{"database": "metadata", "table": "run_metadata", "is_view": false, "human_description_en": "where experiment.library_selection = \"cDNA\", experiment.library_source = \"TRANSCRIPTOMIC SINGLE CELL\" and technology = \"marsseq\"", "rows": [[36249, "SRR34017907", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L001_R1_001.fastq.gz TORCQ_2023_S0_L001_R2_001.fastq.gz", "fastq fastq", 9123251137.0, 118483781.0, "GSM9052756 r1", "0:57 1:20", "A:2003237489;C:1403878506;G:1540717140;T:1805684398;N:2369733604", 57, 20, null, null, 2003237489, 1403878506, 1540717140, 1805684398, 2369733604, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36250, "SRR34017908", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L002_R1_001.fastq.gz TORCQ_2023_S0_L002_R2_001.fastq.gz", "fastq fastq", 9249291128.0, 120120664.0, "GSM9052756 r2", "0:57 1:20", "A:2023532922;C:1427491871;G:1568162363;T:1827659977;N:2402443995", 57, 20, null, null, 2023532922, 1427491871, 1568162363, 1827659977, 2402443995, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36251, "SRR34017909", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L003_R1_001.fastq.gz TORCQ_2023_S0_L003_R2_001.fastq.gz", "fastq fastq", 9438695574.0, 122580462.0, "GSM9052756 r3", "0:57 1:20", "A:2061159862;C:1455510691;G:1599304279;T:1871072315;N:2451648427", 57, 20, null, null, 2061159862, 1455510691, 1599304279, 1871072315, 2451648427, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36252, "SRR34017910", "SRX29213468", "SRS25409913", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells session 2", "GSM9052756", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells session 2", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052756", "GSM9052756: 5 dpf hematopoietic zebrafish cells session 2; Danio rerio; RNA Seq", "GSM9052756 r1", "GSM9052756", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2023_S0_L004_R1_001.fastq.gz TORCQ_2023_S0_L004_R2_001.fastq.gz", "fastq fastq", 9409346870.0, 122199310.0, "GSM9052756 r4", "0:57 1:20", "A:2048111796;C:1451606983;G:1595602008;T:1870010070;N:2444016013", 57, 20, null, null, 2048111796, 1451606983, 1595602008, 1870010070, 2444016013, "SRX29213468", "SRS25409913", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, null, null, null, "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36253, "SRR34017905", "SRX29213467", "SRS25409912", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells session 1", "GSM9052755", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells session 1", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052755", "GSM9052755: 5 dpf hematopoietic zebrafish cells session 1; Danio rerio; RNA Seq", "GSM9052755 r1", "GSM9052755", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2021_S0_R1_001.fastq.gz TORCQ_2021_S0_R2_001.fastq.gz", "fastq fastq", 45817068160.0, 602856160.0, "GSM9052755 r1", "0:56 1:20", "A:12324583812;C:8979463244;G:11486707902;T:13012728622;N:13584580", 56, 20, null, null, 12324583812, 8979463244, 11486707902, 13012728622, 13584580, "SRX29213467", "SRS25409912", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [36254, "SRR34017906", "SRX29213467", "SRS25409912", "SRP592701", "PRJNA1278741", "Single cell and in situ spatial analyses reveal the diversity of newly born hematopoietic stem cells and of their niches [scRNA Seq]", "GSE300039", "Transcriptome Analysis", "Hematopoietic stem cells HSCs and more committed progenitors collectively referred to as HSPCs emerge from vessels during development via Endothelial to Hematopoietic Transition EHT. Recently using the zebrafish embryo we showed that two EHT cell types emerge from the dorsal aorta raising the question of their subsequent fate. To address this issue we established a complex pipeline based on single cell photoconversion and transgenic lines to characterize the abilities of EHT cell progenies to conquer hematopoietic organs and to obtain their transcriptomic profiles. We show that the two EHT cell types lead to partly differentially fated cells with significant differences in thymus colonization and T lymphoid lineage commitment. In addition