metadata: run_metadata: 35 rows where technology = "bulk", tissue_curation = "Thymus" and tissue_curation

35 rows where technology = "bulk", 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.library_strategy	experiment.library_source	experiment.library_selection	experiment.library_layout	experiment.platform	experiment.instrument_model	experiment.study_ref	run.attributes	run.filename	run.semantic_name	run.total_bases	run.total_spots	run.alias	run.read_lengths	run.base_counts	run.r1_length	run.r2_length	run.Acount	run.Ccount	run.Gcount	run.Tcount	run.Ncount	run.experiment	run.pool_member	submission.accession	submission.srasource	submission.bioprojectsource	seqdetective.n_mates	seqdetective.mapping_rate.mate1	seqdetective.mapping_rate.mate2	seqdetective.nofeature_rate.mate1	seqdetective.nofeature_rate.mate2	seqdetective.sparsity.mate1	seqdetective.sparsity.mate2	seqdetective.pos_strand_rate.mate1	seqdetective.pos_strand_rate.mate2	seqdetective.readlen.mate1	seqdetective.readlen.mate2	seqdetective.judgement.mate1	seqdetective.judgement.mate2	seqdetective.judgement.reason	platform_family	instrument_generation	read_bias	selection_class	prep_kit	sc_or_bulk	tech_class	technology	submission.bioprojectsource.country	earliest_date	devstage_curation	devstage_curation_coarse	tissue_curation	tissue_curation_coarse
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
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

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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");;