35_R2.fastq.gz Fsample_35.fastq.gz	fastq fastq	6253893538.0	30959869.0	GSM4591352 r1	0:101 1:101	A:1720308233;C:1397371474;G:1404797248;T:1723210472;N:8206111	101	101		1720308233	1397371474	1404797248	1723210472	8206111	SRX8472317	SRS6772918	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.93192	0.93318	0.35833	0.3632	0.78518	0.78788	0.48278	0.48009	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59534	59534	SRR11926670	SRX8472316	SRS6772917	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	OPL2	GSM4591351	tissue:otg preleukemic thymocytes\|cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	OPL2	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	otg preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591351	GSM4591351: OPL2; Danio rerio; RNA Seq	GSM4591351		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591351	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_34_R2.fastq.gz Fsample_34.fastq.gz	fastq fastq	5351903948.0	26494574.0	GSM4591351 r1	0:101 1:101	A:1442793834;C:1227325750;G:1233975738;T:1440891564;N:6917062	101	101		1442793834	1227325750	1233975738	1440891564	6917062	SRX8472316	SRS6772917	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.92964	0.93101	0.21706	0.2185	0.76497	0.76848	0.47634	0.48247	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59535	59535	SRR11926669	SRX8472315	SRS6772916	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	OPL1	GSM4591350	tissue:otg preleukemic thymocytes\|cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	OPL1	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	otg preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:otg;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591350	GSM4591350: OPL1; Danio rerio; RNA Seq	GSM4591350		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591350	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_33.fastq.gz Fsample_33_R2.fastq.gz	fastq fastq	5499039536.0	27222968.0	GSM4591350 r1	0:101 1:101	A:1515036859;C:1226882670;G:1229198085;T:1520688016;N:7233906	101	101		1515036859	1226882670	1229198085	1520688016	7233906	SRX8472315	SRS6772916	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.92637	0.92762	0.31857	0.32243	0.76769	0.77116	0.46456	0.46584	101	101	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59546	59546	SRR11926658	SRX8472304	SRS6772905	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	MPL3	GSM4591339	tissue:hMYC preleukemic thymocytes\|cell type:thymocytes\|genotype:Tgrag2:hMYC Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	MPL3	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	hMYC preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:hMYC Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591339	GSM4591339: MPL3; Danio rerio; RNA Seq	GSM4591339		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591339	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_21.fastq.gz Fsample_21_R2.fastq.gz	fastq fastq	8876009218.0	29390759.0	GSM4591339 r1	0:151 1:151	A:2397445782;C:2052027740;G:2018874313;T:2405562242;N:2099141	151	151		2397445782	2052027740	2018874313	2405562242	2099141	SRX8472304	SRS6772905	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.92414	0.9227	0.2461	0.23997	0.78841	0.79506	0.50203	0.5018	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59547	59547	SRR11926657	SRX8472303	SRS6772904	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	MPL2	GSM4591338	tissue:hMYC preleukemic thymocytes\|cell type:thymocytes\|genotype:Tgrag2:hMYC Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	MPL2	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	hMYC preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:hMYC Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591338	GSM4591338: MPL2; Danio rerio; RNA Seq	GSM4591338		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591338	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_20.fastq.gz Fsample_20_R2.fastq.gz	fastq fastq	8942441970.0	29610735.0	GSM4591338 r1	0:151 1:151	A:2434196467;C:2047066969;G:2021293350;T:2437752994;N:2132190	151	151		2434196467	2047066969	2021293350	2437752994	2132190	SRX8472303	SRS6772904	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.9147	0.91499	0.22028	0.2117	0.77713	0.78334	0.50243	0.49838	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59548	59548	SRR11926656	SRX8472302	SRS6772903	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	MPL1	GSM4591337	tissue:hMYC preleukemic thymocytes\|cell type:thymocytes\|genotype:Tgrag2:hMYC Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	MPL1	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	hMYC preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:hMYC Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591337	GSM4591337: MPL1; Danio rerio; RNA Seq	GSM4591337		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591337	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_19.fastq.gz Fsample_19_R2.fastq.gz	fastq fastq	9778540144.0	32379272.0	GSM4591337 r1	0:151 1:151	A:2676504038;C:2223347787;G:2177506547;T:2698864055;N:2317717	151	151		2676504038	2223347787	2177506547	2698864055	2317717	SRX8472302	SRS6772903	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.91346	0.91413	0.29555	0.28893	0.79078	0.79825	0.49875	0.50518	151	151	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59549	59549	SRR11926655	SRX8472301	SRS6772902	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	HPL3	GSM4591336	tissue:hulk mutant preleukemic thymocytes\|cell type:thymocytes\|genotype:hulk;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	HPL3	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	hulk mutant preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:hulk;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591336	GSM4591336: HPL3; Danio rerio; RNA Seq	GSM4591336		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591336	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_12.fastq.gz Fsample_12_R2.fastq.gz	fastq fastq	3378760800.0	16893804.0	GSM4591336 r1	0:100 1:100	A:869653801;C:820588210;G:823025653;T:861750769;N:3742367	100	100		869653801	820588210	823025653	861750769	3742367	SRX8472301	SRS6772902	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.93754	0.92151	0.17513	0.16969	0.79922	0.8071	0.63894	0.61913	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59550	59550	SRR11926654	SRX8472300	SRS6772901	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	HPL2	GSM4591335	