run_metadata
119 rows where devstage_curation_coarse = "Multi-stage" and tissue_curation = "Kidney"
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| Link | 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 |
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| 32611 | 32611 | SRR29356860 | SRX24871764 | SRS21581236 | SRP513122 | PRJNA1122499 | An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy | GSE269547 | Transcriptome Analysis | Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL negative control zebrafish were immunized with LPP GFP mRNA immunized twice with two week intervals week 0 and 2.post 12 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group. | pubmed:39759874 | kidneys LPP immunized sample3 | GSM8321946 | source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing | kidneys LPP immunized sample3 | The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample | kidneys | For determination of the host immune response induced by mRNA vaccine immunization adult zebrafish AB strain 3 to 4 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL. post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. | The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. | tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized | GSM8321946 | GSM8321946: kidneys LPP immunized sample3; Danio rerio; RNA Seq | GSM8321946 r1 | GSM8321946 | 1 | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513122 | LPP3.R1.fq.gz LPP3.R2.fq.gz | fastq fastq | 6930388402.0 | 24028386.0 | GSM8321946 r1 | 0:144.22 1:144.21 | A:1741896633;C:1718081658;G:1728245814;T:1742156412;N:7885 | 144 | 144 | 1741896633 | 1718081658 | 1728245814 | 1742156412 | 7885 | SRX24871764 | SRS21581236 | SRA1896369 | Zhang Lab, Department of Microbiology, Fudan University | Zhang Lab, Department of Microbiology, Fudan University | 2 | 0.95561 | 0.95769 | 0.04873 | 0.04831 | 0.70556 | 0.705 | 0.50774 | 0.50807 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2024-06-11 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 32612 | 32612 | SRR29356861 | SRX24871763 | SRS21581235 | SRP513122 | PRJNA1122499 | An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy | GSE269547 | Transcriptome Analysis | Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL negative control zebrafish were immunized with LPP GFP mRNA immunized twice with two week intervals week 0 and 2.post 12 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group. | pubmed:39759874 | kidneys LPP immunized sample2 | GSM8321945 | source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing | kidneys LPP immunized sample2 | The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample | kidneys | For determination of the host immune response induced by mRNA vaccine immunization adult zebrafish AB strain 3 to 4 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL. post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. | The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. | tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized | GSM8321945 | GSM8321945: kidneys LPP immunized sample2; Danio rerio; RNA Seq | GSM8321945 r1 | GSM8321945 | 1 | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513122 | LPP2.R1.fq.gz LPP2.R2.fq.gz | fastq fastq | 6970934950.0 | 24067775.0 | GSM8321945 r1 | 0:144.82 1:144.82 | A:1750927361;C:1729272618;G:1740379247;T:1750348140;N:7584 | 144 | 144 | 1750927361 | 1729272618 | 1740379247 | 1750348140 | 7584 | SRX24871763 | SRS21581235 | SRA1896369 | Zhang Lab, Department of Microbiology, Fudan University | Zhang Lab, Department of Microbiology, Fudan University | 2 | 0.95562 | 0.95799 | 0.04685 | 0.04619 | 0.7067 | 0.7051 | 0.50198 | 0.49861 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2024-06-11 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 32613 | 32613 | SRR29356862 | SRX24871762 | SRS21581234 | SRP513122 | PRJNA1122499 | An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy | GSE269547 | Transcriptome Analysis | Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL negative control zebrafish were immunized with LPP GFP mRNA immunized twice with two week intervals week 0 and 2.post 12 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group. | pubmed:39759874 | kidneys LPP immunized sample1 | GSM8321944 | source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized|geo loc name:missing|collection date:missing | kidneys LPP immunized sample1 | The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample | kidneys | For determination of the host immune response induced by mRNA vaccine immunization adult zebrafish AB strain 3 to 4 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL. post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. | The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. | tissue:kidneys|cell type:whole cell immune cell|group:Vector control immunized group|treatment:2 dose of LPP GFP mRNA immunized | GSM8321944 | GSM8321944: kidneys LPP immunized sample1; Danio rerio; RNA Seq | GSM8321944 r1 | GSM8321944 | 1 | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513122 | LPP1.R1.fq.gz LPP1.R2.fq.gz | fastq fastq | 6946964789.0 | 24016865.0 | GSM8321944 r1 | 0:144.63 1:144.62 | A:1753009524;C:1714194993;G:1724914785;T:1754837582;N:7905 | 144 | 144 | 1753009524 | 1714194993 | 1724914785 | 1754837582 | 7905 | SRX24871762 | SRS21581234 | SRA1896369 | Zhang Lab, Department of Microbiology, Fudan University | Zhang Lab, Department of Microbiology, Fudan University | 2 | 0.94958 | 0.95243 | 0.05857 | 0.05785 | 0.70181 | 0.70074 | 0.5058 | 0.50491 | 150 | 145 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2024-06-11 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 32614 | 32614 | SRR29356863 | SRX24871761 | SRS21581233 | SRP513122 | PRJNA1122499 | An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy | GSE269547 | Transcriptome Analysis | Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL negative control zebrafish were immunized with LPP GFP mRNA immunized twice with two week intervals week 0 and 2.post 12 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group. | pubmed:39759874 | kidneys L3T immunized sample3 | GSM8321943 | source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing | kidneys L3T immunized sample3 | The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample | kidneys | For determination of the host immune response induced by mRNA vaccine immunization adult zebrafish AB strain 3 to 4 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL. post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. | The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. | tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized | GSM8321943 | GSM8321943: kidneys L3T immunized sample3; Danio rerio; RNA Seq | GSM8321943 r1 | GSM8321943 | 1 | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513122 | L3T3.R1.fq.gz L3T3.R2.fq.gz | fastq fastq | 7056672882.0 | 24530821.0 | GSM8321943 r1 | 0:143.84 1:143.83 | A:1768243408;C:1755016636;G:1763993995;T:1769411088;N:7755 | 143 | 143 | 1768243408 | 1755016636 | 1763993995 | 1769411088 | 7755 | SRX24871761 | SRS21581233 | SRA1896369 | Zhang Lab, Department of Microbiology, Fudan University | Zhang Lab, Department of Microbiology, Fudan University | 2 | 0.95045 | 0.95387 | 0.04717 | 0.04638 | 0.712 | 0.71125 | 0.52106 | 0.51883 | 106 | 106 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2024-06-11 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 32615 | 32615 | SRR29356864 | SRX24871760 | SRS21581232 | SRP513122 | PRJNA1122499 | An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy | GSE269547 | Transcriptome Analysis | Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL negative control zebrafish were immunized with LPP GFP mRNA immunized twice with two week intervals week 0 and 2.post 12 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group. | pubmed:39759874 | kidneys L3T immunized sample2 | GSM8321942 | source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing | kidneys L3T immunized sample2 | The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample | kidneys | For determination of the host immune response induced by mRNA vaccine immunization adult zebrafish AB strain 3 to 4 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL. post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. | The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. | tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized | GSM8321942 | GSM8321942: kidneys L3T immunized sample2; Danio rerio; RNA Seq | GSM8321942 r1 | GSM8321942 | 1 | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513122 | L3T2.R1.fq.gz L3T2.R2.fq.gz | fastq fastq | 7021833716.0 | 24281953.0 | GSM8321942 r1 | 0:144.59 1:144.59 | A:1777129692;C:1728181109;G:1738562098;T:1777953935;N:6882 | 144 | 144 | 1777129692 | 1728181109 | 1738562098 | 1777953935 | 6882 | SRX24871760 | SRS21581232 | SRA1896369 | Zhang Lab, Department of Microbiology, Fudan University | Zhang Lab, Department of Microbiology, Fudan University | 2 | 0.9484 | 0.9523 | 0.0532 | 0.05294 | 0.7052 | 0.70362 | 0.51282 | 0.50716 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2024-06-11 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 32616 | 32616 | SRR29356865 | SRX24871759 | SRS21581231 | SRP513122 | PRJNA1122499 | An mRNA vaccine induces antimycobacterial immunity by activating DNA damage repair and autophagy | GSE269547 | Transcriptome Analysis | Effective vaccines are urgently needed for the control of tuberculosis TB. Here we report that a mRNA TB vaccine is highly effective and exhibits both prophylactic and therapeutic activities in the zebrafish model of TB. Adult zebrafish immunized with the mRNA vaccine survived significantly longer than the DNA vaccine post Mycobacterium marinum challenge and post infection treatment with the mRNA vaccine drastically reduced the bacterial burden. The mRNA vaccine activated multiple DNA break repair systems that are essential for the normal development and function of adaptive immunity but not the canonical DNA damage responses that promote cell death demonstrating a profound connection between DNA damage repair and the activation of immune responses under physiological processes of immunization. Remarkably the mRNA vaccine induced autophagy in granulomas coinciding with bacterial killing and cell survival. Collectively these findings demonstrate that the mRNA vaccine elicits potent innate and adaptive immunity conferring effective host protection against mycobacterial challenge. Overall design: To understand the immune protective mechanisms mediated by the L3T vaccine we performed RNA seq analysis of kidneys isolated from zebrafish immunized with the mRNA vaccine and the LPP control. For mRNA vaccination mRNA candidate vaccines were injected with 1µg LPP mRNA in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL negative control zebrafish were immunized with LPP GFP mRNA immunized twice with two week intervals week 0 and 2.post 12 days of the final immunization kidneys from 5 zebrafish were pooled as one sample and three samples total 15 kidneys collected for each group were subjected to RNA seq analysis. Comparative gene expression profiling analysis of RNA seq data for L3T mRNA immunized group and its vector control immunized group LPP GFP mRNA immunized group. | pubmed:39759874 | kidneys L3T immunized sample1 | GSM8321941 | source name:kidneys|tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized|geo loc name:missing|collection date:missing | kidneys L3T immunized sample1 | The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired end reads were generated. Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads. The clean reads were mapped to the reference genome using HISAT2. FPKM of each gene was calculated andthe read counts of each gene were obtained by HTSeq count. PCA analysis were performed using Rv 3.2.0 to evaluate the biological duplication of samples. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files includes FPKM counts for each Sample | kidneys | For determination of the host immune response induced by mRNA vaccine immunization adult zebrafish AB strain 3 to 4 mpf 15 per group were immunized twice with two week intervals week 0 and 2. Dose volumes were 2 μL for intramuscular i.m immunization. 1μg L3T mRNA vaccine or LPP GFP mRNA were injected in the dorsal muscle using PV830 Pneumatic PicoPump microinjector World Precision Instruments Sarasota FL. post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer’s instructions. | The fish were reared in recirculating fish systems obtained from Qingdao Elvin Marine Technology Co. Ltd. Qingdao China and transferred to a flowthrough fish system for the infection experiment. Up to 10 fish were kept in a 3L tank and tanks were maintained under standard conditions for housing zebrafish water temperature ∼28°C pH ∼7.4 and conductivity ∼1500μS. | tissue:kidneys|cell type:whole cell immune cell|group:L3T immunized group|treatment:2 dose of L3T mRNA immunized | GSM8321941 | GSM8321941: kidneys L3T immunized sample1; Danio rerio; RNA Seq | GSM8321941 r1 | GSM8321941 | 1 | post 12 days of the secondary immunization kidneys of adult zebrafish were isolated and placed in 1mL Trizol for RNA extraction. Fifteen kidneys per group were collected and pooled as three samples.Total RNA was extracted using the TRIzol reagent Invitrogen CA USA according to themanufacturer's protocol. RNA purity and quantification were evaluated using the NanoDrop 2000spectrophotometer Thermo Scientific USA. RNA integrity was assessed using the Agilent 2100Bioanalyzer Agilent Technologies Santa Clara CA USA. Then the libraries were constructed usingVAHTS Universal V6 RNA seq Library Prep Kit according to the manufacturer's instructions. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP513122 | L3T1.R1.fq.gz L3T1.R2.fq.gz | fastq fastq | 6941829152.0 | 24117590.0 | GSM8321941 r1 | 0:143.92 1:143.91 | A:1756734172;C:1708781793;G:1718505186;T:1757800293;N:7708 | 143 | 143 | 1756734172 | 1708781793 | 1718505186 | 1757800293 | 7708 | SRX24871759 | SRS21581231 | SRA1896369 | Zhang Lab, Department of Microbiology, Fudan University | Zhang Lab, Department of Microbiology, Fudan University | 2 | 0.95019 | 0.95324 | 0.05797 | 0.05755 | 0.70013 | 0.69934 | 0.5137 | 0.5148 | 147 | 147 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | China | 2024-06-11 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 41873 | 41873 | SRR5320505 | SRX2619910 | SRS2029873 | SRP101556 | PRJNA378487 | Transcriptional profiling of the zebrafish proximal tubule | GSE95808 | Transcriptome Analysis | The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue | pubmed:31188030 | Morpholino 7 | GSM2526320 | tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted | Morpholino 7 | Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts. | larval kidney | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | line:tgPT::EGFP|genotype/variation:Hnf1b depleted | GSM2526320 | GSM2526320: Morpholino 7; Danio rerio; RNA Seq | GSM2526320 | 1 | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | GEO Accession:GSM2526320 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP101556 | C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-06-1-1_CTTGTAAT_L001_R2_001.fastq.gz | fastq fastq | 8670821250.0 | 34683285.0 | GSM2526320 r1 | 0:125 1:125 | A:2285357364;C:2049868144;G:2107192972;T:2225558024;N:2844746 | 125 | 125 | 2285357364 | 2049868144 | 2107192972 | 2225558024 | 2844746 | SRX2619910 | SRS2029873 | SRA543390 | GEO | Molecular Medicine and Pathology, University of Auckland | 2 | 0.96682 | 0.96763 | 0.08369 | 0.08426 | 0.69296 | 0.69493 | 0.47739 | 0.47931 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | New Zealand | 2017-03-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||||
| 41874 | 41874 | SRR5320504 | SRX2619909 | SRS2029872 | SRP101556 | PRJNA378487 | Transcriptional profiling of the zebrafish proximal tubule | GSE95808 | Transcriptome Analysis | The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue | pubmed:31188030 | Morpholino 5 | GSM2526319 | tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted | Morpholino 5 | Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts. | larval kidney | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | line:tgPT::EGFP|genotype/variation:Hnf1b depleted | GSM2526319 | GSM2526319: Morpholino 5; Danio rerio; RNA Seq | GSM2526319 | 1 | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | GEO Accession:GSM2526319 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP101556 | C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R1_001.fastq.gz C6H9AANXX-1531-05-1-1_CAGATCAT_L001_R2_001.fastq.gz | fastq fastq | 9864273500.0 | 39457094.0 | GSM2526319 r1 | 0:125 1:125 | A:2628741477;C:2304848464;G:2364915536;T:2562525014;N:3243009 | 125 | 125 | 2628741477 | 2304848464 | 2364915536 | 2562525014 | 3243009 | SRX2619909 | SRS2029872 | SRA543390 | GEO | Molecular Medicine and Pathology, University of Auckland | 2 | 0.96115 | 0.96161 | 0.10876 | 0.10854 | 0.67495 | 0.67616 | 0.45304 | 0.45767 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | New Zealand | 2017-03-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||||
| 41875 | 41875 | SRR5320503 | SRX2619908 | SRS2029871 | SRP101556 | PRJNA378487 | Transcriptional profiling of the zebrafish proximal tubule | GSE95808 | Transcriptome Analysis | The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue | pubmed:31188030 | Morpholino 4 | GSM2526318 | tissue:larval kidney|line:tgPT::EGFP|genotype/variation:Hnf1b depleted | Morpholino 4 | Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts. | larval kidney | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | line:tgPT::EGFP|genotype/variation:Hnf1b depleted | GSM2526318 | GSM2526318: Morpholino 4; Danio rerio; RNA Seq | GSM2526318 | 1 | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | GEO Accession:GSM2526318 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP101556 | C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R1_001.fastq.gz C6H9AANXX-1531-04-1-1_GCCAATAT_L001_R2_001.fastq.gz | fastq fastq | 8503939500.0 | 34015758.0 | GSM2526318 r1 | 0:125 1:125 | A:2251120561;C:2002327793;G:2052310864;T:2195401798;N:2778484 | 125 | 125 | 2251120561 | 2002327793 | 2052310864 | 2195401798 | 2778484 | SRX2619908 | SRS2029871 | SRA543390 | GEO | Molecular Medicine and Pathology, University of Auckland | 2 | 0.96344 | 0.96379 | 0.09973 | 0.09974 | 0.68043 | 0.68264 | 0.46613 | 0.46851 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | New Zealand | 2017-03-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||||
| 41876 | 41876 | SRR5320502 | SRX2619907 | SRS2029870 | SRP101556 | PRJNA378487 | Transcriptional profiling of the zebrafish proximal tubule | GSE95808 | Transcriptome Analysis | The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue | pubmed:31188030 | Control 3 | GSM2526317 | tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type | Control 3 | Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts. | larval kidney | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | line:tgPT::EGFP|genotype/variation:wild type | GSM2526317 | GSM2526317: Control 3; Danio rerio; RNA Seq | GSM2526317 | 1 | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | GEO Accession:GSM2526317 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP101556 | C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R1_001.fastq.gz C6H9AANXX-1531-03-1-1_ACAGTGAT_L001_R2_001.fastq.gz | fastq fastq | 9619758500.0 | 38479034.0 | GSM2526317 r1 | 0:125 1:125 | A:2561625595;C:2249183851;G:2312313710;T:2493482524;N:3152820 | 125 | 125 | 2561625595 | 2249183851 | 2312313710 | 2493482524 | 3152820 | SRX2619907 | SRS2029870 | SRA543390 | GEO | Molecular Medicine and Pathology, University of Auckland | 2 | 0.96067 | 0.96218 | 0.10832 | 0.10898 | 0.66675 | 0.66866 | 0.47609 | 0.47441 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | New Zealand | 2017-03-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||||
| 41877 | 41877 | SRR5320501 | SRX2619906 | SRS2029869 | SRP101556 | PRJNA378487 | Transcriptional profiling of the zebrafish proximal tubule | GSE95808 | Transcriptome Analysis | The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue | pubmed:31188030 | Control 2 | GSM2526316 | tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type | Control 2 | Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts. | larval kidney | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | line:tgPT::EGFP|genotype/variation:wild type | GSM2526316 | GSM2526316: Control 2; Danio rerio; RNA Seq | GSM2526316 | 1 | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | GEO Accession:GSM2526316 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP101556 | C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R1_001.fastq.gz C6H9AANXX-1531-02-1-1_TGACCAAT_L001_R2_001.fastq.gz | fastq fastq | 8939151000.0 | 35756604.0 | GSM2526316 r1 | 0:125 1:125 | A:2379909844;C:2090182914;G:2143061952;T:2323063658;N:2932632 | 125 | 125 | 2379909844 | 2090182914 | 2143061952 | 2323063658 | 2932632 | SRX2619906 | SRS2029869 | SRA543390 | GEO | Molecular Medicine and Pathology, University of Auckland | 2 | 0.96176 | 0.96203 | 0.10658 | 0.10717 | 0.67087 | 0.67194 | 0.45961 | 0.46137 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | New Zealand | 2017-03-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||||
| 41878 | 41878 | SRR5320500 | SRX2619905 | SRS2029868 | SRP101556 | PRJNA378487 | Transcriptional profiling of the zebrafish proximal tubule | GSE95808 | Transcriptome Analysis | The proximal tubules of the kidney carry out the bulk of solute reabsorption from the glomerular filtrate. They are also highly susceptible to damage as a result of diabetes or other syndromes that affect the kidney. The zebrafish embryonic/larval form of kidney the pronephros represents a simplified form of the mammalian organ yet is easier to access and manipulate. We have recently described the importance of Hnf1b as master regulator in pronephros differentiation. Here we establish a high resolution expression profile of isolated GFP labelled proximal tubules from 3 dpf zebrafish. To enrich the profile in genes of functional relevance during pronephros differentiation proximal tubules from Hnf1b depleted larvae were analysed in parallel and differential expression analysis was performed. Overall design: Examination of wild type and Hnf1b depleted proximal tubule tissue | pubmed:31188030 | Control 1 | GSM2526315 | tissue:larval kidney|line:tgPT::EGFP|genotype/variation:wild type | Control 1 | Read quality was assessed using FastQC. Reads were mapped and quantified together using Salmon ver. 0.8.2. Differential gene expression analysis was carried out using DESeq2 ver. 1.20.0. Genome build: GRCz11 transcriptome Supplementary files format and content: raw counts.csv: Comma separated text file includes gene expression for each sample non normalised raw counts. | larval kidney | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | line:tgPT::EGFP|genotype/variation:wild type | GSM2526315 | GSM2526315: Control 1; Danio rerio; RNA Seq | GSM2526315 | 1 | Approximately 50 dpf 3 dpf larvae were collected in 2 ml eppendorf tubes the E3 embryo medium removed replaced by 10 mM DTT Sigma in E3 plus 0.2% tricaine and incubated for 1hr at RT. DTT preincubation is necessary to degrade the protective mucus layer around the larvae and enable larval tissue digestion. Larvae were washed twice in Ca2+ and Mg2+ containing PBS and subsequently incubated in 5 mg/ml collagenase I Gibco Ca2+/Mg2+ PBS for 3 hrs at 32C. Collagenase was removed by gently washing the larvae twice in DMEM containing 10% FBS. Using a 1000 ul pipette the larvae were gently titurated and transferred into a 3 cm petri dish under a dissecting microscope equipped with epifluorescence. At this stage the larvae are disintegrated into chunks of tissue with intact bright GFP positive proximal tubules floating free of adhering tissue. Pure proximal tubules were collected and placed in lysis buffer of the NucleoSpin RNA XS kit Macherey Nagel and instantly frozen to 80C until further processing. RNA libraries were prepared using the TruSeq stranded total RNA kit for sequencing using standard Illumina protocols | GEO Accession:GSM2526315 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP101556 | C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R1_001.fastq.gz C6H9AANXX-1531-01-1-1_CGATGTAT_L001_R2_001.fastq.gz | fastq fastq | 9579790250.0 | 38319161.0 | GSM2526315 r1 | 0:125 1:125 | A:2520690618;C:2269535412;G:2326632146;T:2459796830;N:3135244 | 125 | 125 | 2520690618 | 2269535412 | 2326632146 | 2459796830 | 3135244 | SRX2619905 | SRS2029868 | SRA543390 | GEO | Molecular Medicine and Pathology, University of Auckland | 2 | 0.96456 | 0.96615 | 0.08928 | 0.09003 | 0.68373 | 0.6856 | 0.46544 | 0.46416 | 125 | 125 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | unknown | unknown | New Zealand | 2017-03-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||||
