rowid,run.accession,experiment.accession,sample.accession,study.accession,bioproject,study.title,study.alias,study.type,study.abstract,study.attributes,study.PMIDs,sample.description,sample.title,sample.alias,sample.centername,sample.attributes,GEOsample.title,GEOsample.dataprocessing,GEOsample.source,GEOsample.treatmentprotocol,GEOsample.extractprotocol,GEOsample.growthprotocol,GEOsample.characteristics,GEOsample.accession,experiment.title,experiment.alias,experiment.library_name,experiment.design_description,experiment.library_construction_protocol,experiment.attributes,experiment.library_strategy,experiment.library_source,experiment.library_selection,experiment.library_layout,experiment.platform,experiment.instrument_model,experiment.spot_descriptor,experiment.study_ref,run.title,run.attributes,run.filename,run.semantic_name,run.total_bases,run.total_spots,run.alias,run.read_lengths,run.base_counts,run.r1_length,run.r2_length,run.r3_length,run.r4_length,run.Acount,run.Ccount,run.Gcount,run.Tcount,run.Ncount,run.experiment,run.pool_member,submission.accession,submission.srasource,submission.bioprojectsource,seqdetective.n_mates,seqdetective.mapping_rate.mate1,seqdetective.mapping_rate.mate2,seqdetective.nofeature_rate.mate1,seqdetective.nofeature_rate.mate2,seqdetective.sparsity.mate1,seqdetective.sparsity.mate2,seqdetective.pos_strand_rate.mate1,seqdetective.pos_strand_rate.mate2,seqdetective.readlen.mate1,seqdetective.readlen.mate2,seqdetective.judgement.mate1,seqdetective.judgement.mate2,seqdetective.judgement.reason,platform_family,instrument_generation,read_bias,selection_class,prep_kit,sc_or_bulk,tech_class,technology,tech_variant,submission.bioprojectsource.country,earliest_date,devstage_curation,devstage_curation_coarse,tissue_curation,tissue_curation_coarse
11130,ERR9979395,ERX9520370,ERS12499848,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 WT GO+BA,SAMEA110401656,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 2 WT GO+BA p,Sample 2 WT GO+BA p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7002_S2_L002_R1_001.fastq.gz P22202_7002_S2_L002_R2_001.fastq.gz,fastq fastq,18144406998.0,153766161.0,E MTAB 11984:P22202 7002 S2 L002,0:28 1:90,A:5277424121;C:3880928155;G:4118706097;T:4866649878;N:698747,28,90,,,5277424121,3880928155,4118706097,4866649878,698747,ERX9520370,ERS12499848,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.0109,0.90145,0.0053,0.21373,0.98746,0.79423,0.41198,0.54447,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11131,ERR9979394,ERX9520370,ERS12499848,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 WT GO+BA,SAMEA110401656,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401656|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 2 WT GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 2 WT GO+BA|sex:not available|stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 2 WT GO+BA p,Sample 2 WT GO+BA p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide 30 ug/mL and butyrate 2.5 mM,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7002_S2_L001_R1_001.fastq.gz P22202_7002_S2_L001_R2_001.fastq.gz,fastq fastq,18458951574.0,156431793.0,E MTAB 11984:P22202 7002 S2 L001,0:28 1:90,A:5372920926;C:3946687814;G:4185647697;T:4953205454;N:489683,28,90,,,5372920926,3946687814,4185647697,4953205454,489683,ERX9520370,ERS12499848,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01037,0.90168,0.0048,0.21246,0.98752,0.79297,0.42601,0.54996,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11132,ERR9979392,ERX9520369,ERS12499847,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 WT control,SAMEA110401655,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 1 WT control p,Sample 1 WT control p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7001_S1_L001_R1_001.fastq.gz P22202_7001_S1_L001_R2_001.fastq.gz,fastq fastq,19396994226.0,164381307.0,E MTAB 11984:P22202 7001 S1 L001,0:28 1:90,A:5665199484;C:4091196594;G:4415211076;T:5224866754;N:520318,28,90,,,5665199484,4091196594,4415211076,5224866754,520318,ERX9520369,ERS12499847,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01093,0.89238,0.00557,0.232,0.98764,0.79444,0.40806,0.54781,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11133,ERR9979393,ERX9520369,ERS12499847,ERP139765,PRJEB54901,Single cell RNA sequencing of germ free zebrafish embryos,E-MTAB-11984,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. We previously evaluated the impact of graphene oxide GO on the gut microbiome in adult zebrafish by performing 16S rRNA gene sequencing in wild type versus AhR deficient zebrafish.  Here  we performed single cell RNA sequencing 10x Genomics on whole dissociated germ free GF zebrafish embryos exposed at 5 dpf to GO plus the microbial metabolite butyrate to gain insight into the impact on specific cell populations in GF zebrafish.,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,,Protocols: The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 WT control,SAMEA110401655,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22|External Id:SAMEA110401655|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 22T16:26:50Z|INSDC last update:2022 07 22T16:26:50Z|INSDC status:public|Submitter Id:E MTAB 11984:Sample 1 WT control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:embryo|genotype:wild type genotype|individual:pool of 80 individuals|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11984:Sample 1 WT control|sex:not available|stimulus:n1|strain:AB,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,E MTAB 11984:Sample 1 WT control p,Sample 1 WT control p,Single cell RNA sequencing of germ free zebrafish embryos,The generation of germ free zebrafish wild type AB followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Twenty larvae were used as one replicate  four replicates  i.e. eighty larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 negative cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed.  The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139765,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of germ free zebrafish embryos,ENA FIRST PUBLIC:2022 07 22|ENA LAST UPDATE:2022 07 22,P22202_7001_S1_L002_R1_001.fastq.gz P22202_7001_S1_L002_R2_001.fastq.gz,fastq fastq,19063958224.0,161558968.0,E MTAB 11984:P22202 7001 S1 L002,0:28 1:90,A:5563588848;C:4022930643;G:4344549562;T:5132136743;N:752428,28,90,,,5563588848,4022930643,4344549562,5132136743,752428,ERX9520369,ERS12499847,ERA16483151,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.01118,0.89308,0.00573,0.23128,0.98737,0.79354,0.39264,0.54552,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-22,Multi-stage,Embryo,Whole Organism,All anatomical structures