tissue:hulk mutant preleukemic thymocytes\|cell type:thymocytes\|genotype:hulk;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	HPL2	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	hulk mutant preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:hulk;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591335	GSM4591335: HPL2; Danio rerio; RNA Seq	GSM4591335		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591335	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_11.fastq.gz Fsample_11_R2.fastq.gz	fastq fastq	3276290400.0	16381452.0	GSM4591335 r1	0:100 1:100	A:909076954;C:730010076;G:728583319;T:904911154;N:3708897	100	100		909076954	730010076	728583319	904911154	3708897	SRX8472300	SRS6772901	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.93409	0.92023	0.18134	0.18141	0.78108	0.78981	0.53659	0.52431	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59551	59551	SRR11926653	SRX8472299	SRS6772900	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	HPL1	GSM4591334	tissue:hulk mutant preleukemic thymocytes\|cell type:thymocytes\|genotype:hulk;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	HPL1	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	hulk mutant preleukemic thymocytes	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:hulk;Tglck:GFP\|tumor stg:preleukemic\|lab of sample collection and sequencing:Frazer lab	GSM4591334	GSM4591334: HPL1; Danio rerio; RNA Seq	GSM4591334		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591334	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 3000	SRP265974		Fsample_10.fastq.gz Fsample_10_R2.fastq.gz	fastq fastq	3700727800.0	18503639.0	GSM4591334 r1	0:100 1:100	A:1028412839;C:821049620;G:815741395;T:1031399520;N:4124426	100	100		1028412839	821049620	815741395	1031399520	4124426	SRX8472299	SRS6772900	SRA1083220	GEO	Center for Medical Genetics, Ghent University	2	0.93381	0.92058	0.22321	0.22223	0.73655	0.74732	0.4822	0.48829	100	100	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59579	59579	SRR11926625	SRX8472271	SRS6772872	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	AB thymus 9	GSM4591306	tissue:Healthy dissected thymus\|cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	AB thymus 9	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy dissected thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	GSM4591306	GSM4591306: AB thymus 9; Danio rerio; RNA Seq	GSM4591306		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591306	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP265974		sample_6.fastq.gz	fastq	2786385619.0	36888152.0	GSM4591306 r1	0:75.54 1:0	A:663089588;C:692060734;G:651825670;T:779197417;N:212210	75	0		663089588	692060734	651825670	779197417	212210	SRX8472271	SRS6772872	SRA1083220	GEO	Center for Medical Genetics, Ghent University	1	0.94942		0.05717		0.73018		0.49009		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59580	59580	SRR11926624	SRX8472270	SRS6772871	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	AB thymus 8	GSM4591305	tissue:Healthy dissected thymus\|cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	AB thymus 8	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy dissected thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	GSM4591305	GSM4591305: AB thymus 8; Danio rerio; RNA Seq	GSM4591305		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591305	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP265974		sample_5.fastq.gz	fastq	2456067469.0	32519095.0	GSM4591305 r1	0:75.53 1:0	A:606304745;C:594426559;G:556316196;T:698842180;N:177789	75	0		606304745	594426559	556316196	698842180	177789	SRX8472270	SRS6772871	SRA1083220	GEO	Center for Medical Genetics, Ghent University	1	0.94282		0.08874		0.70851		0.49253		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59581	59581	SRR11926623	SRX8472269	SRS6772870	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	AB thymus 7	GSM4591304	tissue:Healthy dissected thymus\|cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	AB thymus 7	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy dissected thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	GSM4591304	GSM4591304: AB thymus 7; Danio rerio; RNA Seq	GSM4591304		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591304	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP265974		sample_4.fastq.gz	fastq	2889915115.0	38259114.0	GSM4591304 r1	0:75.54 1:0	A:694082728;C:713330573;G:669832103;T:812454853;N:214858	75	0		694082728	713330573	669832103	812454853	214858	SRX8472269	SRS6772870	SRA1083220	GEO	Center for Medical Genetics, Ghent University	1	0.94794		0.06446		0.72697		0.49962		75		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59582	59582	SRR11926622	SRX8472268	SRS6772869	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	AB thymus 2 3 5 6	GSM4591303	tissue:Healthy dissected thymus\|cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	AB thymus 2 3 5 6	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy dissected thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	GSM4591303	GSM4591303: AB thymus 2 3 5 6; Danio rerio; RNA Seq	GSM4591303		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591303	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP265974		sample_3.fastq.gz	fastq	2338535479.0	30955998.0	GSM4591303 r1	0:75.54 1:0	A:540165709;C:595429439;G:553807340;T:648952381;N:180610	75	0		540165709	595429439	553807340	648952381	180610	SRX8472268	SRS6772869	SRA1083220	GEO	Center for Medical Genetics, Ghent University	1	0.94992		0.04962		0.73032		0.4837		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59583	59583	SRR11926621	SRX8472267	SRS6772868	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	AB thymus 11	GSM4591302	tissue:Healthy dissected thymus\|cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	AB thymus 11	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy dissected thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	GSM4591302	GSM4591302: AB thymus 11; Danio rerio; RNA Seq	GSM4591302		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591302	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP265974		sample_2.fastq.gz	fastq	2942053849.0	38949737.0	GSM4591302 r1	0:75.53 1:0	A:688398915;C:734856328;G:694653408;T:823920342;N:224856	75	0		688398915	734856328	694653408	823920342	224856	SRX8472267	SRS6772868	SRA1083220	GEO	Center for Medical Genetics, Ghent University	1	0.94862		0.06975		0.72224		0.49305		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