| 43499 | 43499 | SRR6020425 | SRX3171489 | SRS2501298 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Trans | GSM2776984 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776984 | GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq | GSM2776984 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776984 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Trans_p01_R1.fastq.gz R4_wkm_Trans_p01_R2.fastq.gz | fastq fastq | 3927170013.0 | 26023917.0 | GSM2776984 r1 | 0:75.41 1:75.50 | A:1129996659;C:572501533;G:611837437;T:1612813099;N:21285 | 75 | 75 | 1129996659 | 572501533 | 611837437 | 1612813099 | 21285 | SRX3171489 | SRS2501298 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.32239 | 0.87342 | 0.20343 | 0.36809 | 0.95722 | 0.82919 | 0.49895 | 0.48491 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43500 | 43500 | SRR6020426 | SRX3171489 | SRS2501298 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Trans | GSM2776984 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776984 | GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq | GSM2776984 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776984 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Trans_p02_R1.fastq.gz R4_wkm_Trans_p02_R2.fastq.gz | fastq fastq | 4030497815.0 | 26709253.0 | GSM2776984 r2 | 0:75.41 1:75.49 | A:1162066088;C:581519292;G:627111524;T:1659778815;N:22096 | 75 | 75 | 1162066088 | 581519292 | 627111524 | 1659778815 | 22096 | SRX3171489 | SRS2501298 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.33073 | 0.87349 | 0.21896 | 0.35721 | 0.96337 | 0.82895 | 0.48607 | 0.49848 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43501 | 43501 | SRR6020427 | SRX3171489 | SRS2501298 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Trans | GSM2776984 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776984 | GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq | GSM2776984 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776984 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Trans_p03_R1.fastq.gz R4_wkm_Trans_p03_R2.fastq.gz | fastq fastq | 3631053942.0 | 24060145.0 | GSM2776984 r3 | 0:75.46 1:75.46 | A:1043256309;C:532046798;G:537476503;T:1518171924;N:102408 | 75 | 75 | 1043256309 | 532046798 | 537476503 | 1518171924 | 102408 | SRX3171489 | SRS2501298 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.32814 | 0.80344 | 0.24082 | 0.39956 | 0.96319 | 0.85831 | 0.49813 | 0.5276 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43502 | 43502 | SRR6020428 | SRX3171489 | SRS2501298 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Trans | GSM2776984 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776984 | GSM2776984: R4 wkm Trans; Danio rerio; RNA Seq | GSM2776984 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776984 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Trans_p04_R1.fastq.gz R4_wkm_Trans_p04_R2.fastq.gz | fastq fastq | 4828053523.0 | 31991602.0 | GSM2776984 r4 | 0:75.42 1:75.50 | A:1401132307;C:703203743;G:750174359;T:1973515875;N:27239 | 75 | 75 | 1401132307 | 703203743 | 750174359 | 1973515875 | 27239 | SRX3171489 | SRS2501298 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.3505 | 0.86169 | 0.26499 | 0.42336 | 0.96027 | 0.8182 | 0.49142 | 0.49842 | 76 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43503 | 43503 | SRR6020421 | SRX3171488 | SRS2501297 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Scar | GSM2776983 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776983 | GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq | GSM2776983 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776983 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Scar_p01_R1.fastq.gz R4_wkm_Scar_p01_R2.fastq.gz | fastq fastq | 614245655.0 | 4041684.0 | GSM2776983 r1 | 0:75.99 1:75.99 | A:107048177;C:178914249;G:231725646;T:96554319;N:3264 | 75 | 75 | 107048177 | 178914249 | 231725646 | 96554319 | 3264 | SRX3171488 | SRS2501297 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 4e-05 | 0.00013 | 1e-05 | 8e-05 | 0.99997 | 0.99991 | 1.0 | 0.875 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43504 | 43504 | SRR6020422 | SRX3171488 | SRS2501297 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Scar | GSM2776983 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776983 | GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq | GSM2776983 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776983 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Scar_p02_R1.fastq.gz R4_wkm_Scar_p02_R2.fastq.gz | fastq fastq | 817459087.0 | 5378786.0 | GSM2776983 r2 | 0:75.99 1:75.99 | A:143806910;C:238933705;G:307736025;T:126978347;N:4100 | 75 | 75 | 143806910 | 238933705 | 307736025 | 126978347 | 4100 | SRX3171488 | SRS2501297 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 3e-05 | 4e-05 | 1e-05 | 1e-05 | 0.99995 | 0.99995 | 0.5 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43505 | 43505 | SRR6020423 | SRX3171488 | SRS2501297 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Scar | GSM2776983 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776983 | GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq | GSM2776983 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776983 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Scar_p03_R1.fastq.gz R4_wkm_Scar_p03_R2.fastq.gz | fastq fastq | 3981890019.0 | 26204072.0 | GSM2776983 r3 | 0:75.98 1:75.97 | A:703462533;C:1148861227;G:1510546877;T:618921234;N:98148 | 75 | 75 | 703462533 | 1148861227 | 1510546877 | 618921234 | 98148 | SRX3171488 | SRS2501297 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 7e-05 | 9e-05 | 4e-05 | 4e-05 | 0.99993 | 0.99987 | 0.25 | 0.42857 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43506 | 43506 | SRR6020424 | SRX3171488 | SRS2501297 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R4 wkm Scar | GSM2776983 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | R4 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R4|tissue:whole kidney marrow|sorted plates:4 | GSM2776983 | GSM2776983: R4 wkm Scar; Danio rerio; RNA Seq | GSM2776983 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776983 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R4_wkm_Scar_p04_R1.fastq.gz R4_wkm_Scar_p04_R2.fastq.gz | fastq fastq | 561112602.0 | 3692109.0 | GSM2776983 r4 | 0:75.98 1:75.99 | A:98682129;C:162936789;G:209922290;T:89568564;N:2830 | 75 | 75 | 98682129 | 162936789 | 209922290 | 89568564 | 2830 | SRX3171488 | SRS2501297 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00016 | 9e-05 | 4e-05 | 5e-05 | 0.99973 | 0.99993 | 0.72727 | 0.75 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43565 | 43565 | SRR6020354 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p01_R2.fastq.gz R2_wkm_Trans_p01_R1.fastq.gz | fastq fastq | 9024550362.0 | 59819416.0 | GSM2776964 r1 | 0:75.43 1:75.43 | A:2680475382;C:1320224241;G:1470728320;T:3553005800;N:116619 | 75 | 75 | 2680475382 | 1320224241 | 1470728320 | 3553005800 | 116619 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.3361 | 0.6658 | 0.26022 | 0.30025 | 0.9655 | 0.84861 | 0.54877 | 0.53502 | 73 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43566 | 43566 | SRR6020355 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p02_R1.fastq.gz R2_wkm_Trans_p02_R2.fastq.gz | fastq fastq | 6846456986.0 | 45296050.0 | GSM2776964 r2 | 0:75.58 1:75.57 | A:1794290868;C:1266097894;G:1480877558;T:2305103809;N:86857 | 75 | 75 | 1794290868 | 1266097894 | 1480877558 | 2305103809 | 86857 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.12369 | 0.58191 | 0.08122 | 0.21507 | 0.96917 | 0.86478 | 0.54436 | 0.52833 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43567 | 43567 | SRR6020356 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p04_R1.fastq.gz R2_wkm_Trans_p04_R2.fastq.gz | fastq fastq | 6833024281.0 | 45038138.0 | GSM2776964 r3 | 0:75.92 1:75.80 | A:1377999605;C:1844050318;G:2309866401;T:1300399227;N:708730 | 75 | 75 | 1377999605 | 1844050318 | 2309866401 | 1300399227 | 708730 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.01228 | 0.03967 | 0.01047 | 0.02854 | 0.996 | 0.98784 | 0.46886 | 0.40014 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43568 | 43568 | SRR6020357 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p05_R1.fastq.gz R2_wkm_Trans_p05_R2.fastq.gz | fastq fastq | 10064318519.0 | 66330889.0 | GSM2776964 r4 | 0:75.93 1:75.80 | A:2012776438;C:2737247628;G:3409080553;T:1904157367;N:1056533 | 75 | 75 | 2012776438 | 2737247628 | 3409080553 | 1904157367 | 1056533 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.01861 | 0.04126 | 0.01632 | 0.03024 | 0.99537 | 0.9852 | 0.46531 | 0.52808 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43569 | 43569 | SRR6020358 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p06_R1.fastq.gz R2_wkm_Trans_p06_R2.fastq.gz | fastq fastq | 6687331360.0 | 44108617.0 | GSM2776964 r5 | 0:75.86 1:75.75 | A:1437098890;C:1744557843;G:2166182975;T:1338781574;N:710078 | 75 | 75 | 1437098890 | 1744557843 | 2166182975 | 1338781574 | 710078 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.02427 | 0.05957 | 0.02134 | 0.04215 | 0.99504 | 0.98561 | 0.59024 | 0.56702 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43570 | 43570 | SRR6020359 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p07_R1.fastq.gz R2_wkm_Trans_p07_R2.fastq.gz | fastq fastq | 5153832004.0 | 34073366.0 | GSM2776964 r6 | 0:75.66 1:75.60 | A:1326888770;C:1102939496;G:1274553839;T:1448364985;N:1084914 | 75 | 75 | 1326888770 | 1102939496 | 1274553839 | 1448364985 | 1084914 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.1589 | 0.37012 | 0.13594 | 0.2937 | 0.96008 | 0.89796 | 0.53952 | 0.50866 | 76 | 75 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43571 | 43571 | SRR6020360 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p08_R1.fastq.gz R2_wkm_Trans_p08_R2.fastq.gz | fastq fastq | 6115949904.0 | 40453679.0 | GSM2776964 r7 | 0:75.63 1:75.55 | A:1597313172;C:1289666072;G:1493416158;T:1734258580;N:1295922 | 75 | 75 | 1597313172 | 1289666072 | 1493416158 | 1734258580 | 1295922 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.13807 | 0.341 | 0.11368 | 0.25445 | 0.96546 | 0.90859 | 0.52718 | 0.49692 | 76 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43572 | 43572 | SRR6020361 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p09_R1.fastq.gz R2_wkm_Trans_p09_R2.fastq.gz | fastq fastq | 5237730043.0 | 34642054.0 | GSM2776964 r8 | 0:75.63 1:75.57 | A:1366106800;C:1100303416;G:1291870046;T:1478328279;N:1121502 | 75 | 75 | 1366106800 | 1100303416 | 1291870046 | 1478328279 | 1121502 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.12743 | 0.30857 | 0.10066 | 0.19993 | 0.96899 | 0.91999 | 0.50164 | 0.55176 | 75 | 76 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43573 | 43573 | SRR6020362 | SRX3171469 | SRS2501278 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Trans | GSM2776964 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776964 | GSM2776964: R2 wkm Trans; Danio rerio; RNA Seq | GSM2776964 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776964 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Trans_p10_R2.fastq.gz R2_wkm_Trans_p10_R1.fastq.gz | fastq fastq | 5966158980.0 | 39481315.0 | GSM2776964 r9 | 0:75.59 1:75.53 | A:1608448002;C:1182029002;G:1349064196;T:1825357615;N:1260165 | 75 | 75 | 1608448002 | 1182029002 | 1349064196 | 1825357615 | 1260165 | SRX3171469 | SRS2501278 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.14278 | 0.40505 | 0.11298 | 0.25782 | 0.96169 | 0.88933 | 0.53335 | 0.51935 | 76 | 75 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43574 | 43574 | SRR6020345 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p01_R1.fastq.gz R2_wkm_Scar_p01_R2.fastq.gz | fastq fastq | 1684853042.0 | 11092789.0 | GSM2776963 r1 | 0:75.97 1:75.92 | A:295001511;C:489169550;G:629447507;T:271215194;N:19280 | 75 | 75 | 295001511 | 489169550 | 629447507 | 271215194 | 19280 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00026 | 0.00111 | 0.00021 | 0.00081 | 0.99983 | 0.99931 | 0.625 | 0.5 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43575 | 43575 | SRR6020346 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p02_R1.fastq.gz R2_wkm_Scar_p02_R2.fastq.gz | fastq fastq | 2167767595.0 | 14269042.0 | GSM2776963 r2 | 0:75.97 1:75.95 | A:393119574;C:622441995;G:803855479;T:348326899;N:23648 | 75 | 75 | 393119574 | 622441995 | 803855479 | 348326899 | 23648 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00015 | 4e-05 | 0.00012 | 2e-05 | 0.99997 | 0.99997 | 0.0 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43576 | 43576 | SRR6020347 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p04_R1.fastq.gz R2_wkm_Scar_p04_R2.fastq.gz | fastq fastq | 949039352.0 | 6246899.0 | GSM2776963 r3 | 0:75.98 1:75.94 | A:168664399;C:275210713;G:354697026;T:150353667;N:113547 | 75 | 75 | 168664399 | 275210713 | 354697026 | 150353667 | 113547 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 5e-05 | 1e-05 | 4e-05 | 0.0 | 0.99997 | 1.0 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||||
| 43577 | 43577 | SRR6020348 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p05_R1.fastq.gz R2_wkm_Scar_p05_R2.fastq.gz | fastq fastq | 708086378.0 | 4660800.0 | GSM2776963 r4 | 0:75.98 1:75.94 | A:125487931;C:204868898;G:265817122;T:111841010;N:71417 | 75 | 75 | 125487931 | 204868898 | 265817122 | 111841010 | 71417 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 5e-05 | 0.0 | 3e-05 | 0.0 | 0.99997 | 1.0 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||||
| 43578 | 43578 | SRR6020349 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p06_R1.fastq.gz R2_wkm_Scar_p06_R2.fastq.gz | fastq fastq | 1334977556.0 | 8786739.0 | GSM2776963 r5 | 0:75.98 1:75.95 | A:236705935;C:386768904;G:500728970;T:210637790;N:135957 | 75 | 75 | 236705935 | 386768904 | 500728970 | 210637790 | 135957 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 2e-05 | 0.0 | 1e-05 | 0.0 | 0.99997 | 1.0 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||||