11134,ERR9981089,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L001_R1_001.fastq.gz P25452_2002_S2_L001_R2_001.fastq.gz,fastq fastq,60177283876.0,509976982.0,E MTAB 11991:P25452 2002 S2 L001,0:28 1:90,A:17254566438;C:13547211711;G:14188233429;T:15185192817;N:2079481,28,90,,,17254566438,13547211711,14188233429,15185192817,2079481,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00671,0.93031,0.00231,0.11028,0.9932,0.82227,0.30887,0.58272,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11135,ERR9981090,ERX9522049,ERS12503451,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 1 lck control,SAMEA110406305,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406305|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 1 lck control|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 1 lck control|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 1 lck control p,Sample 1 lck control p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °,Experimental Factor: stimulus:n1,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2002_S2_L002_R1_001.fastq.gz P25452_2002_S2_L002_R2_001.fastq.gz,fastq fastq,60597886144.0,513541408.0,E MTAB 11991:P25452 2002 S2 L002,0:28 1:90,A:17368154358;C:13649089056;G:14296037620;T:15282869484;N:1735626,28,90,,,17368154358,13649089056,14296037620,15282869484,1735626,ERX9522049,ERS12503451,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00656,0.92899,0.00211,0.11059,0.99334,0.82335,0.32311,0.57644,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11136,ERR9981087,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L001_R1_001.fastq.gz P25452_2001_S1_L001_R2_001.fastq.gz,fastq fastq,20866120186.0,176831527.0,E MTAB 11991:P25452 2001 S1 L001,0:28 1:90,A:5933525376;C:4737179804;G:5025711080;T:5168983880;N:720046,28,90,,,5933525376,4737179804,5025711080,5168983880,720046,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00805,0.92622,0.00259,0.11842,0.99302,0.83027,0.2729,0.57699,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
11137,ERR9981088,ERX9522048,ERS12503450,ERP139797,PRJEB54930,Single cell RNA sequencing of lck GFP transgenic zebrafish,E-MTAB-11991,Transcriptome Analysis,The present study was conducted in the frame of the EU funded Graphene Flagship project. The aim is to evaluate the impact of graphene oxide GO on the innate immune system using zebrafish as a model. We previously performed single cell RNA sequencing of germ free zebrafish embryos exposed to GO plus the microbial metabolite butyrate BA. Here  we performed a follow up experiment using germ free lck GFP transgenic fish in which the zebrafish were exposed to GO plus BA at xxx dpf. The embryos were then dissociated and subsequently sorted on lck and submitted for single cell RNA sequencing using 10x Genomics.,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,,Protocols: The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol. Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Sample 2 lck GO+BA,SAMEA110406304,"Institute of Environmental Medicine, Karolinska Institutet",ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23|External Id:SAMEA110406304|INSDC center alias:Institute of Environmental Medicine  Karolinska Institutet|INSDC center name:Institute of Environmental Medicine  Karolinska Institutet|INSDC first public:2022 07 23T04:33:35Z|INSDC last update:2022 07 23T04:33:35Z|INSDC status:public|Submitter Id:E MTAB 11991:Sample 2 lck GO+BA|age:5|broker name:ArrayExpress|common name:zebrafish|developmental stage:larva|disease:normal|genotype:wild type genotype|isolate:not applicable|organism part:whole organism|sample name:E MTAB 11991:Sample 2 lck GO+BA|strain:Tglck:GFP,,,,,,,,,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,E MTAB 11991:Sample 2 lck GO+BA p,Sample 2 lck GO+BA p,Single cell RNA sequencing of lck GFP transgenic zebrafish,The generation of germ free Tglck:GFP zebrafish followed previously established protocols [1]. In brief  2 hpf embryos were transferred to petri dishes with sterile E3 medium  supplemented with ampicillin 100 μg/mL  kanamycin 5 μg/mL and amphotericin B 250 ng/mL and incubated at 28°C. At 50% epiboly up to shield stage 6 hpf  the embryos were surface disinfected with 0.1% of polyvinylpyrroidone iodine PVP I for exactly 2 min  followed by 0.003% sterile bleach immersion for 18 min. The embryos were then rinsed with sterile E3 medium  transferred to flasks and incubated at 28°C. The viability was monitored  and sterile medium was refreshed daily. At day 4  the hatched embryos were used for the sterility validation. A day 5  germ free Tglck:GFP zebrafish were exposed to the combination of GO 30 µg/mL and butyrate 2.5 mM for 24 h. GO and BA were pre incubated for 1 h prior to the exposure. Fifty larvae were used as one replicate  four replicates  i.e. two hundred larvae in total  were used for each condition. post the exposure  zebrafish larvae were dissociated for single cell suspension following the published protocol [2]. Briefly  zebrafish larvae were euthanized with 0.01% of tricaine for 5 min  collected in 1.5 mL tube  and washed with PBS for three times. The dissociation was initiated by adding 500 μL of pre warmed enzyme mix containing 460 μL of 0.25% trypsin EDTA Gibco and 40 μL of collagenase Sigma Aldrich at the concentration of 100 mg/mL  followed by mechanical dissociation using P1000 and then P200 pipette tips in heat block at 30 °C until the tissue was no longer visible about 10 min. The dissociation was then stopped by adding 800 μL DMEM Corning Cat# 10 013 CV with 10% FBS Fisher Scientific. The cell pellets were collected by centrifuging at 1000 rpm for 5 min at RT  followed by washing with PBS. The cells were next resuspended in 0.5 mL DMEM with 10% FBS. Four replicates from each condition were pooled together at this step and filtered through 40 μm nylon mesh  with an additional washing using DMEM with 10% FBS. The cell suspension was then stained with a fluorescent DNA dye DRAQ7 to exclude non viable cells Invitrogen Cat# D15106 at the dose of 3 μM for 10 min at room temperature before the fluorescence activated cell sorting BD FACSAria III  BD Biosciences  NJ  USA. The sorting was performed using a 100 microns nozzle with the flow rate of 2 and temperature control at 4 °C and gated based on forward scatter and DRAQ7. The DRAQ7 lck+ cells of each sample were FACS sorted into the tubes containing DMEM with 10% FBS and placed on ice immediately post the sorting. The cells were then proceeded with the single cell RNA sequencing analysis. 