59584	59584	SRR11926620	SRX8472266	SRS6772867	SRP265974	PRJNA637328	A novel TLX1 driven T ALL zebrafish model: comparative genomic analysis with other leukemia models	GSE151816	Transcriptome Analysis	We generated a new rag2 TLX1 driven T ALL model in zebrafish. RNA sequencing was preformed on the developed TLX1 T ALLs sequencing performed in the Speleman lab. In addition RNA sequencing was performed on various additional zebrafish T ALL models shrek hulk otg hMYC sequenced in the Frazer lab to look at the molecular differences between the various existing T ALL models. Overall design: RNA sequencing data from TLX1 shrek hulk otg T ALL samples wild type thymocytes sequenced in the Speleman lab wild type thymocytes sequenced in the Frazer lab. Shrek otg hulk hMYC preleukemic thymocytes	pubmed:32591643	AB thymus 10	GSM4591301	tissue:Healthy dissected thymus\|cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	AB thymus 10	First read of Fastq files were aligned to GRCz10 using STARv2.4.2a with esembl GRCz10.91.gtf as guide Counts to GRCz10.91.gtf were generated on the fly by STAR Genome build: GRCz10 Supplementary files format and content: txt file with raw counts	Healthy dissected thymus	Truseq stranded mRNA library prep illumina #20020594		cell type:thymocytes\|genotype:Tgrag2:GFP\|tumor stg:healthy\|lab of sample collection and sequencing:Speleman lab	GSM4591301	GSM4591301: AB thymus 10; Danio rerio; RNA Seq	GSM4591301		1	Truseq stranded mRNA library prep illumina #20020594	GEO Accession:GSM4591301	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500	SRP265974		sample_1.fastq.gz	fastq	2923525817.0	38707354.0	GSM4591301 r1	0:75.53 1:0	A:697204107;C:721945575;G:689048693;T:815100976;N:226466	75	0		697204107	721945575	689048693	815100976	226466	SRX8472266	SRS6772867	SRA1083220	GEO	Center for Medical Genetics, Ghent University	1	0.94964		0.05377		0.71904		0.4902		76		B		usable mapping rate	illumina	nextseq	unknown	cdna_unspecified	trueseq	bulk	unknown	unknown	Belgium	2020-06-04	Undetermined	Undetermined	Thymus	Hematopoietic System
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
68889	68889	SRR18218067	SRX14364507	SRS12177802	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.			Thy rag2 RFP 6	strain:Tu/AB\|age:not collected\|sex:not collected\|tissue:thymus\|birth date: \|death date:02 07 2019\|genotype:rag2:RFP\|biological replicate:Thy rag2 RFP biological replicate 4\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio thymus Tu/AB	Thy rag2 RFP 6	Thy rag2 RFP 6	Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416		FCHT5GHDSXX_L1_HKRDZEBmfpEAAPRABPEI-P86H2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAPRABPEI-P86H2_2.fq.gz	fastq fastq	18061636200.0	60205454.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAPRABPEI P86H2 1.fq.gz	0:150 1:150	A:4749806271;C:4292116510;G:4365562558;T:4654124713;N:26148	150	150		4749806271	4292116510	4365562558	4654124713	26148	SRX14364507	SRS12177802	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.9283	0.92884	0.11636	0.1154	0.77642	0.77697	0.48938	0.49117	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Thymus	Hematopoietic System
68890	68890	SRR18218069	SRX14364506	SRS12177801	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.			Thy rag2 RFP 5	strain:Tu/AB\|age:not collected\|sex:not collected\|tissue:thymus\|birth date: \|death date:02 07 2019\|genotype:rag2:RFP\|biological replicate:Thy rag2 RFP biological replicate 3\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio thymus Tu/AB	Thy rag2 RFP 5	Thy rag2 RFP 5	Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416		FCHT5GHDSXX_L1_HKRDZEBmfpEAAORAAPEI-P74G2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAORAAPEI-P74G2_2.fq.gz	fastq fastq	16916167800.0	56387226.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAORAAPEI P74G2 1.fq.gz	0:150 1:150	A:4469149097;C:4004191756;G:4070955203;T:4371847041;N:24703	150	150		4469149097	4004191756	4070955203	4371847041	24703	SRX14364506	SRS12177801	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.92644	0.92786	0.13071	0.13011	0.77833	0.77792	0.47942	0.4816	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Thymus	Hematopoietic System
68891	68891	SRR18218070	SRX14364505	SRS12177800	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.			Thy rag2 RFP 4	strain:Tu/AB\|age:not collected\|sex:not collected\|tissue:thymus\|birth date: \|death date:02 07 2019\|genotype:rag2:RFP\|biological replicate:Thy rag2 RFP biological replicate 2\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio thymus Tu/AB	Thy rag2 RFP 4	Thy rag2 RFP 4	Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416		FCHT5GHDSXX_L1_HKRDZEBmfpEAANRABPEI-P62F2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAANRABPEI-P62F2_2.fq.gz	fastq fastq	17996947500.0	59989825.0	FCHT5GHDSXX L1 HKRDZEBmfpEAANRABPEI P62F2 1.fq.gz	0:150 1:150	A:4882125302;C:4136332786;G:4194970590;T:4783492952;N:25870	150	150		4882125302	4136332786	4194970590	4783492952	25870	SRX14364505	SRS12177800	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.86095	0.86165	0.25113	0.2504	0.80204	0.80188	0.48309	0.48627	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Thymus	Hematopoietic System
68892	68892	SRR18218071	SRX14364504	SRS12177799	SRP362416	PRJNA812715	Mutant IL7R collaborates with MYC to induce T cell Acute Lymphoblastic Leukemia	PRJNA812715	Other	T cell acute lymphoblastic leukemia T ALL is an aggressive pediatric cancer. Amongst the wide array of driver mutations 10% of T ALL patients display gain of function mutations in the IL 7 receptor alpha chain IL 7Ralpha encoded by IL7R which occur in different molecular subtypes of this disease. However it is still unclear whether IL 7R mutational activation is sufficient to transform T cell precursors. Also which genes cooperate with IL7R to drive leukemogenesis remain poorly defined. Here we demonstrate that mutant IL7R alone is capable of inducing T ALL with long latency in stable transgenic zebrafish and transformation is associated with MYC transcriptional activation. Additionally we find that mutant IL7R collaborates with Myc to induce early onset T ALL in transgenic zebrafish. T ALLs co expressing mutant IL7R and Myc show activation of STAT5 and AKT pathways harbor reduced numbers of apoptotic cells and remake tumors in transplanted zebrafish faster than T ALLs expressing Myc alone. Moreover limiting dilution cell transplantation experiments reveal that activated IL 7R signaling increases the overall frequency of leukemia propagating cells. Our work highlights a synergy between mutant IL7R and Myc in inducing T ALL and demonstrates that mutant IL7R enriches for leukemia propagating potential.			