| 43579 | 43579 | SRR6020350 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p07_R1.fastq.gz R2_wkm_Scar_p07_R2.fastq.gz | fastq fastq | 560151517.0 | 3686527.0 | GSM2776963 r6 | 0:75.99 1:75.96 | A:99216542;C:162559282;G:209970335;T:88295033;N:110325 | 75 | 75 | 99216542 | 162559282 | 209970335 | 88295033 | 110325 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00013 | 0.00031 | 0.0001 | 0.00024 | 0.99989 | 0.99977 | 0.4 | 0.18181 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43580 | 43580 | SRR6020351 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p08_R1.fastq.gz R2_wkm_Scar_p08_R2.fastq.gz | fastq fastq | 581077562.0 | 3824465.0 | GSM2776963 r7 | 0:75.98 1:75.95 | A:103035022;C:167783256;G:218182356;T:91955266;N:121662 | 75 | 75 | 103035022 | 167783256 | 218182356 | 91955266 | 121662 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00012 | 0.00017 | 0.0001 | 0.0001 | 0.99995 | 0.99983 | 0.33333 | 0.75 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43581 | 43581 | SRR6020352 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p09_R1.fastq.gz R2_wkm_Scar_p09_R2.fastq.gz | fastq fastq | 540845179.0 | 3559589.0 | GSM2776963 r8 | 0:75.98 1:75.96 | A:95821696;C:156515054;G:202433894;T:85962271;N:112264 | 75 | 75 | 95821696 | 156515054 | 202433894 | 85962271 | 112264 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00022 | 0.00026 | 0.00017 | 0.00017 | 0.99985 | 0.99975 | 0.42857 | 0.61538 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43582 | 43582 | SRR6020353 | SRX3171468 | SRS2501277 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R2 wkm Scar | GSM2776963 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | R2 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R2|tissue:whole kidney marrow|sorted plates:9 | GSM2776963 | GSM2776963: R2 wkm Scar; Danio rerio; RNA Seq | GSM2776963 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776963 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R2_wkm_Scar_p10_R1.fastq.gz R2_wkm_Scar_p10_R2.fastq.gz | fastq fastq | 839350049.0 | 5524195.0 | GSM2776963 r9 | 0:75.98 1:75.96 | A:148919223;C:243407956;G:314166938;T:132682976;N:172956 | 75 | 75 | 148919223 | 243407956 | 314166938 | 132682976 | 172956 | SRX3171468 | SRS2501277 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00026 | 0.00065 | 0.00022 | 0.00044 | 0.99987 | 0.99935 | 0.5 | 0.69696 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43583 | 43583 | SRR6020335 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p01_R1.fastq.gz R1_wkm_Trans_p01_R2.fastq.gz | fastq fastq | 5973924896.0 | 39414942.0 | GSM2776962 r1 | 0:75.90 1:75.67 | A:1246713886;C:1600299713;G:1930846373;T:1194812009;N:1252915 | 75 | 75 | 1246713886 | 1600299713 | 1930846373 | 1194812009 | 1252915 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.01167 | 0.032 | 0.00909 | 0.02214 | 0.99644 | 0.98829 | 0.31168 | 0.44038 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43584 | 43584 | SRR6020336 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p10_R1.fastq.gz R1_wkm_Trans_p10_R2.fastq.gz | fastq fastq | 2617289615.0 | 17271557.0 | GSM2776962 r10 | 0:75.82 1:75.72 | A:567948720;C:650310169;G:793147028;T:605454241;N:429457 | 75 | 75 | 567948720 | 650310169 | 793147028 | 605454241 | 429457 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.0644 | 0.15708 | 0.05669 | 0.13057 | 0.98198 | 0.94714 | 0.50177 | 0.51068 | 76 | 76 | B | B | mate1-mate2 similar by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43585 | 43585 | SRR6020337 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p02_R1.fastq.gz R1_wkm_Trans_p02_R2.fastq.gz | fastq fastq | 7594280551.0 | 50128244.0 | GSM2776962 r2 | 0:75.86 1:75.63 | A:1634649789;C:1975593425;G:2355482941;T:1626855827;N:1698569 | 75 | 75 | 1634649789 | 1975593425 | 2355482941 | 1626855827 | 1698569 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.01418 | 0.05132 | 0.01052 | 0.03283 | 0.99411 | 0.98096 | 0.42315 | 0.47699 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43586 | 43586 | SRR6020338 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p03_R1.fastq.gz R1_wkm_Trans_p03_R2.fastq.gz | fastq fastq | 10033302083.0 | 66227671.0 | GSM2776962 r3 | 0:75.87 1:75.63 | A:2174708635;C:2640912986;G:3104545578;T:2110890445;N:2244439 | 75 | 75 | 2174708635 | 2640912986 | 3104545578 | 2110890445 | 2244439 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.01909 | 0.05761 | 0.01497 | 0.0388 | 0.99527 | 0.98559 | 0.62157 | 0.383 | 75 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43587 | 43587 | SRR6020339 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p04_R1.fastq.gz R1_wkm_Trans_p04_R2.fastq.gz | fastq fastq | 6711074817.0 | 44294742.0 | GSM2776962 r4 | 0:75.86 1:75.65 | A:1427276784;C:1758105877;G:2110503657;T:1413707482;N:1481017 | 75 | 75 | 1427276784 | 1758105877 | 2110503657 | 1413707482 | 1481017 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.01603 | 0.04728 | 0.01155 | 0.02826 | 0.99537 | 0.98275 | 0.40869 | 0.46908 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43588 | 43588 | SRR6020340 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p05_R1.fastq.gz R1_wkm_Trans_p05_R2.fastq.gz | fastq fastq | 5218937446.0 | 34471555.0 | GSM2776962 r5 | 0:75.81 1:75.59 | A:1215811466;C:1256980753;G:1501056299;T:1243910449;N:1178479 | 75 | 75 | 1215811466 | 1256980753 | 1501056299 | 1243910449 | 1178479 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.02337 | 0.08686 | 0.0188 | 0.05946 | 0.99561 | 0.98139 | 0.29979 | 0.497 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43589 | 43589 | SRR6020341 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p06_R1.fastq.gz R1_wkm_Trans_p06_R2.fastq.gz | fastq fastq | 6108807000.0 | 40436337.0 | GSM2776962 r6 | 0:75.61 1:75.47 | A:1673719828;C:1137235460;G:1275308369;T:2021133061;N:1410282 | 75 | 75 | 1673719828 | 1137235460 | 1275308369 | 2021133061 | 1410282 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.10437 | 0.31204 | 0.0749 | 0.16508 | 0.97881 | 0.92991 | 0.45043 | 0.51006 | 75 | 75 | T | B | mate1 technical by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43590 | 43590 | SRR6020342 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p07_R1.fastq.gz R1_wkm_Trans_p07_R2.fastq.gz | fastq fastq | 4731732871.0 | 31235538.0 | GSM2776962 r7 | 0:75.80 1:75.69 | A:1076749811;C:1116149409;G:1331817067;T:1206252219;N:764365 | 75 | 75 | 1076749811 | 1116149409 | 1331817067 | 1206252219 | 764365 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.06387 | 0.1773 | 0.05441 | 0.13368 | 0.98293 | 0.93825 | 0.51607 | 0.52472 | 75 | 75 | B | B | mate1-mate2 similar by mapping diff | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43591 | 43591 | SRR6020343 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p08_R1.fastq.gz R1_wkm_Trans_p08_R2.fastq.gz | fastq fastq | 4880262283.0 | 32178172.0 | GSM2776962 r8 | 0:75.90 1:75.76 | A:984048995;C:1311633495;G:1623325534;T:960451784;N:802475 | 75 | 75 | 984048995 | 1311633495 | 1623325534 | 960451784 | 802475 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.01625 | 0.04758 | 0.01254 | 0.03334 | 0.99119 | 0.97512 | 0.51741 | 0.48393 | 75 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43592 | 43592 | SRR6020344 | SRX3171467 | SRS2501276 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Trans | GSM2776962 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Trans | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776962 | GSM2776962: R1 wkm Trans; Danio rerio; RNA Seq | GSM2776962 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776962 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Trans_p09_R1.fastq.gz R1_wkm_Trans_p09_R2.fastq.gz | fastq fastq | 2281506515.0 | 15040814.0 | GSM2776962 r9 | 0:75.91 1:75.78 | A:455027935;C:614063661;G:762091600;T:449957278;N:366041 | 75 | 75 | 455027935 | 614063661 | 762091600 | 449957278 | 366041 | SRX3171467 | SRS2501276 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.02501 | 0.0603 | 0.022 | 0.04691 | 0.99159 | 0.97228 | 0.50712 | 0.52872 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43593 | 43593 | SRR6020325 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p01_R1.fastq.gz R1_wkm_Scar_p01_R2.fastq.gz | fastq fastq | 1160781646.0 | 7644126.0 | GSM2776961 r1 | 0:75.98 1:75.87 | A:206133465;C:337727978;G:433057561;T:183619190;N:243452 | 75 | 75 | 206133465 | 337727978 | 433057561 | 183619190 | 243452 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 1e-05 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||||
| 43594 | 43594 | SRR6020326 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p10_R1.fastq.gz R1_wkm_Scar_p10_R2.fastq.gz | fastq fastq | 444321370.0 | 2925523.0 | GSM2776961 r10 | 0:75.98 1:75.89 | A:78895877;C:128614562;G:165020269;T:71718452;N:72210 | 75 | 75 | 78895877 | 128614562 | 165020269 | 71718452 | 72210 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00013 | 0.00022 | 8e-05 | 0.0001 | 0.99995 | 0.99969 | 0.0 | 0.4375 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43595 | 43595 | SRR6020327 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p02_R1.fastq.gz R1_wkm_Scar_p02_R2.fastq.gz | fastq fastq | 1118531897.0 | 7366750.0 | GSM2776961 r2 | 0:75.98 1:75.85 | A:199272195;C:323746349;G:416605188;T:178669664;N:238501 | 75 | 75 | 199272195 | 323746349 | 416605188 | 178669664 | 238501 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 2e-05 | 9e-05 | 0.0 | 2e-05 | 0.99997 | 0.99987 | 1.0 | 0.28571 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43596 | 43596 | SRR6020328 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p03_R1.fastq.gz R1_wkm_Scar_p03_R2.fastq.gz | fastq fastq | 842900122.0 | 5552138.0 | GSM2776961 r3 | 0:75.98 1:75.83 | A:149698513;C:244376973;G:313988330;T:134655045;N:181261 | 75 | 75 | 149698513 | 244376973 | 313988330 | 134655045 | 181261 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 5e-05 | 9e-05 | 2e-05 | 4e-05 | 0.99993 | 0.99989 | 0.66666 | 0.8 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43597 | 43597 | SRR6020329 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p04_R1.fastq.gz R1_wkm_Scar_p04_R2.fastq.gz | fastq fastq | 983580857.0 | 6477811.0 | GSM2776961 r4 | 0:75.98 1:75.86 | A:173458414;C:285222602;G:367968109;T:156722927;N:208805 | 75 | 75 | 173458414 | 285222602 | 367968109 | 156722927 | 208805 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 1e-05 | 0.0 | 0.0 | 0.0 | 1.0 | 1.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||||
| 43598 | 43598 | SRR6020330 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p05_R1.fastq.gz R1_wkm_Scar_p05_R2.fastq.gz | fastq fastq | 542048001.0 | 3570304.0 | GSM2776961 r5 | 0:75.98 1:75.84 | A:96887298;C:156549850;G:201875058;T:86619073;N:116722 | 75 | 75 | 96887298 | 156549850 | 201875058 | 86619073 | 116722 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 5e-05 | 1e-05 | 3e-05 | 0.0 | 0.99997 | 0.99997 | 0.0 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43599 | 43599 | SRR6020331 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p06_R1.fastq.gz R1_wkm_Scar_p06_R2.fastq.gz | fastq fastq | 1331503316.0 | 8770302.0 | GSM2776961 r6 | 0:75.98 1:75.84 | A:239821115;C:383865311;G:491153102;T:216395981;N:267807 | 75 | 75 | 239821115 | 383865311 | 491153102 | 216395981 | 267807 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00035 | 0.00029 | 0.00023 | 0.00015 | 0.99989 | 0.99973 | 0.125 | 0.46153 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43600 | 43600 | SRR6020332 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p07_R1.fastq.gz R1_wkm_Scar_p07_R2.fastq.gz | fastq fastq | 443058723.0 | 2917225.0 | GSM2776961 r7 | 0:75.99 1:75.89 | A:78132383;C:128408112;G:164997328;T:71447465;N:73435 | 75 | 75 | 78132383 | 128408112 | 164997328 | 71447465 | 73435 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00011 | 0.00017 | 8e-05 | 0.00014 | 0.99993 | 0.99991 | 0.25 | 0.5 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43601 | 43601 | SRR6020333 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p08_R1.fastq.gz R1_wkm_Scar_p08_R2.fastq.gz | fastq fastq | 460136778.0 | 3029705.0 | GSM2776961 r8 | 0:75.99 1:75.89 | A:81219078;C:133929839;G:170892657;T:74024644;N:70560 | 75 | 75 | 81219078 | 133929839 | 170892657 | 74024644 | 70560 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 2e-05 | 2e-05 | 1e-05 | 0.0 | 0.99997 | 0.99997 | 0.0 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43602 | 43602 | SRR6020334 | SRX3171466 | SRS2501275 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | R1 wkm Scar | GSM2776961 | source name:wkm single cells|cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | R1 wkm Scar | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence. In transcriptome libraries first read contains UMI 6 first nucleotides and cell barcode from 7 to 14 nucleotides and second reads contains biological information. Second reads with a valid cell barcode in corresponding first read are mapped to the reference transcriptome. Genome build: In scar libraries: eGFP sequence extended with ERCC92; In transcriptome libraries: Danio rerio assembly Zv9 ensemble 74 extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern. *transcriptome.txt.gz: tabular separated files with