we investigated implantation of HSPCs in niches with the support of HSPC signatures gata2b and cd34/podocalyxin retrieved from our single cell datasets. This revealed at unprecedented resolution the homing of HSPCs in niches of entire early larvae including the pronephros the sub aortic and caudal regions as well as the area contacting the supra intestinal artery. Our work provides new insights on fundamental aspects of HSPC fate acquisition from their emergence to their homing in specific niches. Overall design: Single cell transcriptomics analysis of newly born hematopoietic stem and progenitor cells. This dataset comprises progenies of cells photoconverted at 2dpf and sorted by FACS at 5dpf using the Tgkdrl:nls kikume transgenic line as well as sorted FACS hematopoietic cells from transgenic reporter lines namely from the Tgrunx1+23:eGFP and the outcross of the Tgcd41:eGFP and Tggata2b:RFP lines. Larvae were collected post dissection separating the rostral anterior and posterior region along a transversal section at the posterior limit of the elongated yolk and at the posterior limit of the swim bladder dissociation and sorting using a BD FACS AriaIII cell sorter. Progenies of photoconverted cells comprise progenies of single EHT photoconversion either EHT pol+ or EHT pol or whole hemogenic endothelium photoconversion. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019.", null, "pubmed:40501392", null, "5 dpf hematopoietic zebrafish cells session 1", "GSM9052755", null, "tissue:sorted hematopoietic cells|cell type:sorted hematopoietic cells|geo loc name:missing|collection date:missing", "5 dpf hematopoietic zebrafish cells session 1", "Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019 Assembly: zebrafish genome Lawson lab version 4.3.2. Supplementary files format and content: Tab separated value files", "sorted hematopoietic cells", null, "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "cell type:sorted hematopoietic cells", "GSM9052755", "GSM9052755: 5 dpf hematopoietic zebrafish cells session 1; Danio rerio; RNA Seq", "GSM9052755 r1", "GSM9052755", "1", "Single cell suspension for FACS sorting was prepared using an optimized protocol adapted from multiple sources Bresciani et al. 2018; Manoli and Driever 2012; Samsa et al. 2016. All steps were performed with cooled solutions 4\u00b0C and samples were kept on ice throughout the processing to preserve the viability of cells. Briefly 5dpf larvae were anesthetized using balneation in embryo medium supplemented with tricaine at a final concentration of 640 \u00b5g/ml. Larvae between 20 and 30 whole larvae or 60 80 dissected segments per tube were washed twice in PBS before centrifugation 300 x g for 1 min @4\u00b0C and the supernatant was discarded. Larvae were incubated in 1 ml TrypLE medium Life Technologies Cat#: 12605 010 for 10 min on ice with gentle pipetting every 3 mins first with a P1000 pipette and subsequently with a P200 pipette. Samples were then centrifugated for 7 min at 300g before the TrypLE was removed and the cells were resuspended in 500 \u00b5l FACSmax medium Genlantis Cat#: T200100. Ultimately samples were passed through a 40 \u03bcm cell strainer moistened with FACSmax buffer onto a 35 mm cell culture dish using a syringe plunger. The cell strainer and the dish were washed with 300 \u00b5l of FACS max and the flow through was transferred to a FACS tube and kept on ice until sorting within the hour. Cell sorting was performed on a BD FACS AriaIII cell sorter. For all samples gating was done on SSC A vs. FSC A to collect cells then on FSC W vs. FSC A to keep only singlets and on APC A to remove dead cells marked by Draq7 Thermofisher Cat#: D15106. Cells were sorted in 384 wells plates 28 plates in 2 independent sessions of 14 plates each and the transcriptomic library was prepared according to the MARS seq protocol 2.0 Keren Shaul et al. 2019. Libraries were then sequenced using the NextSeq 500/550 High Output Kit v2 75 cycles Illumina. Raw reads were converted to fastq files using bcl2fastq package 2.20.0. Reads were demultiplexed and mapped to the Lawson Lab