Thy rag2 RFP 3	strain:Tu/AB\|age:not collected\|sex:not collected\|tissue:thymus\|birth date: \|death date:02 07 2019\|genotype:rag2:RFP\|biological replicate:Thy rag2 RFP biological replicate 1\|BioSampleModel:Model organism or animal								RNA seq of Danio rerio thymus Tu/AB	Thy rag2 RFP 3	Thy rag2 RFP 3	Tu/AB WT zebrafish were sacrificed to harvest the thymus visible through RFP staining for further analysis. The RNA was extracted from sorted thymic cells using the RNeasy Mini Kit according to the manufacturers instructions Qiagen. mRNA was enriched using magnetic beads with Oligo dT fragmented and converted to cDNA size selected and PCR amplified generating paired end 100 bp sequences using a Illumina NovaSeq 6000.			RNA-Seq	TRANSCRIPTOMIC	PolyA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP362416		FCHT5GHDSXX_L1_HKRDZEBmfpEAAMRABPEI-P50E2_1.fq.gz FCHT5GHDSXX_L1_HKRDZEBmfpEAAMRABPEI-P50E2_2.fq.gz	fastq fastq	18041602200.0	60138674.0	FCHT5GHDSXX L1 HKRDZEBmfpEAAMRABPEI P50E2 1.fq.gz	0:150 1:150	A:4726391295;C:4303349397;G:4380843440;T:4630991494;N:26574	150	150		4726391295	4303349397	4380843440	4630991494	26574	SRX14364504	SRS12177799	SRA1380603	Instituto de Medicina Molecular Joao Lobo Antunes\|JBarata lab	Instituto de Medicina Molecular Joao Lobo Antunes	2	0.93138	0.9316	0.11291	0.11196	0.78143	0.78261	0.4799	0.47958	150	150	B	B	biological fallback assumption	illumina	novaseq_era	unknown	poly_a	unknown	bulk	unknown	unknown	Portugal	2022-03-04	Undetermined	Undetermined	Thymus	Hematopoietic System
76641	76641	SRR25247899	SRX20994109	SRS18268516	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T4 Sample 53	GSM7595974	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T4 Sample 53	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595974	GSM7595974: Thymus lckmCherry cd79aGFP Population T4 Sample 53; Danio rerio; RNA Seq	GSM7595974 r1	GSM7595974	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	53_S65_R2_001.fastq.gz 53_S65_R1_001.fastq.gz	fastq fastq	10257924978.0	33966639.0	GSM7595974 r1	0:151 1:151	A:3041876002;C:1856778277;G:2077467609;T:3281762421;N:40669	151	151		3041876002	1856778277	2077467609	3281762421	40669	SRX20994109	SRS18268516	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.74686	0.55687	0.09361	0.09952	0.88538	0.94302	0.6544	0.6924	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76642	76642	SRR25247900	SRX20994108	SRS18268515	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T4 Sample 52	GSM7595973	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T4 Sample 52	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595973	GSM7595973: Thymus lckmCherry cd79aGFP Population T4 Sample 52; Danio rerio; RNA Seq	GSM7595973 r1	GSM7595973	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	52_S64_R1_001.fastq.gz 52_S64_R2_001.fastq.gz	fastq fastq	10369663770.0	34336635.0	GSM7595973 r1	0:151 1:151	A:3082270824;C:1842032766;G:2098848870;T:3346470075;N:41235	151	151		3082270824	1842032766	2098848870	3346470075	41235	SRX20994108	SRS18268515	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.7463	0.55849	0.12388	0.14088	0.88028	0.94369	0.6854	0.70968	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76643	76643	SRR25247901	SRX20994107	SRS18268513	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T4 Sample 51	GSM7595972	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T4 Sample 51	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595972	GSM7595972: Thymus lckmCherry cd79aGFP Population T4 Sample 51; Danio rerio; RNA Seq	GSM7595972 r1	GSM7595972	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	51_S63_R2_001.fastq.gz 51_S63_R1_001.fastq.gz	fastq fastq	10986483972.0	36379086.0	GSM7595972 r1	0:151 1:151	A:3203989538;C:2032991258;G:2291606935;T:3457852653;N:43588	151	151		3203989538	2032991258	2291606935	3457852653	43588	SRX20994107	SRS18268513	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.75607	0.57028	0.09825	0.09786	0.87992	0.93795	0.66505	0.68991	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76644	76644	SRR25247905	SRX20994106	SRS18268514	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T2 Sample 50	GSM7595971	source name:Thymus\|tissue:Thymus\|cell type:T Stage IV\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T2 Sample 50	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage IV\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595971	GSM7595971: Thymus lckmCherry cd79aGFP Population T2 Sample 50; Danio rerio; RNA Seq	GSM7595971 r1	GSM7595971	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	50_S62_R1_001.fastq.gz 50_S62_R2_001.fastq.gz	fastq fastq	11149582998.0	36919149.0	GSM7595971 r1	0:151 1:151	A:3234571276;C:2073976116;G:2356352649;T:3484638408;N:44549	151	151		3234571276	2073976116	2356352649	3484638408	44549	SRX20994106	SRS18268514	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.7664	0.58289	0.1324	0.11697	0.89181	0.94119	0.60945	0.65676	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76645	76645	SRR25247902	SRX20994105	SRS18268512	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T2 Sample 49	GSM7595970	source name:Thymus\|tissue:Thymus\|cell type:T Stage IV\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T2 Sample 49	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage IV\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595970	GSM7595970: Thymus lckmCherry cd79aGFP Population T2 Sample 49; Danio rerio; RNA Seq	GSM7595970 r1	GSM7595970	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	49_S61_R1_001.fastq.gz 49_S61_R2_001.fastq.gz	fastq fastq	9322695908.0	30869854.0	GSM7595970 r1	0:151 1:151	A:2726922200;C:1719173931;G:1967587692;T:2908975055;N:37030	151	151		2726922200	1719173931	1967587692	2908975055	37030	SRX20994105	SRS18268512	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.7069	0.50745	0.13643	0.11444	0.88562	0.93415	0.61812	0.62999	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76646	76646	SRR25247903	SRX20994104	SRS18268510	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T2 Sample 48	GSM7595969	source name:Thymus\|tissue:Thymus\|cell type:T Stage