transcript count rows per cell columns. Cells in each file are labeled according to barcode ID plate organ and fish of origin. *tsne.txt.gz: tsne map coordinates obtained post running RaceID Grun D. et al. Nature 525 251 255 2015 and cell type assigned to each cell. Cells are labeled as in the *transcriptome.txt.gz files. | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:mRNA|FISH id:R1|tissue:whole kidney marrow|sorted plates:10 | GSM2776961 | GSM2776961: R1 wkm Scar; Danio rerio; RNA Seq | GSM2776961 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2776961 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | R1_wkm_Scar_p09_R1.fastq.gz R1_wkm_Scar_p09_R2.fastq.gz | fastq fastq | 495182451.0 | 3261129.0 | GSM2776961 r9 | 0:75.98 1:75.87 | A:89479589;C:142929535;G:181791653;T:80902228;N:79446 | 75 | 75 | 89479589 | 142929535 | 181791653 | 80902228 | 79446 | SRX3171466 | SRS2501275 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00037 | 0.00149 | 0.00026 | 0.00096 | 0.99969 | 0.99855 | 0.22222 | 0.3647 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-09-08 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 43634 | 43634 | SRR5961758 | SRX3119870 | SRS2454729 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | P1 wkm Scars | GSM2752193 | source name:wkm single cells|cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2 | P1 wkm Scars | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2 | GSM2752193 | GSM2752193: P1 wkm Scars; Danio rerio; RNA Seq | GSM2752193 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2752193 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | P1_wkm_Scar_p01_R1.fastq.gz P1_wkm_Scar_p01_R2.fastq.gz | fastq fastq | 995569951.0 | 6550623.0 | GSM2752193 r1 | 0:75.99 1:75.99 | A:179447412;C:292592664;G:370193004;T:153293464;N:43407 | 75 | 75 | 179447412 | 292592664 | 370193004 | 153293464 | 43407 | SRX3119870 | SRS2454729 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00015 | 4e-05 | 0.00013 | 3e-05 | 0.99997 | 1.0 | 0.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-08-23 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||||
| 43635 | 43635 | SRR5961759 | SRX3119870 | SRS2454729 | SRP116018 | PRJNA399711 | Whole organism clone tracing using single cell sequencing | GSE102990 | Transcriptome Analysis | We present ScarTrace a single cell sequencing strategy that allows us to simultaneously quantify information on clonal history and cell type for thousands of single cells obtained from different organs from adult zebrafish. Using this approach we show that all blood cells types in the kidney marrow arise from a small set of multipotent embryonic. In contrast we find that cells in the eyes brain and caudal tail fin arise from many embryonic progenitors which are more restricted and produce specific cell types in the adult tissue. Next we use ScarTrace to explore when embryonic cells commit to forming either left or right organs using the eyes and brain as a model system. Lastly we monitor regeneration of the caudal tail fin and identify a subpopulation of resident macrophages that have a clonal origin that is distinct from other blood cell types. Overall design: Single cell sequencing data from cells isolated from zebrafish organs whole kidney marrow forebrain hindbrain left eye right eye left midbrain right midbrain and regenerated fin. For each cell we provide libraries with transcritpome and with clonal information respectively. | pubmed:29590089 | P1 wkm Scars | GSM2752193 | source name:wkm single cells|cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2 | P1 wkm Scars | In scar libraries first read contains cell barcode 8 first nucleotides and second read contains the scar. Second reads with a valid cell barcode in first read are mapped to the reference GFP sequence and only reads that map to GFP and contain the reverse PCR primer with at least three mismatches are taken into account for downstream analysis. These reads are mapped again using the pairwise2.align.globalms function from Biopython with match score set to 1; mismatch score to 0.25; open gap penalty to 1; and extending gap penalty to 0.1. Subsequently we pool scars per cell and by cigar. For each scar library a double Gaussian is fitted to the distribution of reads per cell to find the threshold in number of reads to select cells. Next scars were filtered according to their frequency of detection in the full library. For each cell reads are normalized to 100 and scars representing less than 3.5% are removed. Genome build: In scar libraries: eGFP sequence extended with ERCC92 Supplementary files format and content: *scarclones.txt: tabular separated files with scar percentage columns per cell rows. Cells from the same fish have been named according to barcode ID plate and organ of origin. Last column hclust referes to ID for the clone cells sharing hclust label have the same scar pattern | wkm single cells | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | cas9 injection:protein|FISH id:P1|tissue:whole kidney marrow|sorted plates:2 | GSM2752193 | GSM2752193: P1 wkm Scars; Danio rerio; RNA Seq | GSM2752193 | 1 | post organ isolation live single cells are sorted into 384 well plates containing mineral oil uniquely barcoded cell specific primers for independent scar and mRNA detection Spike in controls and and RNAse inhibitor. Scartrace Illumina TruSeq adapaters | GEO Accession:GSM2752193 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | NextSeq 500 | SRP116018 | P1_wkm_Scar_p02_R1.fastq.gz P1_wkm_Scar_p02_R2.fastq.gz | fastq fastq | 941664617.0 | 6196187.0 | GSM2752193 r2 | 0:75.99 1:75.99 | A:170094338;C:275555653;G:348702043;T:147269855;N:42728 | 75 | 75 | 170094338 | 275555653 | 348702043 | 147269855 | 42728 | SRX3119870 | SRS2454729 | SRA602108 | GEO | AVO, Hubrecht Institue | 2 | 0.00033 | 0.0001 | 0.00027 | 8e-05 | 0.99987 | 0.99993 | 0.625 | 1.0 | 76 | 76 | T | T | mates < 9% mapping rate | illumina | nextseq | unknown | random_priming | trueseq | sc | other_seq | scartrace | Netherlands | 2017-08-23 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 49079 | 49079 | SRR7659034 | SRX4520651 | SRS3639026 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | ABc 4: WT control rep4 | GSM3324252 | source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | ABc 4: WT control rep4 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | GSM3324252 | GSM3324252: ABc 4: WT control rep4; Danio rerio; RNA Seq | GSM3324252 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324252 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | ABc_4_1.fq.gz ABc_4_2.fq.gz | fastq fastq | 8338149600.0 | 27793832.0 | GSM3324252 r1 | 0:150 1:150 | A:2217593021;C:1962526726;G:1956500797;T:2200674254;N:854802 | 150 | 150 | 2217593021 | 1962526726 | 1956500797 | 2200674254 | 854802 | SRX4520651 | SRS3639026 | SRA755536 | GEO | University of Tampere | 2 | 0.92493 | 0.91975 | 0.05312 | 0.0528 | 0.69603 | 0.70005 | 0.52953 | 0.5259 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49080 | 49080 | SRR7659033 | SRX4520650 | SRS3639025 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | ABc 3: WT control rep3 | GSM3324251 | source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | ABc 3: WT control rep3 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | GSM3324251 | GSM3324251: ABc 3: WT control rep3; Danio rerio; RNA Seq | GSM3324251 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324251 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | ABc_3_1.fq.gz ABc_3_2.fq.gz | fastq fastq | 7748608500.0 | 25828695.0 | GSM3324251 r1 | 0:150 1:150 | A:2069797407;C:1816718033;G:1809358876;T:2051944143;N:790041 | 150 | 150 | 2069797407 | 1816718033 | 1809358876 | 2051944143 | 790041 | SRX4520650 | SRS3639025 | SRA755536 | GEO | University of Tampere | 2 | 0.91798 | 0.90987 | 0.04896 | 0.04859 | 0.74166 | 0.74418 | 0.53544 | 0.54232 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49081 | 49081 | SRR7659032 | SRX4520649 | SRS3639024 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | ABc 2: WT control rep2 | GSM3324250 | source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | ABc 2: WT control rep2 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | GSM3324250 | GSM3324250: ABc 2: WT control rep2; Danio rerio; RNA Seq | GSM3324250 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324250 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | ABc_2_1.fq.gz ABc_2_2.fq.gz | fastq fastq | 8114032500.0 | 27046775.0 | GSM3324250 r1 | 0:150 1:150 | A:2194610150;C:1876718372;G:1867025193;T:2174858493;N:820292 | 150 | 150 | 2194610150 | 1876718372 | 1867025193 | 2174858493 | 820292 | SRX4520649 | SRS3639024 | SRA755536 | GEO | University of Tampere | 2 | 0.91423 | 0.90996 | 0.06031 | 0.05939 | 0.73095 | 0.7345 | 0.53902 | 0.53559 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49082 | 49082 | SRR7659031 | SRX4520648 | SRS3639023 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | ABc 1: WT control rep1 | GSM3324249 | source name:zebrafish kidney|genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | ABc 1: WT control rep1 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:n1 control|tissue:zebrafish kidney | GSM3324249 | GSM3324249: ABc 1: WT control rep1; Danio rerio; RNA Seq | GSM3324249 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324249 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | ABc_1_2.fq.gz ABc_1_1.fq.gz | fastq fastq | 7048214700.0 | 23494049.0 | GSM3324249 r1 | 0:150 1:150 | A:1872405650;C:1662441748;G:1654726958;T:1857920176;N:720168 | 150 | 150 | 1872405650 | 1662441748 | 1654726958 | 1857920176 | 720168 | SRX4520648 | SRS3639023 | SRA755536 | GEO | University of Tampere | 2 | 0.90831 | 0.89864 | 0.04895 | 0.04839 | 0.7419 | 0.74501 | 0.54589 | 0.55048 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49083 | 49083 | SRR7659030 | SRX4520647 | SRS3639020 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | AB 4: WT inf rep4 | GSM3324248 | source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | AB 4: WT inf rep4 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | GSM3324248 | GSM3324248: AB 4: WT inf rep4; Danio rerio; RNA Seq | GSM3324248 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324248 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | AB_4_1.fq.gz AB_4_2.fq.gz | fastq fastq | 7339619100.0 | 24465397.0 | GSM3324248 r1 | 0:150 1:150 | A:1956014376;C:1724124671;G:1723654528;T:1935080058;N:745467 | 150 | 150 | 1956014376 | 1724124671 | 1723654528 | 1935080058 | 745467 | SRX4520647 | SRS3639020 | SRA755536 | GEO | University of Tampere | 2 | 0.91872 | 0.90787 | 0.04809 | 0.04729 | 0.74241 | 0.74698 | 0.5326 | 0.53365 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49084 | 49084 | SRR7659029 | SRX4520646 | SRS3639022 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | AB 3: WT inf rep3 | GSM3324247 | source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | AB 3: WT inf rep3 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | GSM3324247 | GSM3324247: AB 3: WT inf rep3; Danio rerio; RNA Seq | GSM3324247 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324247 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | AB_3_1.fq.gz AB_3_2.fq.gz | fastq fastq | 7424949300.0 | 24749831.0 | GSM3324247 r1 | 0:150 1:150 | A:1964882946;C:1754326057;G:1752010860;T:1952971662;N:757775 | 150 | 150 | 1964882946 | 1754326057 | 1752010860 | 1952971662 | 757775 | SRX4520646 | SRS3639022 | SRA755536 | GEO | University of Tampere | 2 | 0.9196 | 0.91227 | 0.04829 | 0.04781 | 0.72232 | 0.72594 | 0.52261 | 0.51343 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49085 | 49085 | SRR7659028 | SRX4520645 | SRS3639021 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | AB 2: WT inf rep2 | GSM3324246 | source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | AB 2: WT inf rep2 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | GSM3324246 | GSM3324246: AB 2: WT inf rep2; Danio rerio; RNA Seq | GSM3324246 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324246 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | AB_2_2.fq.gz AB_2_1.fq.gz | fastq fastq | 7060829400.0 | 23536098.0 | GSM3324246 r1 | 0:150 1:150 | A:1875609739;C:1663056551;G:1660410877;T:1861028532;N:723701 | 150 | 150 | 1875609739 | 1663056551 | 1660410877 | 1861028532 | 723701 | SRX4520645 | SRS3639021 | SRA755536 | GEO | University of Tampere | 2 | 0.92483 | 0.9177 | 0.04614 | 0.04584 | 0.73012 | 0.73389 | 0.52324 | 0.52808 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49086 | 49086 | SRR7659027 | SRX4520644 | SRS3639019 | SRP156734 | PRJNA485080 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish | GSE118288 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. As expected based on the literature our results showed the induction of genes coding proteins associated to immune signaling cell migration and acute phase response indicating that the immune response to M. marinum infection in zebrafish is similar than the response to tuberculosis causing Mycobacterium tuberculosis in humans. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 8 samples were analyzed four biological replicates in each group. | pubmed:31626817 | AB 1: WT inf rep1 | GSM3324245 | source name:zebrafish kidney|genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | AB 1: WT inf rep1 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. Control samples were collected from unchallenged wild type AB fish of the smame litter which was used for infections. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | genotype:wild type AB|agent:Mycobacterium marinum|tissue:zebrafish kidney | GSM3324245 | GSM3324245: AB 1: WT inf rep1; Danio rerio; RNA Seq | GSM3324245 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3324245 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156734 | AB_1_1.fq.gz AB_1_2.fq.gz | fastq fastq | 7909740000.0 | 26365800.0 | GSM3324245 r1 | 0:150 1:150 | A:2093646099;C:1870851418;G:1866389764;T:2078055144;N:797575 | 150 | 150 | 2093646099 | 1870851418 | 1866389764 | 2078055144 | 797575 | SRX4520644 | SRS3639019 | SRA755536 | GEO | University of Tampere | 2 | 0.92137 | 0.90717 | 0.04875 | 0.04769 | 0.73783 | 0.74219 | 0.53376 | 0.5364 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-08 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49087 | 49087 | SRR7664345 | SRX4524952 | SRS3643046 | SRP156914 | PRJNA485334 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463] | GSE118350 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. In addition we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed four biological replicates in each group. | pubmed:31626817 | mutant463 inf rep4 | GSM3325717 | tissue:zebrafish kidney|strain:mutant463 | mutant463 inf rep4 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct. | strain:mutant463 | GSM3325717 | GSM3325717: mutant463 inf rep4; Danio rerio; RNA Seq | GSM3325717 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3325717 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156914 | F1_463_4_1.fq.gz F1_463_4_2.fq.gz | fastq fastq | 7892745600.0 | 26309152.0 | GSM3325717 r1 | 0:150 1:150 | A:2102605709;C:1854325558;G:1849161474;T:2085489415;N:1163444 | 150 | 150 | 2102605709 | 1854325558 | 1849161474 | 2085489415 | 1163444 | SRX4524952 | SRS3643046 | SRA756218 | GEO | University of Tampere | 2 | 0.9279 | 0.91721 | 0.05059 | 0.0497 | 0.7302 | 0.73448 | 0.51354 | 0.51569 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-09 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49088 | 49088 | SRR7664344 | SRX4524951 | SRS3643047 | SRP156914 | PRJNA485334 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463] | GSE118350 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. In addition we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed four biological replicates in each group. | pubmed:31626817 | mutant463 inf rep3 | GSM3325716 | tissue:zebrafish kidney|strain:mutant463 | mutant463 inf rep3 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct. | strain:mutant463 | GSM3325716 | GSM3325716: mutant463 inf rep3; Danio rerio; RNA Seq | GSM3325716 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3325716 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156914 | F1_463_3_1.fq.gz F1_463_3_2.fq.gz | fastq fastq | 8128128900.0 | 27093763.0 | GSM3325716 r1 | 0:150 1:150 | A:2183432859;C:1890349432;G:1885512767;T:2167999703;N:834139 | 150 | 150 | 2183432859 | 1890349432 | 1885512767 | 2167999703 | 834139 | SRX4524951 | SRS3643047 | SRA756218 | GEO | University of Tampere | 2 | 0.92534 | 0.91699 | 0.0575 | 0.05751 | 0.72368 | 0.72675 | 0.53219 | 0.53162 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-09 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49089 | 49089 | SRR7664343 | SRX4524950 | SRS3643045 | SRP156914 | PRJNA485334 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463] | GSE118350 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. In addition we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed four biological replicates in each group. | pubmed:31626817 | mutant463 inf rep2 | GSM3325715 | tissue:zebrafish kidney|strain:mutant463 | mutant463 inf rep2 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct. | strain:mutant463 | GSM3325715 | GSM3325715: mutant463 inf rep2; Danio rerio; RNA Seq | GSM3325715 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3325715 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156914 | F1_463_2_1.fq.gz F1_463_2_2.fq.gz | fastq fastq | 8481546900.0 | 28271823.0 | GSM3325715 r1 | 0:150 1:150 | A:2274428903;C:1976862267;G:1971746746;T:2257250093;N:1258891 | 150 | 150 | 2274428903 | 1976862267 | 1971746746 | 2257250093 | 1258891 | SRX4524950 | SRS3643045 | SRA756218 | GEO | University of Tampere | 2 | 0.9244 | 0.91499 | 0.05718 | 0.05626 | 0.72941 | 0.73379 | 0.53004 | 0.53034 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-09 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 49090 | 49090 | SRR7664342 | SRX4524949 | SRS3643043 | SRP156914 | PRJNA485334 | Characterization of the immune response to Mycobacterium marinum infection in zebrafish [mutant 463] | GSE118350 | Transcriptome Analysis | Mycobacterium marinum infection in zebrafish Danio rerio has been widely used to study human tuberculosis because the bacteria causing these two diseases are close relatives. We studied the zebrafish immune response to M. marinum infection through a whole genome level transcriptome analysis. In addition we carried out a medium scale forward genetic screen to identify genes underlying defense mechanisms against M. marinum infection in zebrafish. Our aim was to gain more information about the genetic mechanisms important in the immune defense against human tuberculosis. In this screen we identified a mutant zebrafish line with impaired resistance to a low dose M. marinum infection. In this line the transcriptome analysis at 14 days post infection revealed decreased expression of a gene homologous to human UNC119 which has been shown to have a role in T cell activation. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in zebrafish. 4 samples were analyzed four biological replicates in each group. | pubmed:31626817 | mutant463 inf rep1 | GSM3325714 | tissue:zebrafish kidney|strain:mutant463 | mutant463 inf rep1 | Read alignment to reference genome was done using STAR Raw expression estimates raw read counts for genes Danio rerio.GRCz10.91 were counted using FeatureCounts Raw expression estimates were normalized using median of rations implemented in R packages DESeq2 Genome build: Danio rerio.GRCz10 Supplementary files format and content: The raw expression values obtained from FeatureCounts and the median of ratios normalized expression values for each gene are provided in tab delimited text files. The first column includes the gene represented by its Gencode id. The remaining columns indicate the read counts such that each column represents a sample. | zebrafish kidney | 5 mpf to 6 mpf zebrafish were infected with 5 9 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 2 weeks post infection. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer’s instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. The mutant zebrafish line was produced with the gene breaking transposon based mutagenesis using the RP2 construct. | strain:mutant463 | GSM3325714 | GSM3325714: mutant463 inf rep1; Danio rerio; RNA Seq | GSM3325714 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Kit ID: 74104 according to the manufacturer's instructions. The genomic DNA was removed from the samples using the RapidOut DNA removal Kit K2981. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM3325714 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | HiSeq X Ten | SRP156914 | F1_463_1_2.fq.gz F1_463_1_1.fq.gz | fastq fastq | 7430278200.0 | 24767594.0 | GSM3325714 r1 | 0:150 1:150 | A:1981941438;C:1739863325;G:1736512377;T:1970856840;N:1104220 | 150 | 150 | 1981941438 | 1739863325 | 1736512377 | 1970856840 | 1104220 | SRX4524949 | SRS3643043 | SRA756218 | GEO | University of Tampere | 2 | 0.91811 | 0.90734 | 0.04866 | 0.04819 | 0.70512 | 0.70966 | 0.50962 | 0.50717 | 150 | 150 | B | B | biological fallback assumption | illumina | hiseq_era | full_length | random_priming | unknown | bulk | unknown | unknown | Finland | 2018-08-09 | Multi-stage | Multi-stage | Kidney | Renal System | ||||||||||
| 52204 | 52204 | SRR8991401 | SRX5770469 | SRS4704579 | SRP194254 | PRJNA540466 | Characterization of the zebrafish cell landscape at single cell resolution | GSE130487 | Transcriptome Analysis | Zebrafish have been found to be a premier model organism in biological and regeneration research. However the comprehensive cell compositions and molecular dynamics during tissue regeneration in zebrafish remain poorly understood. Here we utilized Microwell seq to analyze more than 250 000 single cells covering major zebrafish cell types and constructed a systematic zebrafish cell landscape. We revealed single cell compositions for 18 zebrafish tissue types covering both embryo and adult stages. Single cell mapping of caudal fin regeneration revealed a unique characteristic of blastema population and key genetic regulation involved in zebrafish tissue repair. Overall our single cell datasets demonstrate the utility of zebrafish cell landscape resources in various fields of biological research. Overall design: Expression profiling by high throughput sequencing of major zebrafish organ types. Please note that 19 samples were added and 9 samples were deleted on Mar 1 2022. | pubmed:34660600 | Kidney3 | GSM3740954 | source name:kidney|strain:Tubingen|genotype:wild type|tissue:kidney | Kidney3 | The drop seq core computational tool was used for preprocessing of the Microwell seq data. The implementation is described in the Drop seq computational cookbook http://mccarrolllab.org/dropseq/. Base calls were performed with Illumina bcl2fastq Sequenced reads were trimmed for adaptor sequence.Then reads in bam files were tagged with the cell and molecular UMI barcode sequences using Drop seq tools 1.12.The cell barcodes are tagged as XC in the bam file and the UMI is tagged as XM in the bam file. The reads quality under 10 were removed. ScRNA seq reads were aligned to the Danio rerio GRCz10 genome assembly using STAR version 2.5.2a with default configurations. Next merge the STAR alignment tagged bam SAM to recover cell /molecular barcodes and the reads are annotated with exon tags. Last we demultiplexed all cell barcodes taken into consideration for the analysis from the exon tagged bam files to get a digital expression matrix based on UMI counts. Genome build: http://dec2017.archive.ensembl.org/Danio rerio/Info/Index Supplementary files format and content: tab delimited text files of digital expression matrix dge based on raw UMI counts columns are cells and rows are genes. | kidney | Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol | strain:Tubingen|genotype:wild type|tissue:kidney | GSM3740954 | GSM3740954: Kidney3; Danio rerio; RNA Seq | GSM3740954 | 1 | Tissue dissociation and single cell lysate Library preparations were performed with the Microwell seq protocol | GEO Accession:GSM3740954 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq X Ten | SRP194254 | assembly:Danio rerio GRCz10 | Kidney3.bam | bam | 47181267324.0 | 156229362.0 | GSM3740954 r1 | 0:151 1:151 | A:11942883398;C:7663399672;G:7892086087;T:19671671186;N:11226981 | 151 | 151 | 11942883398 | 7663399672 | 7892086087 | 19671671186 | 11226981 | SRX5770469 | SRS4704579 | SRA880843 | GEO | Zhejiang University | 2 | 0.0 | 0.74871 | 0.0 | 0.03049 | 1.0 | 0.8658 | 0.55011 | 151 | 151 | T | B | mate1 technical by mapping diff | illumina | hiseq_era | unknown | cdna_unspecified | unknown | sc | single_cell_plate | microwellseq | China | 2019-04-30 | Undetermined | Multi-stage | Kidney | Renal System | ||||||||||||