curated genome [Lawson et al. 2020 v4.3.2] using the MARS seq pipeline scripts Keren Shaul et al. 2019. Briefly a first step of reverse transcription RT SuperScript III Thermo Fisher Cat#: 18080085 was conducted to barcode the transcripts with unique cell and UMI barcodes. post RT primers were removed with an exonuclease ExoI NEB Cat#: M0293L and the barcoded cDNAs for each single cell in a half plate were pooled together for the next steps. cDNA was converted to dsDNA Second Strand synthesis kit NEB Cat#: E611L and linearly amplified by in vitro transcription HiScribe T7 High Yield RNA Synthesis Kit NEB Cat#: E2040S. The dsDNA was degraded TURBO DNase Fisher Cat#: 10646175 and the amplified RNA fragmented for sequencing Fisher Cat#: 10426914. A pool barcode with Illumina adapters for each half plate was added by RNA DNA ligation before a second RT step AffinityScript Multiple Temperature reverse transcriptase Agilent Cat#: 600109. Final amplification by PCR was performed KAPA HiFi HotStart ReadyMix Roche Diagnostics Cat#: 7958935001. The resulting libraries were controlled by qPCR amplification of housekeeping genes ef1a and \u00df actin DNA quality control using a TapeStation Agilent and DNA concentration using the Qubit dsDNA high sensitivity assay.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "NextSeq 500", null, "SRP592701", null, null, "TORCQ_2021_S0_R1_001_small.fastq.gz TORCQ_2021_S0_R2_001_small.fastq.gz", "fastq fastq", 190000.0, 2500.0, "GSM9052755 r2", "0:56 1:20", "A:50399;C:36081;G:47775;T:53618;N:2127", 56, 20, null, null, 50399, 36081, 47775, 53618, 2127, "SRX29213467", "SRS25409912", "SRA2151098", "Institut Pasteur", "Institut Pasteur", null, null, null, null, null, null, null, null, null, null, null, "B", "T", "sc-like readlen", "illumina", "nextseq", "unknown", "random_priming", "unknown", "sc", "single_cell_plate", "marsseq", null, "France", "2025-06-17", "Larval", "Larval", "Blood", "Hematopoietic System"], [69988, "SRR19217299", "SRX15281308", "SRS13012753", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9278", "GSM6153483", null, "source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing", "AB9278", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\" scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\" \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month", "GSM6153483", "GSM6153483: AB9278; Danio rerio; RNA Seq", "GSM6153483 r1", "GSM6153483", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9278_SB390_R1_01.fastq.gz AB9278_SB390_R2_01.fastq.gz", "fastq fastq", 1259447780.0, 11770540.0, "GSM6153483 r1", "0:92 1:15", "A:305608913;C:313550706;G:363197186;T:277079546;N:11429", 92, 15, null, null, 305608913, 313550706, 363197186, 277079546, 11429, "SRX15281308", "SRS13012753", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.94767, 0.0, 0.32091, 0.0, 0.89796, 1.0, 0.7545, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69989, "SRR19217300", "SRX15281307", "SRS13012752", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9277", "GSM6153482", null, "source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month|geo loc name:missing|collection date:missing", "AB9277", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\" scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\" \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:7 month", "GSM6153482", "GSM6153482: AB9277; Danio rerio; RNA Seq", "GSM6153482 r1", "GSM6153482", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9277_SB390_R1_01.fastq.gz AB9277_SB390_R2_01.fastq.gz", "fastq fastq", 1130776107.0, 10568001.0, "GSM6153482 r1", "0:92 1:15", "A:288600700;C:269726443;G:310844405;T:261594352;N:10207", 92, 15, null, null, 288600700, 269726443, 310844405, 261594352, 10207, "SRX15281307", "SRS13012752", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.94379, 0.0, 0.28638, 0.0, 0.86415, 1.0, 0.63321, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69990, "SRR19217301", "SRX15281306", "SRS13012751", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9280", "GSM6153481", null, "source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing", "AB9280", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\" scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\" \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month", "GSM6153481", "GSM6153481: AB9280; Danio rerio; RNA Seq", "GSM6153481 r1", "GSM6153481", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9280_SB390_R1_01.fastq.gz AB9280_SB390_R2_01.fastq.gz", "fastq fastq", 1172966528.0, 10962304.0, "GSM6153481 r1", "0:92 1:15", "A:311089180;C:274626206;G:310304031;T:276936052;N:11059", 92, 15, null, null, 311089180, 274626206, 310304031, 276936052, 11059, "SRX15281306", "SRS13012751", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.92936, 0.0, 0.23628, 0.0, 0.86147, 1.0, 0.74656, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69991, "SRR19217302", "SRX15281305", "SRS13012750", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB9279", "GSM6153480", null, "source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month|geo loc name:missing|collection date:missing", "AB9279", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\" scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\" \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:5 month", "GSM6153480", "GSM6153480: AB9279; Danio rerio; RNA Seq", "GSM6153480 r1", "GSM6153480", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, "loader:fastq load.py", "AB9279_SB390_R1_01.fastq.gz AB9279_SB390_R2_01.fastq.gz", "fastq fastq", 1383147163.0, 12926609.0, "GSM6153480 r1", "0:92 1:15", "A:364575971;C:320901229;G:367626618;T:330030659;N:12686", 92, 15, null, null, 364575971, 320901229, 367626618, 330030659, 12686, "SRX15281305", "SRS13012750", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.92462, 0.0, 0.26743, 0.0, 0.8493, 1.0, 0.74133, null, 92, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Adult", "Adult", "Pituitary Gland", "Endocrine System"], [69992, "SRR19217303", "SRX15281304", "SRS13012749", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB7418", "GSM6153479", null, "source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing", "AB7418", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\" scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\" \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf", "GSM6153479", "GSM6153479: AB7418; Danio rerio; RNA Seq", "GSM6153479 r1", "GSM6153479", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, null, "AB7418_SB350_S35_R1_001.fastq.gz AB7418_SB350_S35_R2_001.fastq.gz", "fastq fastq", 2468773944.0, 29390166.0, "GSM6153479 r1", "0:69 1:15", "A:764359919;C:520031317;G:592699381;T:591594655;N:88672", 69, 15, null, null, 764359919, 520031317, 592699381, 591594655, 88672, "SRX15281304", "SRS13012749", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.85786, 0.0, 0.15143, 0.0, 0.84885, 1.0, 0.67021, null, 69, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", "Juvenile", "Juvenile", "Pituitary Gland", "Endocrine System"], [69993, "SRR19217304", "SRX15281303", "SRS13012748", "SRP375342", "PRJNA838481", "Neural plate progenitors give rise to both anterior and posterior pituitary cells", "GSE203075", "Transcriptome Analysis", "The pituitary is the master neuroendocrine tissue which regulates body homeostasis. It consists of the adenohypophysis AH which harbors hormones producing cells and the neurohypophysis NH which relays the direct passage of hormones from the brain to the periphery. We previously characterized the mouse NH cell identities Chen Q et al. 2020. However the zebrafish NH cell types remained unknown owning to surgical inaccessible and limited amount of the tissue. Using Mars Seq single cell sequencing Jaitin et al. 2014 we characterized the cell types of the neurohypophyseal enriched population from the juvenile and adult zebrafish pituitaries which laid the foundation for further lineage and functional research in this study. Overall design: 3 pools of 37 dpf 5 month and 7 mpf Tgpomca:EGFP zebrafish were prepared for Mars seq single cell RNA Seq. Two 348 well plates were collected for each age group.", null, "pubmed:37683631", null, "AB7417", "GSM6153478", null, "source