IV\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T2 Sample 48	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage IV\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595969	GSM7595969: Thymus lckmCherry cd79aGFP Population T2 Sample 48; Danio rerio; RNA Seq	GSM7595969 r1	GSM7595969	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	48_S60_R1_001.fastq.gz 48_S60_R2_001.fastq.gz	fastq fastq	7830804432.0	25929816.0	GSM7595969 r1	0:151 1:151	A:2320164600;C:1418924520;G:1593915842;T:2497768242;N:31228	151	151		2320164600	1418924520	1593915842	2497768242	31228	SRX20994104	SRS18268510	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.74989	0.56664	0.13383	0.11897	0.86947	0.92626	0.63359	0.63884	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76647	76647	SRR25247904	SRX20994103	SRS18268511	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T1 Sample 47	GSM7595968	source name:Thymus\|tissue:Thymus\|cell type:T State III\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T1 Sample 47	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T State III\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595968	GSM7595968: Thymus lckmCherry cd79aGFP Population T1 Sample 47; Danio rerio; RNA Seq	GSM7595968 r1	GSM7595968	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	47_S59_R1_001.fastq.gz 47_S59_R2_001.fastq.gz	fastq fastq	8746939552.0	28963376.0	GSM7595968 r1	0:151 1:151	A:2581719668;C:1603400764;G:1776556616;T:2785228356;N:34148	151	151		2581719668	1603400764	1776556616	2785228356	34148	SRX20994103	SRS18268511	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.74197	0.56047	0.10187	0.099	0.88481	0.93701	0.67376	0.69505	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76648	76648	SRR25247906	SRX20994102	SRS18268509	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T1 Sample 46	GSM7595967	source name:Thymus\|tissue:Thymus\|cell type:T State III\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T1 Sample 46	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T State III\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595967	GSM7595967: Thymus lckmCherry cd79aGFP Population T1 Sample 46; Danio rerio; RNA Seq	GSM7595967 r1	GSM7595967	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	46_S58_R2_001.fastq.gz 46_S58_R1_001.fastq.gz	fastq fastq	11602233886.0	38417993.0	GSM7595967 r1	0:151 1:151	A:3413897763;C:2146046716;G:2373195191;T:3669047894;N:46322	151	151		3413897763	2146046716	2373195191	3669047894	46322	SRX20994102	SRS18268509	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.72323	0.53899	0.12972	0.13114	0.88458	0.93959	0.69874	0.72809	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76649	76649	SRR25247907	SRX20994101	SRS18268508	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79aGFP Population T1 Sample 45	GSM7595966	source name:Thymus\|tissue:Thymus\|cell type:T State III\|genotype:lckmCherry cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79aGFP Population T1 Sample 45	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T State III\|genotype:lckmCherry cd79aGFP\|treatment:NA	GSM7595966	GSM7595966: Thymus lckmCherry cd79aGFP Population T1 Sample 45; Danio rerio; RNA Seq	GSM7595966 r1	GSM7595966	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	45_S57_R1_001.fastq.gz 45_S57_R2_001.fastq.gz	fastq fastq	8407299480.0	27838740.0	GSM7595966 r1	0:151 1:151	A:2458010874;C:1568377940;G:1764963889;T:2615913460;N:33317	151	151		2458010874	1568377940	1764963889	2615913460	33317	SRX20994101	SRS18268508	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.73863	0.56362	0.11999	0.10773	0.89501	0.94418	0.66398	0.67575	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76657	76657	SRR25247915	SRX20994093	SRS18268500	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T4 Sample 35	GSM7595958	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T4 Sample 35	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595958	GSM7595958: Thymus rag2RFP cd79aGFP Population T4 Sample 35; Danio rerio; RNA Seq	GSM7595958 r1	GSM7595958	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	35_S47_R2_001.fastq.gz 35_S47_R1_001.fastq.gz	fastq fastq	7950117082.0	26324891.0	GSM7595958 r1	0:151 1:151	A:2332817459;C:1484005026;G:1661277987;T:2471985200;N:31410	151	151		2332817459	1484005026	1661277987	2471985200	31410	SRX20994093	SRS18268500	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.70931	0.52058	0.10349	0.10014	0.90481	0.94809	0.71184	0.74817	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76658	76658	SRR25247916	SRX20994092	SRS18268498	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T4 Sample 34	GSM7595957	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T4 Sample 34	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595957	GSM7595957: Thymus rag2RFP cd79aGFP Population T4 Sample 34; Danio rerio; RNA Seq	GSM7595957 r1	GSM7595957	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	34_S46_R2_001.fastq.gz 34_S46_R1_001.fastq.gz	fastq fastq	7966171704.0	26378052.0	GSM7595957 r1	0:151 1:151	A:2329420986;C:1477961313;G:1664561539;T:2494196526;N:31340	151	151		2329420986	1477961313	1664561539	2494196526	31340	SRX20994092	SRS18268498	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.71845	0.50928	0.0957	0.09999	0.90384	0.95312	0.74113	0.75866	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76659	76659	SRR25247917	SRX20994091	SRS18268499	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T4 Sample 33	GSM7595956	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T4 Sample 33	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595956	GSM7595956: Thymus rag2RFP cd79aGFP Population T4 Sample 33; Danio rerio; RNA Seq	GSM7595956 r1	GSM7595956	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	33_S45_R1_001.fastq.gz 33_S45_R2_001.fastq.gz	fastq fastq	8314572796.0	27531698.0	GSM7595956 r1	0:151 1:151	A:2452587590;C:1535172003;G:1743148608;T:2583631469;N:33126	151	151		2452587590	1535172003	1743148608	2583631469	33126	SRX20994091	SRS18268499	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.62571	0.44431	0.112	0.09476	0.91405	0.9487	0.71132	0.74047	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76660	76660	SRR25247918	SRX20994090	SRS18268497	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T3 Sample 32	GSM7595955	source name:Thymus\|tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T3 Sample 32	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595955	