1. Pham LN  Kanther M  Semova I & Rawls JF. Methods for generating and colonizing gnotobiotic zebrafish. Nat. Protoc. 3  1862 1875 2008. 2. Bresciani E  Broadbridge E  Liu PP An efficient dissociation protocol for generation of single cell suspension from zebrafish embryos and larvae  MethodsX. 5  1287 1290 2018. Single cell RNA sequencing scRNA seq was performed by Eukaryotic Single Cell Genomics Facility at SciLifeLab  Stockholm. The single cells collected from FACS sorting were loaded on a 10x GemCode Single Cell Instrument 10x Genomics  Pleasanton  USA to generate single cell gel beads in emulsion GEMs using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics following the manufacture's protocol.  Briefly  GEMs were generated by combining barcoded Single Cell three prime v3.1 Gel Beads  a Master Mix containing cells  and Partitioning Oil onto Chromium Next GEM Chip G. Following GEMs generation  the Gel Bead was dissolved  primers containing an Illumina TruSeq Read 1read 1 sequencing primer  16 nt 10x Barcode  12 nt unique molecular identifier UMI and 30 nt polydT sequence were released  and the co partitioned cells were lysed. The nucleic acid library construction was performed using the Chromium Next GEM Single Cell three prime GEM  Library & Gel Bead Kit v3.1 10x Genomics  16 rxns PN 1000268 following the manufacture's protocol. post GEMs generation  primers were mixed with the cell lysate and a Master Mix containing reverse transcription RT reagents to produce barcoded  full length cDNA from polyadenylated mRNA. Silane magnetic beads were used to purify the first strand cDNA from the post GEM RT reaction mixture  which included leftover biochemical reagents and primers. Barcoded  full length cDNA was amplified via PCR to generate sufficient mass for library construction. Enzymatic fragmentation and size selection were used to optimize the cDNA amplicon size. P5  P7  i7 and i5 sample indexes  and TruSeq Read 2 read 2 primer sequence were added via End Repair  A tailing  Adaptor Ligation  and PCR. The final libraries containing the P5 and P7 primers used in Illumina amplification were prepared for an estimated 5000 nuclei per sample.,Experimental Factor: stimulus:graphene oxide  30 microgram per milliliter|Experimental Factor: compound:butyrate|Experimental Factor: dose:2.5,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,size fractionation,PAIRED,ILLUMINA,Illumina NovaSeq 6000,,ERP139797,Illumina NovaSeq 6000 paired end sequencing; Single cell RNA sequencing of lck GFP transgenic zebrafish,ENA FIRST PUBLIC:2022 07 23|ENA LAST UPDATE:2022 07 23,P25452_2001_S1_L002_R1_001.fastq.gz P25452_2001_S1_L002_R2_001.fastq.gz,fastq fastq,21068682172.0,178548154.0,E MTAB 11991:P25452 2001 S1 L002,0:28 1:90,A:5987758267;C:4786100132;G:5078292970;T:5215926275;N:604528,28,90,,,5987758267,4786100132,5078292970,5215926275,604528,ERX9522048,ERS12503450,ERA16488297,"Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive","Institute of Environmental Medicine, Karolinska Institutet|European Nucleotide Archive",2,0.00813,0.92702,0.00264,0.11874,0.99283,0.82737,0.30228,0.56929,28,90,T,B,sc-like readlen,illumina,novaseq_era,full_length,size_fractionation,trueseq,sc,single_cell_droplet,10x,,Sweden,2022-07-23,Larval,Larval,Whole Organism,All anatomical structures
40376,SRR3166964,SRX1583817,SRS1295580,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 28d Calm4,,breed:AB|chain:alpha|index:26|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 28d Calm4,116 28d Calm4 alpha,116 28d Calm4 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_116_28d_Calm4_alpha.fq.gz read2_116_28d_Calm4_alpha.fq.gz,fastq fastq,12052440600.0,40174802.0,116 28d Calm4 alpha files,0:150 1:150,A:3274476247;C:2324807837;G:3578878507;T:2848354560;N:25923449,150,150,,,3274476247,2324807837,3578878507,2848354560,25923449,SRX1583817,SRS1295580,SRA353254,SRA,Bar-Ilan University,2,0.00096,0.22917,0.00017,0.19822,0.99906,0.99762,0.35172,0.6189,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40377,SRR3166963,SRX1583816,SRS1295581,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 28d Calm2,,breed:AB|chain:alpha|index:25|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 28d Calm2,114 28d Calm2 alpha,114 28d Calm2 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_114_28d_Calm2_alpha.fq.gz read2_114_28d_Calm2_alpha.fq.gz,fastq fastq,4957122900.0,16523743.0,114 28d Calm2 alpha files,0:150 1:150,A:1398510544;C:988027281;G:1244120221;T:1316350204;N:10114650,150,150,,,1398510544,988027281,1244120221,1316350204,10114650,SRX1583816,SRS1295581,SRA353254,SRA,Bar-Ilan University,2,0.00167,0.03332,0.00146,0.028,0.99967,0.99896,0.15789,0.60731,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40378,SRR3166962,SRX1583815,SRS1295582,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 28d KLH6,,breed:AB|chain:alpha|index:21|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 28d KLH6,110 28d KLH6 alpha,110 28d KLH6 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_110_28d_KLH6_alpha.fq.gz read2_110_28d_KLH6_alpha.fq.gz,fastq fastq,6270530700.0,20901769.0,110 28d KLH6 alpha files,0:150 1:150,A:1802311183;C:1236560108;G:1561615962;T:1659163742;N:10879705,150,150,,,1802311183,1236560108,1561615962,1659163742,10879705,SRX1583815,SRS1295582,SRA353254,SRA,Bar-Ilan University,2,0.00179,0.13512,0.00073,0.11592,0.99967,0.99855,0.21568,0.87835,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40379,SRR3166961,SRX1583814,SRS1295583,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 28d PHA6,,breed:AB|chain:alpha|index:32|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 28d PHA6,102 28d PHA6 alpha,102 28d PHA6 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_102_28d_PHA6_alpha.fq.gz read2_102_28d_PHA6_alpha.fq.gz,fastq fastq,10067723700.0,33559079.0,102 28d PHA6 alpha files,0:150 1:150,A:2803515995;C:2027880463;G:2649055724;T:2566963260;N:20308258,150,150,,,2803515995,2027880463,2649055724,2566963260,20308258,SRX1583814,SRS1295583,SRA353254,SRA,Bar-Ilan University,2,0.00158,0.04576,0.00056,0.03839,0.99922,0.99831,0.3246,0.40078,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-02-14,Undetermined,Undetermined,Whole Organism,All anatomical structures