name:Neurohypophysis enriched cells|strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf loc name:missing|collection date:missing", "AB7417", "bcl2fastq/2.15.0.4 Sequences with RMT with minimum Phred score of less than 27 were filtered out. Pool barcode and well barcode RMT were extracted from the first and second end of the read respectively and concatenated to the fastq header delimited by a underscore i.e. POOL BARCODE WELL BARCODE RMT. Reads were separated by POOL BARCODE WELL BARCODE header data allowing 1 sequencing error. This process created a single fastq file for each source well. Single cell analysis was performed using the Seurat package v 3.1.5 Butler et al. 2018. Cells with >30% mitochondria gene expression as well as cells with extreme top or bottom UMI expression were removed leaving a total of 1281 cells from all samples. Expression values were normalized and scaled using the functions NormalizeData normalization.method=\"LogNormalize\" scale.factor= 10000 and ScaleData vars.to.regress = c\"nCount RNA\" \"percent.mito\". Clusters were determined using FindNeighbors dims=1:6 and FindClusters reduction.type = \"pca\" resolution = 0.6. paired end read2 used to read cell and molecule barcodes only Assembly: DanRer10 Supplementary files format and content: Text file containing the gene average log normalized expression per cluster", "Neurohypophysis enriched cells", "5ul of 4.6mM \u03b2 Ala Lys N\u03b5 AMCA Biotrend #BP0352 was injected into 37 dpf juvenile or 10ul into 5 or 7 mpf male Tgpomca:EGFP. post 3 hours the pituitaries of each age group were dissected and dispersed into single cell suspensions as described below.", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", "37 dpf 5 & 7 month zebrafish were raised at the Weizmann Institute fish facility.", "strain:AB Tgpomca:EGFP|tissue:Neurohypophysis|age:37 dpf", "GSM6153478", "GSM6153478: AB7417; Danio rerio; RNA Seq", "GSM6153478 r1", "GSM6153478", "1", "5 pituitaries from each age group were dissected and pooled in 1ml ice cold HEPES buffered saline HBS which was later changed to 250\u03bcl ice cold PBS+/+ with prewarmed Liberase TM for 12 minutes at 30 degrees C. The tissues were then further dissociated with 750\u03bcl of TrypLE Express and 16\u03bcl DNaseI for 6 minutes at room temperature and stopped with 50\u03bcl FBS. Dissociated cells were pelleted at 500g for 5 minutes at 4 degree C therepost resuspended in 500\u03bcl ice cold resuspension buffer Leibovitz L 15 with 0.3mM Glutamine penicillin 50 U/mL + streptomycin 0.05 mg/mL FBS 1% BSA 0.04% and passed through a 40\u03bcm strainer. Cells were stained with propidium iodide then sorted into 384 well plates. The Mars Seq single cell library was prepared according to Jaitin et al. 2014. In short mRNA from the single cell was barcoded and converted to cDNA in the 384 well plate then pooled and in vitro transcribed to RNA before fragmented into a library. The library was then ligated reverse transcribed and PCR amplified to attach the pool barcodes and Illumina sequencing codes. The library quality and concentration for each pool were checked before sequencing using an Illumina NextSeq 500 machine Illumina USA at a median sequencing depth around 40 000 reads per cell.", null, "RNA-Seq", "TRANSCRIPTOMIC SINGLE CELL", "cDNA", "PAIRED", "ILLUMINA", "Illumina NovaSeq 6000", null, "SRP375342", null, null, "AB7417_SB350_S24_R1_001.fastq.gz AB7417_SB350_S24_R2_001.fastq.gz", "fastq fastq", 2586526488.0, 30791982.0, "GSM6153478 r1", "0:69 1:15", "A:833353097;C:525447349;G:601496569;T:626135990;N:93483", 69, 15, null, null, 833353097, 525447349, 601496569, 626135990, 93483, "SRX15281303", "SRS13012748", "SRA1420605", "Molecular Cell Biology, Weizmann Institute of Science", "Molecular Cell Biology, Weizmann Institute of Science", 2, 0.84125, 0.0, 0.10717, 0.0, 0.84768, 1.0, 0.63154, null, 69, 15, "B", "T", "sc-like readlen", "illumina", "novaseq_era", "unknown", "cdna_unspecified", "unknown", "sc", "single_cell_plate", "marsseq", null, "Israel", "2022-05-16", 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