GSM7595955: Thymus rag2RFP cd79aGFP Population T3 Sample 32; Danio rerio; RNA Seq	GSM7595955 r1	GSM7595955	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	32_S44_R1_001.fastq.gz 32_S44_R2_001.fastq.gz	fastq fastq	10270435026.0	34008063.0	GSM7595955 r1	0:151 1:151	A:3072285253;C:1829169076;G:2174184861;T:3194754612;N:41224	151	151		3072285253	1829169076	2174184861	3194754612	41224	SRX20994090	SRS18268497	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.68076	0.52889	0.18916	0.16273	0.87144	0.9303	0.5977	0.60526	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76661	76661	SRR25247919	SRX20994089	SRS18268496	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T3 Sample 31	GSM7595954	source name:Thymus\|tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T3 Sample 31	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595954	GSM7595954: Thymus rag2RFP cd79aGFP Population T3 Sample 31; Danio rerio; RNA Seq	GSM7595954 r1	GSM7595954	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	31_S43_R1_001.fastq.gz 31_S43_R2_001.fastq.gz	fastq fastq	8576339752.0	28398476.0	GSM7595954 r1	0:151 1:151	A:2575134911;C:1518644685;G:1746645548;T:2735880553;N:34055	151	151		2575134911	1518644685	1746645548	2735880553	34055	SRX20994089	SRS18268496	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.75636	0.6119	0.26758	0.23065	0.86801	0.92807	0.60587	0.61722	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76662	76662	SRR25247920	SRX20994088	SRS18268495	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T3 Sample 30	GSM7595953	source name:Thymus\|tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T3 Sample 30	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595953	GSM7595953: Thymus rag2RFP cd79aGFP Population T3 Sample 30; Danio rerio; RNA Seq	GSM7595953 r1	GSM7595953	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	30_S42_R1_001.fastq.gz 30_S42_R2_001.fastq.gz	fastq fastq	10957925040.0	36284520.0	GSM7595953 r1	0:151 1:151	A:3260030485;C:1943181567;G:2272932117;T:3481737311;N:43560	151	151		3260030485	1943181567	2272932117	3481737311	43560	SRX20994088	SRS18268495	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.75404	0.62746	0.32062	0.27288	0.87588	0.93123	0.63498	0.66153	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76663	76663	SRR25247921	SRX20994087	SRS18268494	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T2 Sample 29	GSM7595952	source name:Thymus\|tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T2 Sample 29	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595952	GSM7595952: Thymus rag2RFP cd79aGFP Population T2 Sample 29; Danio rerio; RNA Seq	GSM7595952 r1	GSM7595952	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	29_S41_R1_001.fastq.gz 29_S41_R2_001.fastq.gz	fastq fastq	10621822898.0	35171599.0	GSM7595952 r1	0:151 1:151	A:3115594114;C:1963383687;G:2242332489;T:3300470381;N:42227	151	151		3115594114	1963383687	2242332489	3300470381	42227	SRX20994087	SRS18268494	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.71819	0.58604	0.20876	0.18902	0.88554	0.93482	0.62188	0.63983	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76664	76664	SRR25247922	SRX20994086	SRS18268492	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T2 Sample 28	GSM7595951	source name:Thymus\|tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T2 Sample 28	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595951	GSM7595951: Thymus rag2RFP cd79aGFP Population T2 Sample 28; Danio rerio; RNA Seq	GSM7595951 r1	GSM7595951	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	28_S40_R2_001.fastq.gz 28_S40_R1_001.fastq.gz	fastq fastq	8727889694.0	28900297.0	GSM7595951 r1	0:151 1:151	A:2547391532;C:1595452476;G:1834559014;T:2750452130;N:34542	151	151		2547391532	1595452476	1834559014	2750452130	34542	SRX20994086	SRS18268492	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.74557	0.58372	0.26466	0.23691	0.88623	0.93344	0.65795	0.66615	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76665	76665	SRR25247923	SRX20994085	SRS18268493	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T2 Sample 27	GSM7595950	source name:Thymus\|tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T2 Sample 27	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage I\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595950	GSM7595950: Thymus rag2RFP cd79aGFP Population T2 Sample 27; Danio rerio; RNA Seq	GSM7595950 r1	GSM7595950	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	27_S39_R1_001.fastq.gz 27_S39_R2_001.fastq.gz	fastq fastq	9477428024.0	31382212.0	GSM7595950 r1	0:151 1:151	A:2824829196;C:1691241542;G:1990496690;T:2970823258;N:37338	151	151		2824829196	1691241542	1990496690	2970823258	37338	SRX20994085	SRS18268493	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.72602	0.56304	0.29776	0.23812	0.89021	0.93888	0.62393	0.62679	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76666	76666	SRR25247924	SRX20994084	SRS18268491	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T1 Sample 26	GSM7595949	source name:Thymus\|tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T1 Sample 26	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595949	GSM7595949: Thymus rag2RFP cd79aGFP Population T1 Sample 26; Danio rerio; RNA Seq	GSM7595949 r1	GSM7595949	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	26_S38_R1_001.fastq.gz 26_S38_R2_001.fastq.gz	fastq fastq	9995699586.0	33098343.0	GSM7595949 r1	0:151 1:151	A:2895036004;C:1859983984;G:2130779126;T:3109860999;N:39473	151	151		2895036004	1859983984	2130779126	3109860999	39473	SRX20994084	SRS18268491	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.71196	0.53328	0.13463	0.12387	0.8761	0.93111	0.60964	0.62685	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76667	76667	SRR25247928	SRX20994083	SRS18268490	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T1 Sample 25	GSM7595948	source name:Thymus\|tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T1 Sample 25	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595948	GSM7595948: Thymus rag2RFP cd79aGFP Population T1 Sample 25; Danio rerio; RNA Seq	GSM7595948 r1	GSM7595948	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	25_S37_R1_001.fastq.gz 25_S37_R2_001.fastq.gz	fastq fastq	8574030660.0	28390830.0	GSM7595948 r1	0:151 1:151	A:2488813358;C:1589002672;G:1801315676;T:2694865137;N:33817	151	151		2488813358	1589002672	1801315676	2694865137	33817	SRX20994083	SRS18268490	