40380,SRR3166960,SRX1583813,SRS1295584,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 7d KLH2,,breed:AB|chain:alpha|index:34|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 7d KLH2,16 7d KLH2 alpha,16 7d KLH2 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_16_7d_KLH2_alpha.fq.gz read2_16_7d_KLH2_alpha.fq.gz,fastq fastq,2783317500.0,9277725.0,16 7d KLH2 alpha files,0:150 1:150,A:761370556;C:556705024;G:719835894;T:727504605;N:17901421,150,150,,,761370556,556705024,719835894,727504605,17901421,SRX1583813,SRS1295584,SRA353254,SRA,Bar-Ilan University,2,0.00143,0.13658,0.0008,0.11879,0.99935,0.99876,0.25409,0.87567,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-02-14,Undetermined,Undetermined,Whole Organism,All anatomical structures
40381,SRR3166959,SRX1583812,SRS1295585,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 21d KLH6,,breed:AB|chain:alpha|index:24|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 21d KLH6,78 21d KLH6 alpha,78 21d KLH6 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_78_21d_KLH6_alpha.fq.gz read2_78_21d_KLH6_alpha.fq.gz,fastq fastq,7720614900.0,25735383.0,78 21d KLH6 alpha files,0:150 1:150,A:2163229607;C:1591913203;G:1963558161;T:1998596363;N:3317566,150,150,,,2163229607,1591913203,1963558161,1998596363,3317566,SRX1583812,SRS1295585,SRA353254,SRA,Bar-Ilan University,2,0.00105,0.04913,0.00036,0.04186,0.99937,0.99835,0.14393,0.4819,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40382,SRR3166958,SRX1583811,SRS1295586,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 7d Calm6,,breed:AB|chain:alpha|index:33|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 7d Calm6,27 7d Calm6 alpha,27 7d Calm6 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_27_7d_Calm6_alpha.fq.gz read2_27_7d_Calm6_alpha.fq.gz,fastq fastq,4337226600.0,14457422.0,27 7d Calm6 alpha files,0:150 1:150,A:1174401516;C:871068073;G:1145864920;T:1118174763;N:27717328,150,150,,,1174401516,871068073,1145864920,1118174763,27717328,SRX1583811,SRS1295586,SRA353254,SRA,Bar-Ilan University,2,0.002,0.032,0.0007,0.02494,0.99924,0.99912,0.38,0.38606,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-02-14,Undetermined,Undetermined,Whole Organism,All anatomical structures
40383,SRR3166957,SRX1583810,SRS1295587,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 7d PHA7,,breed:AB|chain:alpha|index:36|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 7d PHA7,14 7d PHA7 alpha,14 7d PHA7 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_14_7d_PHA7_alpha.fq.gz read2_14_7d_PHA7_alpha.fq.gz,fastq fastq,3401366100.0,11337887.0,14 7d PHA7 alpha files,,,,,,,,,,,,SRX1583810,SRS1295587,SRA353254,SRA,Bar-Ilan University,2,0.00357,0.02242,0.00202,0.01952,0.99902,0.99811,0.35016,0.5424,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40384,SRR3166956,SRX1583809,SRS1295588,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRA library 7d PHA3,,breed:AB|chain:alpha|index:35|sex:male|time point:7d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRa sequencing of zebrafish:  whole zebrafish: Sample TCRA library 7d PHA3,10 7d PHA3 alpha,10 7d PHA3 alpha,five prime RACE amplification of TCRa transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_10_7d_PHA3_alpha.fq.gz read1_10_7d_PHA3_alpha.fq.gz,fastq fastq,4293459300.0,14311531.0,10 7d PHA3 alpha files,0:150 1:150,A:1208054755;C:855800391;G:1072212534;T:1129932131;N:27459489,150,150,,,1208054755,855800391,1072212534,1129932131,27459489,SRX1583809,SRS1295588,SRA353254,SRA,Bar-Ilan University,2,0.00174,0.05155,0.0009,0.0472,0.99937,0.9989,0.2256,0.60714,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40385,SRR3166955,SRX1583808,SRS1295589,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d Calm7,,breed:AB|chain:beta|index:56|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d Calm7,119 28d Calm7 beta,119 28d Calm7 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_119_28d_Calm7_beta.fq.gz read2_119_28d_Calm7_beta.fq.gz,fastq fastq,3494941800.0,11649806.0,119 28d Calm7 beta files,0:150 1:150,A:1262121526;C:602497563;G:790544892;T:738346792;N:101431027,150,150,,,1262121526,602497563,790544892,738346792,101431027,SRX1583808,SRS1295589,SRA353254,SRA,Bar-Ilan University,2,3e-05,0.00179,0.0,7e-05,0.99997,0.99831,0.0,0.42009,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40386,SRR3166954,SRX1583807,SRS1295590,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d Calm5,,breed:AB|chain:beta|index:55|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d Calm5,117 28d Calm5 beta,117 28d Calm5 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_117_28d_Calm5_beta.fq.gz read1_117_28d_Calm5_beta.fq.gz,fastq fastq,2950876200.0,9836254.0,117 28d Calm5 beta files,0:150 1:150,A:1025845698;C:505599350;G:688977765;T:634738210;N:95715177,150,150,,,1025845698,505599350,688977765,634738210,95715177,SRX1583807,SRS1295590,SRA353254,SRA,Bar-Ilan University,2,0.0,0.00023,0.0,0.0,1.0,0.99987,,0.07692,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40387,SRR3166953,SRX1583806,SRS1295591,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d Calm3,,breed:AB|chain:beta|index:54|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d Calm3,115 28d Calm3 beta,115 28d Calm3 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_115_28d_Calm3_beta.fq.gz read2_115_28d_Calm3_beta.fq.gz,fastq fastq,1913218200.0,6377394.0,115 28d Calm3 beta files,0:150 