| 63833 | 63833 | SRR14077612 | SRX10451897 | SRS8583182 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | WT kidney3 [runx1] | GSM5212431 | source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | WT kidney3 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212431 | GSM5212431: WT kidney3 [runx1]; Danio rerio; RNA Seq | GSM5212431 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212431 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.5.8142700.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142700.2.cln.fq.gz | fastq fastq | 5620598490.0 | 22731446.0 | GSM5212431 r1 | 0:123.63 1:123.63 | A:1519385372;C:1283859179;G:1297145256;T:1520155478;N:53205 | 123 | 123 | 1519385372 | 1283859179 | 1297145256 | 1520155478 | 53205 | SRX10451897 | SRS8583182 | SRA1210911 | GEO | NHGRI | 2 | 0.94209 | 0.94365 | 0.1093 | 0.10867 | 0.7655 | 0.76471 | 0.52137 | 0.52991 | 57 | 57 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63834 | 63834 | SRR14077613 | SRX10451897 | SRS8583182 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | WT kidney3 [runx1] | GSM5212431 | source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | WT kidney3 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212431 | GSM5212431: WT kidney3 [runx1]; Danio rerio; RNA Seq | GSM5212431 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212431 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.4.8142700.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142700.2.cln.fq.gz | fastq fastq | 5653835646.0 | 22866105.0 | GSM5212431 r2 | 0:123.63 1:123.63 | A:1528563748;C:1291263140;G:1304651524;T:1529275913;N:81321 | 123 | 123 | 1528563748 | 1291263140 | 1304651524 | 1529275913 | 81321 | SRX10451897 | SRS8583182 | SRA1210911 | GEO | NHGRI | 2 | 0.94227 | 0.9433 | 0.10809 | 0.1082 | 0.7654 | 0.76629 | 0.46698 | 0.51583 | 120 | 120 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63835 | 63835 | SRR14077610 | SRX10451896 | SRS8583181 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | WT kidney2 [runx1] | GSM5212430 | source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | WT kidney2 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212430 | GSM5212430: WT kidney2 [runx1]; Danio rerio; RNA Seq | GSM5212430 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212430 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.4.8142702.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142702.2.cln.fq.gz | fastq fastq | 5711423980.0 | 23122476.0 | GSM5212430 r1 | 0:123.50 1:123.50 | A:1541001316;C:1305691699;G:1320208515;T:1544438912;N:83538 | 123 | 123 | 1541001316 | 1305691699 | 1320208515 | 1544438912 | 83538 | SRX10451896 | SRS8583181 | SRA1210911 | GEO | NHGRI | 2 | 0.95092 | 0.95171 | 0.07601 | 0.07547 | 0.73584 | 0.73665 | 0.45011 | 0.45353 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63836 | 63836 | SRR14077611 | SRX10451896 | SRS8583181 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | WT kidney2 [runx1] | GSM5212430 | source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | WT kidney2 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212430 | GSM5212430: WT kidney2 [runx1]; Danio rerio; RNA Seq | GSM5212430 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212430 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.5.8142702.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142702.2.cln.fq.gz | fastq fastq | 5674131430.0 | 22971228.0 | GSM5212430 r2 | 0:123.51 1:123.51 | A:1530898067;C:1297222710;G:1311658561;T:1534297201;N:54891 | 123 | 123 | 1530898067 | 1297222710 | 1311658561 | 1534297201 | 54891 | SRX10451896 | SRS8583181 | SRA1210911 | GEO | NHGRI | 2 | 0.95066 | 0.95158 | 0.07593 | 0.07608 | 0.73263 | 0.7343 | 0.44607 | 0.44584 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63837 | 63837 | SRR14077608 | SRX10451895 | SRS8583180 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | WT kidney1 [runx1] | GSM5212429 | source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | WT kidney1 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212429 | GSM5212429: WT kidney1 [runx1]; Danio rerio; RNA Seq | GSM5212429 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212429 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.5.8142698.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142698.2.cln.fq.gz | fastq fastq | 6048097920.0 | 24370362.0 | GSM5212429 r1 | 0:124.09 1:124.09 | A:1630531156;C:1385676653;G:1399270262;T:1632562524;N:57325 | 124 | 124 | 1630531156 | 1385676653 | 1399270262 | 1632562524 | 57325 | SRX10451895 | SRS8583180 | SRA1210911 | GEO | NHGRI | 2 | 0.94669 | 0.94821 | 0.09654 | 0.09706 | 0.73537 | 0.73606 | 0.49615 | 0.49775 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63838 | 63838 | SRR14077609 | SRX10451895 | SRS8583180 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | WT kidney1 [runx1] | GSM5212429 | source name:adult kidney|genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | WT kidney1 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:WT|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212429 | GSM5212429: WT kidney1 [runx1]; Danio rerio; RNA Seq | GSM5212429 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212429 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.4.8142698.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142698.2.cln.fq.gz | fastq fastq | 6086298924.0 | 24523879.0 | GSM5212429 r2 | 0:124.09 1:124.09 | A:1640963544;C:1394293929;G:1408031161;T:1642922398;N:87892 | 124 | 124 | 1640963544 | 1394293929 | 1408031161 | 1642922398 | 87892 | SRX10451895 | SRS8583180 | SRA1210911 | GEO | NHGRI | 2 | 0.94597 | 0.94665 | 0.09708 | 0.09725 | 0.73744 | 0.73839 | 0.49464 | 0.49315 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63839 | 63839 | SRR14077616 | SRX10451894 | SRS8583179 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | runx1 / kidney6 [runx1] | GSM5212433 | source name:adult kidney|genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | runx1 / kidney6 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212433 | GSM5212433: runx1 / kidney6 [runx1]; Danio rerio; RNA Seq | GSM5212433 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212433 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.4.8142704.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142704.2.cln.fq.gz | fastq fastq | 5830417310.0 | 23547116.0 | GSM5212433 r1 | 0:123.80 1:123.80 | A:1528065414;C:1374560308;G:1389503409;T:1538204560;N:83619 | 123 | 123 | 1528065414 | 1374560308 | 1389503409 | 1538204560 | 83619 | SRX10451894 | SRS8583179 | SRA1210911 | GEO | NHGRI | 2 | 0.94227 | 0.9443 | 0.0312 | 0.03106 | 0.7305 | 0.73198 | 0.4564 | 0.45229 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63840 | 63840 | SRR14077617 | SRX10451894 | SRS8583179 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | runx1 / kidney6 [runx1] | GSM5212433 | source name:adult kidney|genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | runx1 / kidney6 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212433 | GSM5212433: runx1 / kidney6 [runx1]; Danio rerio; RNA Seq | GSM5212433 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212433 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.5.8142704.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142704.2.cln.fq.gz | fastq fastq | 5801368354.0 | 23428774.0 | GSM5212433 r2 | 0:123.81 1:123.81 | A:1520440154;C:1367723047;G:1382629888;T:1530520601;N:54664 | 123 | 123 | 1520440154 | 1367723047 | 1382629888 | 1530520601 | 54664 | SRX10451894 | SRS8583179 | SRA1210911 | GEO | NHGRI | 2 | 0.94318 | 0.94442 | 0.03018 | 0.0303 | 0.72835 | 0.72906 | 0.44351 | 0.44657 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63841 | 63841 | SRR14077614 | SRX10451893 | SRS8583178 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | runx1 / kidney5 [runx1] | GSM5212432 | source name:adult kidney|genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | runx1 / kidney5 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212432 | GSM5212432: runx1 / kidney5 [runx1]; Danio rerio; RNA Seq | GSM5212432 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212432 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.5.8142695.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.5.8142695.2.cln.fq.gz | fastq fastq | 5768438696.0 | 23423221.0 | GSM5212432 r1 | 0:123.14 1:123.14 | A:1566209291;C:1310337702;G:1323216779;T:1568619957;N:54967 | 123 | 123 | 1566209291 | 1310337702 | 1323216779 | 1568619957 | 54967 | SRX10451893 | SRS8583178 | SRA1210911 | GEO | NHGRI | 2 | 0.94778 | 0.94948 | 0.0935 | 0.09399 | 0.72157 | 0.72299 | 0.49608 | 0.49634 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 63842 | 63842 | SRR14077615 | SRX10451893 | SRS8583178 | SRP312298 | PRJNA717672 | Redundant mechanisms driven independently by RUNX1 and GATA2 for hematopoietic development [zebrafish bulk RNA seq2] | GSE169689 | Transcriptome Analysis | Here we used RNAsequencing to characterize the transcriptional profile of the kidney of runx1 knock out zebrafish adult compared to wild type. Overall design: Bulk RNAseq was performed on surgically dissected the kidneys from wild type and runx1 / siblings 2.5 mpf pool of 3 kidneys/replicate. | parent bioproject:PRJNA663961 | pubmed:34492681 | runx1 / kidney5 [runx1] | GSM5212432 | source name:adult kidney|genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | runx1 / kidney5 [runx1] | RNA seq reads were aligned to the zebrafish genome reference GRCz11 and transcript reference GRCz11.99 using hisat2 2.2.1.0 We used htseq count v0.11.4 to generate gene expression estimates from the aligned reads. Alignment and expression estimation of our dataset. DESeq2 was implemented in R to perform differential gene expression analysis from gene count matrix. Genome build: GRCz11 Supplementary files format and content: raw counts | adult kidney | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | genotype:runx1 / del8 hg96|strain:EK|tissue:kidney|biopsy time:2.5 month | GSM5212432 | GSM5212432: runx1 / kidney5 [runx1]; Danio rerio; RNA Seq | GSM5212432 | 1 | Rnaseq on kidney: Wild type and runx1del8/del8 kidneys were dissected from 2.5 mpf fish pool of 3 kidneys/replicate and immediately collected in Trizol #15596018 Invitrogen. Samples were then put in a heatblock at 52C for 10 min and then overnight in 80C RNA was extracted following the manufacturer protocol using Direct zolTM RNA MiniPrep Kit Zymo Research #R2051. Sequencing libraries were prepaired using paired end library preparation TruSeq RNA Library Prep Kit v2 | GEO Accession:GSM5212432 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP312298 | 141031_OPTIMUS_C5M4FANXX.4.8142695.1.cln.fq.gz 141031_OPTIMUS_C5M4FANXX.4.8142695.2.cln.fq.gz | fastq fastq | 5808145902.0 | 23584233.0 | GSM5212432 r2 | 0:123.14 1:123.14 | A:1576938864;C:1319376550;G:1332344310;T:1579402358;N:83820 | 123 | 123 | 1576938864 | 1319376550 | 1332344310 | 1579402358 | 83820 | SRX10451893 | SRS8583178 | SRA1210911 | GEO | NHGRI | 2 | 0.94737 | 0.94902 | 0.09296 | 0.09311 | 0.72228 | 0.7236 | 0.49544 | 0.48947 | 126 | 126 | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | trueseq | bulk | bulk | bulk | United States | 2021-03-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||||
| 65128 | 65128 | SRR14935651 | SRX11248280 | SRS9294818 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep9 | GSM5406802 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep9 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406802 | GSM5406802: kidney pdx1 heterozygous ko rep9; Danio rerio; RNA Seq | GSM5406802 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406802 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_18_R1_001.fastq.gz 8724R1_18_R2_001.fastq.gz | fastq fastq | 11176979232.0 | 37097872.0 | GSM5406802 r1 | 0:150.64 1:150.65 | A:2835225993;C:2589629327;G:2820499304;T:2931557102;N:67506 | 150 | 150 | 2835225993 | 2589629327 | 2820499304 | 2931557102 | 67506 | SRX11248280 | SRS9294818 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87724 | 0.87448 | 0.31729 | 0.31569 | 0.73716 | 0.73933 | 0.62206 | 0.62398 | 151 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65129 | 65129 | SRR14935650 | SRX11248279 | SRS9294817 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep8 | GSM5406801 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep8 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406801 | GSM5406801: kidney pdx1 heterozygous ko rep8; Danio rerio; RNA Seq | GSM5406801 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406801 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_17_R1_001.fastq.gz 8724R1_17_R2_001.fastq.gz | fastq fastq | 11394814456.0 | 37822298.0 | GSM5406801 r1 | 0:150.65 1:150.62 | A:2870553528;C:2617084802;G:2858252766;T:3048861279;N:62081 | 150 | 150 | 2870553528 | 2617084802 | 2858252766 | 3048861279 | 62081 | SRX11248279 | SRS9294817 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.88351 | 0.88116 | 0.29453 | 0.29339 | 0.72908 | 0.73012 | 0.59959 | 0.60047 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65130 | 65130 | SRR14935649 | SRX11248278 | SRS9294816 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep7 | GSM5406800 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep7 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406800 | GSM5406800: kidney pdx1 heterozygous ko rep7; Danio rerio; RNA Seq | GSM5406800 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406800 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_16_R1_001.fastq.gz 8724R1_16_R2_001.fastq.gz | fastq fastq | 10795664046.0 | 35825557.0 | GSM5406800 r1 | 0:150.66 1:150.68 | A:2699673063;C:2430598463;G:2795587348;T:2869745840;N:59332 | 150 | 150 | 2699673063 | 2430598463 | 2795587348 | 2869745840 | 59332 | SRX11248278 | SRS9294816 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87086 | 0.8686 | 0.31803 | 0.31528 | 0.73517 | 0.73752 | 0.60984 | 0.61136 | 151 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65131 | 65131 | SRR14935648 | SRX11248277 | SRS9294815 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep6 | GSM5406799 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep6 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406799 | GSM5406799: kidney pdx1 heterozygous ko rep6; Danio rerio; RNA Seq | GSM5406799 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406799 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_15_R1_001.fastq.gz 