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.76128	0.60104	0.2036	0.19091	0.86896	0.92368	0.63325	0.64052	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76668	76668	SRR25247925	SRX20994082	SRS18268489	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79aGFP Population T1 Sample 24	GSM7595947	source name:Thymus\|tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79aGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79aGFP Population T1 Sample 24	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79aGFP\|treatment:NA	GSM7595947	GSM7595947: Thymus rag2RFP cd79aGFP Population T1 Sample 24; Danio rerio; RNA Seq	GSM7595947 r1	GSM7595947	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	24_S36_R1_001.fastq.gz 24_S36_R2_001.fastq.gz	fastq fastq	10245271178.0	33924739.0	GSM7595947 r1	0:151 1:151	A:3027828661;C:1881531100;G:2109776614;T:3226094586;N:40217	151	151		3027828661	1881531100	2109776614	3226094586	40217	SRX20994082	SRS18268489	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.74318	0.57154	0.19699	0.18085	0.87008	0.92683	0.60011	0.60753	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76672	76672	SRR25247930	SRX20994078	SRS18268485	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79bGFP Population T4 Sample 20	GSM7595943	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79bGFP Population T4 Sample 20	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79bGFP\|treatment:NA	GSM7595943	GSM7595943: Thymus lckmCherry cd79bGFP Population T4 Sample 20; Danio rerio; RNA Seq	GSM7595943 r1	GSM7595943	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	20_S32_R1_001.fastq.gz 20_S32_R2_001.fastq.gz	fastq fastq	7357232796.0	24361698.0	GSM7595943 r1	0:151 1:151	A:2156745950;C:1361406858;G:1502397402;T:2336653301;N:29285	151	151		2156745950	1361406858	1502397402	2336653301	29285	SRX20994078	SRS18268485	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.76466	0.59032	0.13633	0.14407	0.89457	0.94126	0.70613	0.73475	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76673	76673	SRR25247931	SRX20994077	SRS18268484	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus lckmCherry cd79bGFP Population T4 Sample 19	GSM7595942	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus lckmCherry cd79bGFP Population T4 Sample 19	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:lckmCherry cd79bGFP\|treatment:NA	GSM7595942	GSM7595942: Thymus lckmCherry cd79bGFP Population T4 Sample 19; Danio rerio; RNA Seq	GSM7595942 r1	GSM7595942	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	19_S31_R1_001.fastq.gz 19_S31_R2_001.fastq.gz	fastq fastq	7835569992.0	25945596.0	GSM7595942 r1	0:151 1:151	A:2285864595;C:1463161267;G:1656089782;T:2430423318;N:31030	151	151		2285864595	1463161267	1656089782	2430423318	31030	SRX20994077	SRS18268484	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.68242	0.50364	0.13384	0.12452	0.91192	0.94803	0.71089	0.72547	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76685	76685	SRR25247942	SRX20994065	SRS18268472	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79bGFP Population T4 Sample 6	GSM7595930	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79bGFP Population T4 Sample 6	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79bGFP\|treatment:NA	GSM7595930	GSM7595930: Thymus rag2RFP cd79bGFP Population T4 Sample 6; Danio rerio; RNA Seq	GSM7595930 r1	GSM7595930	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	6_S18_R1_001.fastq.gz 6_S18_R2_001.fastq.gz	fastq fastq	8390217454.0	27782177.0	GSM7595930 r1	0:151 1:151	A:2421221360;C:1601232886;G:1787641759;T:2580087936;N:33513	151	151		2421221360	1601232886	1787641759	2580087936	33513	SRX20994065	SRS18268472	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.69069	0.52877	0.14308	0.13948	0.91693	0.94724	0.72517	0.38475	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76686	76686	SRR25247943	SRX20994064	SRS18268471	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79bGFP Population T4 Sample 5	GSM7595929	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79bGFP Population T4 Sample 5	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79bGFP\|treatment:NA	GSM7595929	GSM7595929: Thymus rag2RFP cd79bGFP Population T4 Sample 5; Danio rerio; RNA Seq	GSM7595929 r1	GSM7595929	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	5_S17_R1_001.fastq.gz 5_S17_R2_001.fastq.gz	fastq fastq	8158834114.0	27016007.0	GSM7595929 r1	0:151 1:151	A:2339327280;C:1558094669;G:1747369217;T:2514010546;N:32402	151	151		2339327280	1558094669	1747369217	2514010546	32402	SRX20994064	SRS18268471	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.65335	0.48523	0.15841	0.15278	0.92368	0.95177	0.6743	0.67965	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76687	76687	SRR25247945	SRX20994063	SRS18268470	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79bGFP Population T4 Sample 4	GSM7595928	source name:Thymus\|tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79bGFP Population T4 Sample 4	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:Thymic B\|genotype:rag2RFP cd79bGFP\|treatment:NA	GSM7595928	GSM7595928: Thymus rag2RFP cd79bGFP Population T4 Sample 4; Danio rerio; RNA Seq	GSM7595928 r1	GSM7595928	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	4_S16_R1_001.fastq.gz 4_S16_R2_001.fastq.gz	fastq fastq	8704163064.0	28821732.0	GSM7595928 r1	0:151 1:151	A:2466210983;C:1690333059;G:1912063529;T:2635521209;N:34284	151	151		2466210983	1690333059	1912063529	2635521209	34284	SRX20994063	SRS18268470	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.54845	0.35725	0.13255	0.1049	0.9445	0.96327	0.66031	0.66937	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76688	76688	SRR25247946	SRX20994062	SRS18268469	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79bGFP Population T1 Sample 3	GSM7595927	source name:Thymus\|tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79bGFP Population T1 Sample 3	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79bGFP\|treatment:NA	GSM7595927	GSM7595927: Thymus rag2RFP cd79bGFP Population T1 Sample 3; Danio rerio; RNA Seq	GSM7595927 r1	GSM7595927	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	3_S15_R1_001.fastq.gz 3_S15_R2_001.fastq.gz	fastq fastq	9629450294.0	31885597.0	GSM7595927 r1	0:151 1:151	A:2813374436;C:1804435410;G:2009975925;T:3001626142;N:38381	151	151		2813374436	1804435410	2009975925	3001626142	38381	SRX20994062	SRS18268469	