1:150,A:637646003;C:349779874;G:435732113;T:430619528;N:59440682,150,150,,,637646003,349779874,435732113,430619528,59440682,SRX1583806,SRS1295591,SRA353254,SRA,Bar-Ilan University,2,0.0,0.02438,0.0,0.00184,1.0,0.99908,,0.01511,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40388,SRR3166952,SRX1583805,SRS1295592,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d KLH6,,breed:AB|chain:beta|index:27|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d KLH6,110 28d KLH6 beta,110 28d KLH6 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_110_28d_KLH6_beta.fq.gz read2_110_28d_KLH6_beta.fq.gz,fastq fastq,2689206600.0,8964022.0,110 28d KLH6 beta files,0:150 1:150,A:807762783;C:503825062;G:585283183;T:703818890;N:88516682,150,150,,,807762783,503825062,585283183,703818890,88516682,SRX1583805,SRS1295592,SRA353254,SRA,Bar-Ilan University,2,0.00014,0.3078,0.0,0.02202,0.99975,0.99095,0.38888,0.10297,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40389,SRR3166951,SRX1583804,SRS1295593,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d KLH2,,breed:AB|chain:beta|index:23|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d KLH2,106 28d KLH2 beta,106 28d KLH2 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_106_28d_KLH2_beta.fq.gz read1_106_28d_KLH2_beta.fq.gz,fastq fastq,2795086200.0,9316954.0,106 28d KLH2 beta files,0:150 1:150,A:897420089;C:470460508;G:621809014;T:712999451;N:92397138,150,150,,,897420089,470460508,621809014,712999451,92397138,SRX1583804,SRS1295593,SRA353254,SRA,Bar-Ilan University,2,0.0,0.05106,0.0,0.00859,1.0,0.99943,,0.01388,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40390,SRR3166950,SRX1583803,SRS1295594,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d KLH1,,breed:AB|chain:beta|index:22|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d KLH1,105 28d KLH1 beta,105 28d KLH1 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_105_28d_KLH1_beta.fq.gz read2_105_28d_KLH1_beta.fq.gz,fastq fastq,1768628700.0,5895429.0,105 28d KLH1 beta files,0:150 1:150,A:486366963;C:366398128;G:389871583;T:478235213;N:47756813,150,150,,,486366963,366398128,389871583,478235213,47756813,SRX1583803,SRS1295594,SRA353254,SRA,Bar-Ilan University,2,4e-05,0.09054,3e-05,0.01597,1.0,0.99931,,0.00767,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40391,SRR3166949,SRX1583802,SRS1295595,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d PHA7,,breed:AB|chain:beta|index:30|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d PHA7,103 28d PHA7 beta,103 28d PHA7 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_103_28d_PHA7_beta.fq.gz read2_103_28d_PHA7_beta.fq.gz,fastq fastq,2234344500.0,7447815.0,103 28d PHA7 beta files,0:150 1:150,A:628358242;C:462371909;G:526170885;T:548473987;N:68969477,150,150,,,628358242,462371909,526170885,548473987,68969477,SRX1583802,SRS1295595,SRA353254,SRA,Bar-Ilan University,2,0.00104,0.68691,5e-05,0.01999,0.99894,0.97281,0.23076,0.44172,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40392,SRR3166948,SRX1583801,SRS1295596,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d PHA5,,breed:AB|chain:beta|index:29|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d PHA5,101 28d PHA5 beta,101 28d PHA5 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_101_28d_PHA5_beta.fq.gz read2_101_28d_PHA5_beta.fq.gz,fastq fastq,1356278400.0,4520928.0,101 28d PHA5 beta files,0:150 1:150,A:372190640;C:278464953;G:294268430;T:378226253;N:33128124,150,150,,,372190640,278464953,294268430,378226253,33128124,SRX1583801,SRS1295596,SRA353254,SRA,Bar-Ilan University,2,0.00254,0.10913,0.0001,0.01715,0.99995,0.99904,0.01106,0.01084,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40393,SRR3166947,SRX1583800,SRS1295597,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d PHA2,,breed:AB|chain:beta|index:28|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d PHA2,98 28d PHA2 beta,98 28d PHA2 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_98_28d_PHA2_beta.fq.gz read1_98_28d_PHA2_beta.fq.gz,fastq fastq,4533755400.0,15112518.0,98 28d PHA2 beta files,0:150 1:150,A:1508096116;C:749853448;G:1051562277;T:1142392486;N:81851073,150,150,,,1508096116,749853448,1051562277,1142392486,81851073,SRX1583800,SRS1295597,SRA353254,SRA,Bar-Ilan University,2,0.0,0.33493,0.0,0.02388,1.0,0.99758,,0.15819,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40394,SRR3166946,SRX1583799,SRS1295598,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d IFA 5,,breed:AB|chain:beta|index:11|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d IFA 5,93 28d IFA 5 beta,93 28d IFA 5 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_93_28d_IFA_5_beta.fq.gz read2_93_28d_IFA_5_beta.fq.gz,fastq fastq,1526394600.0,5087982.0,93 28d IFA 5 beta files,0:150 1:150,A:431910708;C:323148774;G:334806769;T:417586287;N:18942062,150,150,,,431910708,323148774,334806769,417586287,18942062,SRX1583799,SRS1295598,SRA353254,SRA,Bar-Ilan University,2,0.00039,0.31457,0.00015,0.00771,0.99963,0.98468,0.28947,0.16209,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40395,SRR3166945,SRX1583798,SRS1295599,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d IFA 2,,breed:AB|chain:beta|index:10|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d IFA 2,90 28d IFA 2 beta,90 28d IFA 2 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_90_28d_IFA_2_beta.fq.gz read2_90_28d_IFA_2_beta.fq.gz,fastq fastq,2345298300.0,7817661.0,90 28d IFA 2 beta files,0:150 1:150,A:753823005;C:419081900;G:516233583;T:613533931;N:42625881,150,150,,,753823005,419081900,516233583,613533931,42625881,SRX1583798,SRS1295599,SRA353254,SRA,Bar-Ilan University,2,0.00015,0.38592,3e-05,0.00508,0.99985,0.99385,0.33333,0.06202,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40396,SRR3166944,SRX1583797,SRS1295600,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 28d IFA 1,,breed:AB|chain:beta|index:28|sex:male|time point:28d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 28d IFA 1,89 28d IFA 1 beta,89 28d IFA 1 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_89_28d_IFA_1_beta.fq.gz read2_89_28d_IFA_1_beta.fq.gz,fastq fastq,2029349400.0,6764498.0,89 28d IFA 1 beta files,0:150 1:150,A:714287901;C:360307311;G:472841677;T:446872160;N:35040351,150,150,,,714287901,360307311,472841677,446872160,35040351,SRX1583797,SRS1295600,SRA353254,SRA,Bar-Ilan University,2,0.0,0.06313,0.0,0.01031,1.0,0.99703,,0.15591,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40397,SRR3166943,SRX1583796,SRS1295601,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d Calm6,,breed:AB|chain:beta|index:44|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d Calm6,86 21d Calm6 beta,86 21d Calm6 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_86_21d_Calm6_beta.fq.gz read1_86_21d_Calm6_beta.fq.gz,fastq fastq,2610499200.0,8701664.0,86 21d Calm6 beta files,0:150 1:150,A:764524163;C:544491001;G:601533912;T:654396223;N:45553901,150,150,,,764524163,544491001,601533912,654396223,45553901,SRX1583796,SRS1295601,SRA353254,SRA,Bar-Ilan University,2,0.00108,0.63356,0.00012,0.12284,0.99837,0.96193,0.21768,0.38237,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40398,SRR3166942,SRX1583795,SRS1295602,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d Calm5,,breed:AB|chain:beta|index:43|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d Calm5,85 21d Calm5 beta,85 21d Calm5 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_85_21d_Calm5_beta.fq.gz read2_85_21d_Calm5_beta.fq.gz,fastq fastq,2700056100.0,9000187.0,85 21d Calm5 beta files,0:150 1:150,A:755011216;C:593419169;G:623123170;T:688658373;N:39844172,150,150,,,755011216,593419169,623123170,688658373,39844172,SRX1583795,SRS1295602,SRA353254,SRA,Bar-Ilan University,2,0.00244,0.68155,0.00026,0.01492,0.99766,0.96597,0.24863,0.31823,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40399,SRR3166941,SRX1583794,SRS1295603,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d Calm1,,breed:AB|chain:beta|index:42|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d Calm1,81 21d Calm1 beta,81 21d Calm1 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_81_21d_Calm1_beta.fq.gz read2_81_21d_Calm1_beta.fq.gz,fastq fastq,2296683900.0,7655613.0,81 21d Calm1 beta files,0:150 1:150,A:776751441;C:430253074;G:528909259;T:525320137;N:35449989,150,150,,,776751441,430253074,528909259,525320137,35449989,SRX1583794,SRS1295603,SRA353254,SRA,Bar-Ilan University,2,2e-05,0.0464,0.0,0.00091,0.99997,0.99882,0.0,0.0134,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40400,SRR3166940,SRX1583793,SRS1295604,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d KLH6,,breed:AB|chain:beta|index:50|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d KLH6,78 21d KLH6 beta,78 21d KLH6 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_78_21d_KLH6_beta.fq.gz read2_78_21d_KLH6_beta.fq.gz,fastq fastq,1500221100.0,5000737.0,78 21d KLH6 beta files,0:150 1:150,A:435807096;C:294707078;G:337922064;T:361615328;N:70169534,150,150,,,435807096,294707078,337922064,361615328,70169534,SRX1583793,SRS1295604,SRA353254,SRA,Bar-Ilan University,2,5e-05,0.37212,3e-05,0.03128,0.99997,0.99358,0.0,0.11962,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40401,SRR3166939,SRX1583792,SRS1295605,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d KLH5,,breed:AB|chain:beta|index:49|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d KLH5,77 21d KLH5 beta,77 21d KLH5 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_77_21d_KLH5_beta.fq.gz read2_77_21d_KLH5_beta.fq.gz,fastq fastq,2106732600.0,7022442.0,77 21d KLH5 beta files,0:150 1:150,A:696373936;C:376059887;G:465978414;T:465485185;N:102835178,150,150,,,696373936,376059887,465978414,465485185,102835178,SRX1583792,SRS1295605,SRA353254,SRA,Bar-Ilan University,2,0.0,0.04625,0.0,0.00381,1.0,0.99979,,0.00123,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40402,SRR3166938,SRX1583791,SRS1295606,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d KLH1,,breed:AB|chain:beta|index:48|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d KLH1,73 21d KLH1 beta,73 21d KLH1 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_73_21d_KLH1_beta.fq.gz read1_73_21d_KLH1_beta.fq.gz,fastq fastq,3554391900.0,11847973.0,73 21d KLH1 beta files,0:150 1:150,A:1312477977;C:598886813;G:787337227;T:686894043;N:168795840,150,150,,,1312477977,598886813,787337227,686894043,168795840,SRX1583791,SRS1295606,SRA353254,SRA,Bar-Ilan University,2,6e-05,0.00136,5e-05,0.00019,1.0,0.99983,,0.0303,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40403,SRR3166937,SRX1583790,SRS1295607,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d PHA6,,breed:AB|chain:beta|index:53|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d PHA6,70 21d PHA6 beta,70 21d PHA6 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_70_21d_PHA6_beta.fq.gz read1_70_21d_PHA6_beta.fq.gz,fastq fastq,4238076900.0,14126923.0,70 21d PHA6 beta files,0:150 1:150,A:1519543327;C:710498920;G:932091678;T:844220454;N:231722521,150,150,,,1519543327,710498920,932091678,844220454,231722521,SRX1583790,SRS1295607,SRA353254,SRA,Bar-Ilan University,2,0.00023,0.00772,7e-05,0.00068,0.99991,0.99851,0.25,0.08615,150,150,T,T,mates < 9% mapping rate,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40404,SRR3166936,SRX1583789,SRS1295608,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d PHA4,,breed:AB|chain:beta|index:52|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d PHA4,68 21d PHA4 beta,68 21d PHA4 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_68_21d_PHA4_beta.fq.gz read2_68_21d_PHA4_beta.fq.gz,fastq fastq,2030511600.0,6768372.0,68 21d PHA4 beta files,0:150 1:150,A:659873688;C:307551211;G:388669539;T:566328083;N:108089079,150,150,,,659873688,307551211,388669539,566328083,108089079,SRX1583789,SRS1295608,SRA353254,SRA,Bar-Ilan University,2,0.00029,0.24246,3e-05,0.05929,0.99971,0.99214,0.4,0.16492,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40405,SRR3166935,SRX1583788,SRS1295609,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d PHA1,,breed:AB|chain:beta|index:51|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d PHA1,65 21d PHA1 beta,65 21d PHA1 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_65_21d_PHA1_beta.fq.gz read2_65_21d_PHA1_beta.fq.gz,fastq fastq,930240600.0,3100802.0,65 21d PHA1 beta files,0:150 1:150,A:259486434;C:184043790;G:197463162;T:250422190;N:38825024,150,150,,,259486434,184043790,197463162,250422190,38825024,SRX1583788,SRS1295609,SRA353254,SRA,Bar-Ilan