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.6865	0.47098	0.18726	0.14724	0.88349	0.93563	0.63844	0.65717	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76689	76689	SRR25247947	SRX20994061	SRS18268468	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79bGFP Population T1 Sample 2	GSM7595926	source name:Thymus\|tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79bGFP Population T1 Sample 2	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79bGFP\|treatment:NA	GSM7595926	GSM7595926: Thymus rag2RFP cd79bGFP Population T1 Sample 2; Danio rerio; RNA Seq	GSM7595926 r1	GSM7595926	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	2_S14_R1_001.fastq.gz 2_S14_R2_001.fastq.gz	fastq fastq	9283788946.0	30741023.0	GSM7595926 r1	0:151 1:151	A:2741738440;C:1702138319;G:1938033936;T:2901841449;N:36802	151	151		2741738440	1702138319	1938033936	2901841449	36802	SRX20994061	SRS18268468	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.72627	0.59001	0.22607	0.20684	0.88556	0.93249	0.65227	0.66481	151	151	B	B	biological fallback assumption	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	Thymus	Hematopoietic System
76690	76690	SRR25247948	SRX20994060	SRS18268467	SRP448831	PRJNA994052	Dynamic Changes in Lymphocyte Populations Establish Zebrafish as a Thymic Involution Model	GSE237139	Transcriptome Analysis	The thymus is the site of T lymphocyte development and T cell education to recognize foreign but not self antigens. B cells also reside and develop in the thymus although their functions are less clear. During 'thymic involution ' a process of lymphoid atrophy and adipose replacement linked to sexual maturation thymic cells decline. However thymic B cells decrease far less than T cells such that B cells comprise 1% of neonatal thymocytes but up to 10% in maturity in humans. All jawed vertebrates possess a thymus and we and others have shown that zebrafish Danio rerio also have thymic B cells. Here we investigated the precise identities of zebrafish thymic T and B cells and how they change with involution. We assessed the timing and specific details of zebrafish thymic involution using multiple lymphocyte specific fluorophore labeled transgenic lines quantifying changes in thymic lymphocytes pre vs. post involution. Our results prove that as in humans zebrafish thymic B cells increase relative to T cells post involution. We also performed RNA sequencing RNA seq on D. rerio thymic and marrow lymphocytes of four novel double transgenic lines identifying distinct populations of immature T and B cells. Collectively this is the first comprehensive analysis of zebrafish thymic involution demonstrating its similarity to human involution and establishing the highly genetically manipulatable zebrafish model as a template for involution studies. Overall design: This experimental study aimed to investigate the gene expression profiles of lymphocytes in zebrafish using bulk RNA sequencing RNA seq analysis. Specifically four different double transgenic zebrafish lines were utilized each expressing specific fluorescent markers to label distinct cell populations. The double transgenic lines included rag2:RFP × cd79a:GFP rag2:RFP × cd79b:GFP cd79a:GFP × lck:mCherry and cd79b:GFP × lck:mCherry. These transgenic lines allowed for the identification and isolation of specific cell types for subsequent transcrip…	pubmed:38656392	Thymus rag2RFP cd79bGFP Population T1 Sample 1	GSM7595925	source name:Thymus\|tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79bGFP\|treatment:NA\|geo loc name:missing\|collection date:missing	Thymus rag2RFP cd79bGFP Population T1 Sample 1	Raw read quality was first assessed using FastQC v.0.11.8. BBDuk from the BBMap suite v.38.22 was used for adapter trimming per manufacturer recommendations. rRNA mapping reads were also filtered at this step. Read quality was assessed post trimming as well. Trimmed reads were mapped to the GRCz11 genome using STAR using default settings. Note that due to the nature of three prime tagged RNA sequencing the R2 files containg low quality reads that are not typically used during processing. Read counts per gene were generated with FeatureCounts from Rsubread v.2.12.2 using the D.rerio Ensembl transcriptome release v.92 with a min. alignment quality threshold of 10. DESeq2 v.1.38.3 was used for downstream processing library normalization and DE testing. Assembly: GRCz11 Supplementary files format and content: Tab delimited file containing raw gene counts for each Sample Supplementary files format and content: Tab delimited file containing normalized gene counts and variance stabilized gene counts separate files for each Sample	Thymus	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq 3’ mRNA Seq Library Prep Kit FWD following manufacturer's protocols.	For procedures zebrafish subjects were anesthetized with 0.02% tricaine methanesulfonate. Thymi and marrow samples were dissected and placed in 500 ul cell media RPMI + 1% FBS + 1% Pen/Strep. Single cell suspensions were prepped by dissociating thymic and marrow tissue 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.	tissue:Thymus\|cell type:T Stage II\|genotype:rag2RFP cd79bGFP\|treatment:NA	GSM7595925	GSM7595925: Thymus rag2RFP cd79bGFP Population T1 Sample 1; Danio rerio; RNA Seq	GSM7595925 r1	GSM7595925	1	Total RNA extraction was performed using Promega Reliprep RNA extraction kit per manufacturer's protocol. RNA QC was checked by Bioanalyzer prior to sequencing. The average amount of RNA used to prepare each library of 2.5 ug/sample. RNA libraries for sequencing were prepared using the QuantSeq three prime mRNA Seq Library Prep Kit FWD following manufacturer's protocols.		RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000	SRP448831	loader:fastq load.py	1_S13_R1_001.fastq.gz 1_S13_R2_001.fastq.gz	fastq fastq	9464822242.0	31340471.0	GSM7595925 r1	0:151 1:151	A:2638585573;C:1886184090;G:2274314822;T:2665699767;N:37990	151	151		2638585573	1886184090	2274314822	2665699767	37990	SRX20994060	SRS18268467	SRA1671790	Pediatrics, University of Oklahoma Health Sciences Center	Pediatrics, University of Oklahoma Health Sciences Center	2	0.59028	0.41513	0.22607	0.21014	0.89134	0.94298	0.64355	0.60145	151	151	B	B	mate2-mate1 similar by mapping diff	illumina	novaseq_era	3prime	cdna_unspecified	lexogen	bulk	bulk	bulk	United States	2023-07-12	Undetermined	Undetermined	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");;