University,2,0.00012,0.14868,0.0,0.02051,0.99963,0.99111,0.36842,0.258,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40406,SRR3166934,SRX1583787,SRS1295610,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d IFA 8,,breed:AB|chain:beta|index:47|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d IFA 8,64 21d IFA 8 beta,64 21d IFA 8 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_64_21d_IFA_8_beta.fq.gz read2_64_21d_IFA_8_beta.fq.gz,fastq fastq,1461868800.0,4872896.0,64 21d IFA 8 beta files,0:150 1:150,A:462418747;C:247121586;G:284662907;T:394116911;N:73548649,150,150,,,462418747,247121586,284662907,394116911,73548649,SRX1583787,SRS1295610,SRA353254,SRA,Bar-Ilan University,2,0.0001,0.17532,0.0,0.04988,0.99983,0.99843,0.25,0.01908,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40407,SRR3166933,SRX1583786,SRS1295611,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d IFA 4,,breed:AB|chain:beta|index:46|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d IFA 4,60 21d IFA 4 beta,60 21d IFA 4 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_60_21d_IFA_4_beta.fq.gz read1_60_21d_IFA_4_beta.fq.gz,fastq fastq,4128399900.0,13761333.0,60 21d IFA 4 beta files,0:150 1:150,A:1332478795;C:800389451;G:937176538;T:950735272;N:107619844,150,150,,,1332478795,800389451,937176538,950735272,107619844,SRX1583786,SRS1295611,SRA353254,SRA,Bar-Ilan University,2,0.00043,0.19668,5e-05,0.00597,0.99953,0.9782,0.2647,0.35656,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40408,SRR3166932,SRX1583785,SRS1295612,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 21d IFA 2,,breed:AB|chain:beta|index:45|sex:male|time point:21d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 21d IFA 2,58 21d IFA 2 beta,58 21d IFA 2 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_58_21d_IFA_2_beta.fq.gz read1_58_21d_IFA_2_beta.fq.gz,fastq fastq,5035078800.0,16783596.0,58 21d IFA 2 beta files,0:150 1:150,A:1714919930;C:839542402;G:1121993893;T:1220614755;N:138007820,150,150,,,1714919930,839542402,1121993893,1220614755,138007820,SRX1583785,SRS1295612,SRA353254,SRA,Bar-Ilan University,2,0.0,0.17551,0.0,0.00318,1.0,0.99833,,0.10802,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40409,SRR3166931,SRX1583784,SRS1295613,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 14d Calm6,,breed:AB|chain:beta|index:37|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 14d Calm6,55 14d Calm6 beta,55 14d Calm6 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_55_14d_Calm6_beta.fq.gz read2_55_14d_Calm6_beta.fq.gz,fastq fastq,1028012700.0,3426709.0,55 14d Calm6 beta files,0:150 1:150,A:295958360;C:207583542;G:216651025;T:284035600;N:23784173,150,150,,,295958360,207583542,216651025,284035600,23784173,SRX1583784,SRS1295613,SRA353254,SRA,Bar-Ilan University,2,5e-05,0.16498,0.0,0.01748,0.99989,0.99253,0.33333,0.12385,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40410,SRR3166930,SRX1583783,SRS1295614,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library Naive6,,breed:AB|chain:beta|index:31|sex:male|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library Naive6,126 Naive6 beta,126 Naive6 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_126_Naive6_beta.fq.gz read1_126_Naive6_beta.fq.gz,fastq fastq,1984909800.0,6616366.0,126 Naive6 beta files,0:150 1:150,A:574002364;C:411972224;G:452963561;T:493883048;N:52088603,150,150,,,574002364,411972224,452963561,493883048,52088603,SRX1583783,SRS1295614,SRA353254,SRA,Bar-Ilan University,2,0.0007,0.73767,5e-05,0.01562,0.99928,0.9754,0.16,0.44061,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40411,SRR3166929,SRX1583782,SRS1295615,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 14d IFA1,,breed:AB|chain:beta|index:38|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 14d IFA1,36 14d IFA1 beta,36 14d IFA1 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_36_14d_IFA1_beta.fq.gz read1_36_14d_IFA1_beta.fq.gz,fastq fastq,2641709400.0,8805698.0,36 14d IFA1 beta files,0:150 1:150,A:828430279;C:516389015;G:603137557;T:652458512;N:41294037,150,150,,,828430279,516389015,603137557,652458512,41294037,SRX1583782,SRS1295615,SRA353254,SRA,Bar-Ilan University,2,6e-05,0.17777,1e-05,0.00441,0.99991,0.99243,0.5,0.07212,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40412,SRR3166928,SRX1583781,SRS1295616,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 14d PHA7,,breed:AB|chain:beta|index:41|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 14d PHA7,35 14d PHA7 beta,35 14d PHA7 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read2_35_14d_PHA7_beta.fq.gz read1_35_14d_PHA7_beta.fq.gz,fastq fastq,2481744900.0,8272483.0,35 14d PHA7 beta files,0:150 1:150,A:684148801;C:534638425;G:555073374;T:671216692;N:36667608,150,150,,,684148801,534638425,555073374,671216692,36667608,SRX1583781,SRS1295616,SRA353254,SRA,Bar-Ilan University,2,0.00054,0.3447,8e-05,0.03511,0.9991,0.97049,0.29411,0.37357,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2017-02-12,Undetermined,Undetermined,Whole Organism,All anatomical structures
40413,SRR3166927,SRX1583780,SRS1295617,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 14d PHA6,,breed:AB|chain:beta|index:40|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 14d PHA6,34 14d PHA6 beta,34 14d PHA6 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_34_14d_PHA6_beta.fq.gz read2_34_14d_PHA6_beta.fq.gz,fastq fastq,2149899000.0,7166330.0,34 14d PHA6 beta files,0:150 1:150,A:603640552;C:452244383;G:474826068;T:587177894;N:32010103,150,150,,,603640552,452244383,474826068,587177894,32010103,SRX1583780,SRS1295617,SRA353254,SRA,Bar-Ilan University,2,4e-05,0.16994,0.0,0.14727,0.99991,0.99342,0.0,0.31047,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
40414,SRR3166926,SRX1583779,SRS1295618,SRP070056,PRJNA309588,Analysis of the T cell response in Zebrafish,PRJNA309588,Other,Our understanding of T cell receptor TCR repertoire diversity and response tochallenge is still incomplete. For example  TCR clones shared by different individuals withminimal alteration to germline gene sequences public clones are detectable in all vertebrates but their significance is unknown. We exploited the experimental advantages offered by thezebrafish to analyze the complete TCR repertoire and its response to self and foreign antigens.We found that cross reactive public TCRs dominate the T cell response  endowing the TCRrepertoire with the ability to cope with diverse antigenic challenges. These features of vertebratepublic TCRs provide a mechanism for the rapid generation of protective T cell immunityallowing a short temporal window for the development of more specific private T cell responses.,,,,,TCRB library 14d PHA5,,breed:AB|chain:beta|index:39|sex:male|time point:14d|tissue:whole fish|age:1y|BioSampleModel:Model organism or animal,,,,,,,,,TCRb sequencing of zebrafish:  whole zebrafish: Sample TCRB library 14d PHA5,33 14d PHA5 beta,33 14d PHA5 beta,five prime RACE amplification of TCRb transcript,,,AMPLICON,TRANSCRIPTOMIC,RACE,PAIRED,ILLUMINA,Illumina HiSeq 2000,<SPOT_DESCRIPTOR><SPOT_DECODE_SPEC><SPOT_LENGTH>300</SPOT_LENGTH><READ_SPEC><READ_INDEX>0</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Forward</READ_TYPE><BASE_COORD>1</BASE_COORD></READ_SPEC><READ_SPEC><READ_INDEX>1</READ_INDEX><READ_CLASS>Application Read</READ_CLASS><READ_TYPE>Reverse</READ_TYPE><BASE_COORD>151</BASE_COORD></READ_SPEC></SPOT_DECODE_SPEC></SPOT_DESCRIPTOR>,SRP070056,,,read1_33_14d_PHA5_beta.fq.gz read2_33_14d_PHA5_beta.fq.gz,fastq fastq,4781329500.0,15937765.0,33 14d PHA5 beta files,0:150 1:150,A:1564269921;C:790001191;G:1015752339;T:1331170138;N:80135911,150,150,,,1564269921,790001191,1015752339,1331170138,80135911,SRX1583779,SRS1295618,SRA353254,SRA,Bar-Ilan University,2,0.00034,0.20127,0.00018,0.00887,0.99989,0.99567,0.05263,0.08667,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,bulk,unknown,unknown,,Israel,2016-03-02,Undetermined,Undetermined,Whole Organism,All anatomical structures
58873,SRR11509894,SRX8082006,SRS6450124,SRP255712,PRJNA623798,Single cell lineage tracing on endogenous scarring sites scLOESS,PRJNA623798,Other,Lineage recording of zebrafish embryogenesis reveals early cell fate commitment,,,1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles  and purified amplicons were pooled into an equimolar mixture.  3 independent replicates in total.,Target specific Amplification of Single Cell cDNA Library,SCC,,strain:AB line|age:7dpf|dev stage:larvae|sex:not applicable|tissue:Whole organism|collection date:2018 07 26|BioSampleModel:Model organism or animal,,,,,,,,,Single cell cDNA library Amplicon of zebrafish larva  replicate 3,SCC replicate3,SCC replicate3,1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles  and purified amplicons were pooled into an equimolar mixture.  PCR replicate 3.,,,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP255712,,,SCC-replicate3_R1.fq.gz SCC-replicate3_R2.fq.gz,fastq fastq,14811756300.0,49372521.0,SCC replicate3 R1.fq.gz,0:150 1:150,A:3255250699;C:3018244265;G:3088919277;T:5446140655;N:3201404,150,150,,,3255250699,3018244265,3088919277,5446140655,3201404,SRX8082006,SRS6450124,SRA1063780,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.01015,0.97122,0.00049,0.00158,0.99841,0.97569,0.54867,0.48858,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2020-04-10,Larval,Larval,Whole Organism,All anatomical structures
58874,SRR11509895,SRX8082005,SRS6450124,SRP255712,PRJNA623798,Single cell lineage tracing on endogenous scarring sites scLOESS,PRJNA623798,Other,Lineage recording of zebrafish embryogenesis reveals early cell fate commitment,,,1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles  and purified amplicons were pooled into an equimolar mixture.  3 independent replicates in total.,Target specific Amplification of Single Cell cDNA Library,SCC,,strain:AB line|age:7dpf|dev stage:larvae|sex:not applicable|tissue:Whole organism|collection date:2018 07 26|BioSampleModel:Model organism or animal,,,,,,,,,Single cell cDNA library Amplicon of zebrafish larva  replicate 2,SCC replicate2,SCC replicate2,1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles  and purified amplicons were pooled into an equimolar mixture.  PCR replicate 2.,,,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP255712,,,SCC-replicate2_R2.fq.gz SCC-replicate2_R1.fq.gz,fastq fastq,19858547700.0,66195159.0,SCC replicate2 R1.fq.gz,0:150 1:150,A:4363166112;C:4066433314;G:4155737160;T:7269480395;N:3730719,150,150,,,4363166112,4066433314,4155737160,7269480395,3730719,SRX8082005,SRS6450124,SRA1063780,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.025,0.97152,0.00079,0.00143,0.99746,0.97668,0.74358,0.46727,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2020-04-09,Larval,Larval,Whole Organism,All anatomical structures
58875,SRR11509896,SRX8082004,SRS6450124,SRP255712,PRJNA623798,Single cell lineage tracing on endogenous scarring sites scLOESS,PRJNA623798,Other,Lineage recording of zebrafish embryogenesis reveals early cell fate commitment,,,1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles  and purified amplicons were pooled into an equimolar mixture.  3 independent replicates in total.,Target specific Amplification of Single Cell cDNA Library,SCC,,strain:AB line|age:7dpf|dev stage:larvae|sex:not applicable|tissue:Whole organism|collection date:2018 07 26|BioSampleModel:Model organism or animal,,,,,,,,,Single cell cDNA library Amplicon of zebrafish larva  replicate 1,SCC replicate1,SCC replicate1,1g cDNA library fetch from 10x Genomics Chromium Single Cell 3 Library was amplified by extra 15 cycles. and then split into 90 equal aliquots to amplify each target by 25 cycles  and purified amplicons were pooled into an equimolar mixture.  PCR replicate 1.,,,AMPLICON,TRANSCRIPTOMIC SINGLE CELL,PCR,PAIRED,ILLUMINA,HiSeq X Ten,,SRP255712,,,SCC-replicate1_R1.fq.gz SCC-replicate1_R2.fq.gz,fastq fastq,18191440200.0,60638134.0,SCC replicate1 R1.fq.gz,0:150 1:150,A:3994446536;C:3726446852;G:3814798796;T:6652431833;N:3316183,150,150,,,3994446536,3726446852,3814798796,6652431833,3316183,SRX8082004,SRS6450124,SRA1063780,Sun Yat- sen University|Life Sicence School,Sun Yat- sen University,2,0.03094,0.97334,0.00045,0.00127,0.99774,0.97824,0.80981,0.45378,150,150,T,B,mate1 technical by mapping diff,illumina,hiseq_era,unknown,random_priming,unknown,sc,single_cell_droplet,10x,,China,2020-04-09,Larval,Larval,Whole Organism,All anatomical structures