8724R1_15_R2_001.fastq.gz | fastq fastq | 10760871119.0 | 35714100.0 | GSM5406799 r1 | 0:150.66 1:150.65 | A:2739382001;C:2429434631;G:2669749643;T:2922244501;N:60343 | 150 | 150 | 2739382001 | 2429434631 | 2669749643 | 2922244501 | 60343 | SRX11248277 | SRS9294815 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.8687 | 0.86692 | 0.3287 | 0.32779 | 0.73405 | 0.73486 | 0.60891 | 0.61291 | 151 | 150 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65132 | 65132 | SRR14935647 | SRX11248276 | SRS9294814 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep5 | GSM5406798 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep5 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406798 | GSM5406798: kidney pdx1 heterozygous ko rep5; Danio rerio; RNA Seq | GSM5406798 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406798 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_14_R1_001.fastq.gz 8724R1_14_R2_001.fastq.gz | fastq fastq | 10649537104.0 | 35349599.0 | GSM5406798 r1 | 0:150.64 1:150.62 | A:2731221488;C:2409467117;G:2701711963;T:2807076164;N:60372 | 150 | 150 | 2731221488 | 2409467117 | 2701711963 | 2807076164 | 60372 | SRX11248276 | SRS9294814 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87441 | 0.87237 | 0.29421 | 0.29338 | 0.72693 | 0.72955 | 0.5953 | 0.59497 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65133 | 65133 | SRR14935646 | SRX11248275 | SRS9294813 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep4 | GSM5406797 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep4 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406797 | GSM5406797: kidney pdx1 heterozygous ko rep4; Danio rerio; RNA Seq | GSM5406797 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406797 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_13_R1_001.fastq.gz 8724R1_13_R2_001.fastq.gz | fastq fastq | 10694204698.0 | 35493814.0 | GSM5406797 r1 | 0:150.66 1:150.64 | A:2702728213;C:2453895836;G:2650869868;T:2886649326;N:61455 | 150 | 150 | 2702728213 | 2453895836 | 2650869868 | 2886649326 | 61455 | SRX11248275 | SRS9294813 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87706 | 0.87455 | 0.30298 | 0.30085 | 0.73492 | 0.73499 | 0.60664 | 0.61545 | 149 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65134 | 65134 | SRR14935645 | SRX11248274 | SRS9294812 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep3 | GSM5406796 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406796 | GSM5406796: kidney pdx1 heterozygous ko rep3; Danio rerio; RNA Seq | GSM5406796 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406796 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_12_R1_001.fastq.gz 8724R1_12_R2_001.fastq.gz | fastq fastq | 10345053183.0 | 34342254.0 | GSM5406796 r1 | 0:150.63 1:150.60 | A:2688355747;C:2362640622;G:2528888231;T:2765108367;N:60216 | 150 | 150 | 2688355747 | 2362640622 | 2528888231 | 2765108367 | 60216 | SRX11248274 | SRS9294812 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.86578 | 0.86485 | 0.32858 | 0.32741 | 0.74022 | 0.74192 | 0.6202 | 0.62802 | 150 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65135 | 65135 | SRR14935644 | SRX11248273 | SRS9294811 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep2 | GSM5406795 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406795 | GSM5406795: kidney pdx1 heterozygous ko rep2; Danio rerio; RNA Seq | GSM5406795 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406795 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_11_R1_001.fastq.gz 8724R1_11_R2_001.fastq.gz | fastq fastq | 10918902659.0 | 36232610.0 | GSM5406795 r1 | 0:150.67 1:150.68 | A:2720295545;C:2469360250;G:2821457214;T:2907726754;N:62896 | 150 | 150 | 2720295545 | 2469360250 | 2821457214 | 2907726754 | 62896 | SRX11248273 | SRS9294811 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87461 | 0.87362 | 0.33405 | 0.33405 | 0.74024 | 0.73994 | 0.60898 | 0.60832 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65136 | 65136 | SRR14935643 | SRX11248272 | SRS9294810 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney pdx1 heterozygous ko rep1 | GSM5406794 | source name:total kidney|genotype:PDX1mut|tissue:kidney | kidney pdx1 heterozygous ko rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:PDX1mut|tissue:kidney | GSM5406794 | GSM5406794: kidney pdx1 heterozygous ko rep1; Danio rerio; RNA Seq | GSM5406794 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406794 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_10_R1_001.fastq.gz 8724R1_10_R2_001.fastq.gz | fastq fastq | 11557818156.0 | 38359672.0 | GSM5406794 r1 | 0:150.63 1:150.67 | A:2923769735;C:2594538133;G:2968671202;T:3070777088;N:61998 | 150 | 150 | 2923769735 | 2594538133 | 2968671202 | 3070777088 | 61998 | SRX11248272 | SRS9294810 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.8705 | 0.86891 | 0.33241 | 0.3311 | 0.7363 | 0.73835 | 0.61699 | 0.62373 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65137 | 65137 | SRR14935642 | SRX11248271 | SRS9294809 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney wildtype rep3 | GSM5406793 | source name:total kidney|genotype:WT|tissue:kidney | kidney wildtype rep3 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:WT|tissue:kidney | GSM5406793 | GSM5406793: kidney wildtype rep3; Danio rerio; RNA Seq | GSM5406793 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406793 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_3_R1_001.fastq.gz 8724R1_3_R2_001.fastq.gz | fastq fastq | 10759333910.0 | 35709735.0 | GSM5406793 r1 | 0:150.63 1:150.67 | A:2742030248;C:2405074908;G:2740896620;T:2871268925;N:63209 | 150 | 150 | 2742030248 | 2405074908 | 2740896620 | 2871268925 | 63209 | SRX11248271 | SRS9294809 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87736 | 0.875 | 0.29165 | 0.29063 | 0.73261 | 0.73361 | 0.51754 | 0.51714 | 150 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65138 | 65138 | SRR14935641 | SRX11248270 | SRS9294808 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney wildtype rep2 | GSM5406792 | source name:total kidney|genotype:WT|tissue:kidney | kidney wildtype rep2 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:WT|tissue:kidney | GSM5406792 | GSM5406792: kidney wildtype rep2; Danio rerio; RNA Seq | GSM5406792 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406792 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_2_R1_001.fastq.gz 8724R1_2_R2_001.fastq.gz | fastq fastq | 11014631579.0 | 36552301.0 | GSM5406792 r1 | 0:150.65 1:150.68 | A:2786726244;C:2457413219;G:2801015846;T:2969414816;N:61454 | 150 | 150 | 2786726244 | 2457413219 | 2801015846 | 2969414816 | 61454 | SRX11248270 | SRS9294808 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.87866 | 0.87699 | 0.31394 | 0.31278 | 0.73588 | 0.73726 | 0.61713 | 0.61801 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 65139 | 65139 | SRR14935640 | SRX11248269 | SRS9294807 | SRP325966 | PRJNA742218 | Transcriptome analysis of adult wildtype and pdx1+/ zebrafish kidneys through next generation RNA sequencing | GSE179104 | Transcriptome Analysis | The pdx1 knockout zebrafish mutant has been established as an animal model of diabetic retinopathy. Due to a disturbed beta cell development these mutants develop hyperglycaemia leading to an activation of angiogenesis in the retina of larval and adult stages. This study addresses the questions if the pdx1 heterozygous mutant kidney is also affected by similar changes of the microvasculature and if the expression patterns of signaling pathways and mechanisms associated with the development of diabetic conditions are changed in these kidneys. For this purpose we performed RNA sequencing with the mRNA of total adult kidneys of heterozygous pdx1 mutants and their wildtype littermates. Overall design: RNA expression profiles of adult wildtype and heterozygous pdx1 mutant zebrafish kidneys | pubmed:35100334 | kidney wildtype rep1 | GSM5406791 | source name:total kidney|genotype:WT|tissue:kidney | kidney wildtype rep1 | trimmed with trim galore version 0.6.4. Parameters: length 26 phred33 Get raw counts with kallisto quant version 0.4.6. TPM abundance estimates generated with kallisto quant 0.4.6 Genome build: GRCz11 Supplementary files format and content: TPM abundance estimates and raw counts generated with kallisto. | total kidney | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer’s protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | genotype:WT|tissue:kidney | GSM5406791 | GSM5406791: kidney wildtype rep1; Danio rerio; RNA Seq | GSM5406791 | 1 | Kidneys were removed and stored at 20°C in RNAlater. Total RNA was isolated using the RNeasy Kit with a QIAcube following the manufacturer's protocol. RNA libraries were prepared for sequencing using standard BGISeq 500 protocols | GEO Accession:GSM5406791 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | BGISEQ | BGISEQ-500 | SRP325966 | loader:fastq load.py | 8724R1_1_R1_001.fastq.gz 8724R1_1_R2_001.fastq.gz | fastq fastq | 10413411371.0 | 34567408.0 | GSM5406791 r1 | 0:150.65 1:150.60 | A:2697353558;C:2358512324;G:2568693377;T:2788789911;N:62201 | 150 | 150 | 2697353558 | 2358512324 | 2568693377 | 2788789911 | 62201 | SRX11248269 | SRS9294807 | SRA1251952 | GEO | ZMF, University Heidelberg | 2 | 0.86943 | 0.8664 | 0.31108 | 0.30889 | 0.73815 | 0.74034 | 0.56789 | 0.60471 | 151 | 151 | B | B | biological fallback assumption | bgi | bgi | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Germany | 2021-06-29 | Undetermined | Multi-stage | Kidney | Renal System | |||||||||||
| 67062 | 67062 | SRR17048184 | SRX13237924 | SRS11162468 | SRP348087 | PRJNA783915 | RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection | GSE189627 | Transcriptome Analysis | Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected mutant PBS injected WT M. marinum infected mutant M. marinum infected. | pubmed:39916610 | Mut Inf 7 [210019 24 Mut Inf 42 s24 S235] | GSM5704997 | source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | Mut Inf 7 [210019 24 Mut Inf 42 s24 S235] | Automatic adapter trimming Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx | Mut Inf kidney | 9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish treated with identical protocol were used as controls. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | GSM5704997 | GSM5704997: Mut Inf 7 [210019 24 Mut Inf 42 s24 S235]; Danio rerio; RNA Seq | GSM5704997 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM5704997 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP348087 | loader:fastq load.py | 210019_24_Mut_Inf_42_s24_S235_L004_R1_001.fastq.gz 210019_24_Mut_Inf_42_s24_S235_L004_R2_001.fastq.gz | fastq fastq | 7032894927.0 | 35884038.0 | GSM5704997 r1 | 0:97.96 1:98.03 | A:1731100028;C:1788276798;G:1809972002;T:1694957455;N:8588644 | 97 | 98 | 1731100028 | 1788276798 | 1809972002 | 1694957455 | 8588644 | SRX13237924 | SRS11162468 | SRA1335306 | GEO | Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center | 2 | 0.95915 | 0.96169 | 0.11158 | 0.10796 | 0.80955 | 0.80827 | 0.66594 | 0.66734 | 100 | 99 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Finland | 2021-11-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||
| 67063 | 67063 | SRR17048183 | SRX13237923 | SRS11162467 | SRP348087 | PRJNA783915 | RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection | GSE189627 | Transcriptome Analysis | Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected mutant PBS injected WT M. marinum infected mutant M. marinum infected. | pubmed:39916610 | Mut Inf 6 [210019 23 Mut Inf 40 s23 S234] | GSM5704996 | source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | Mut Inf 6 [210019 23 Mut Inf 40 s23 S234] | Automatic adapter trimming Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx | Mut Inf kidney | 9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish treated with identical protocol were used as controls. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | GSM5704996 | GSM5704996: Mut Inf 6 [210019 23 Mut Inf 40 s23 S234]; Danio rerio; RNA Seq | GSM5704996 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM5704996 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP348087 | loader:fastq load.py | 210019_23_Mut_Inf_40_s23_S234_L004_R1_001.fastq.gz 210019_23_Mut_Inf_40_s23_S234_L004_R2_001.fastq.gz | fastq fastq | 5863554559.0 | 30352906.0 | GSM5704996 r1 | 0:96.52 1:96.66 | A:1426131519;C:1483378471;G:1506857016;T:1396909564;N:50277989 | 96 | 96 | 1426131519 | 1483378471 | 1506857016 | 1396909564 | 50277989 | SRX13237923 | SRS11162467 | SRA1335306 | GEO | Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center | 2 | 0.95854 | 0.95918 | 0.12378 | 0.12045 | 0.8171 | 0.81631 | 0.64334 | 0.68212 | 100 | 100 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Finland | 2021-11-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||
| 67064 | 67064 | SRR17048182 | SRX13237922 | SRS11162466 | SRP348087 | PRJNA783915 | RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection | GSE189627 | Transcriptome Analysis | Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected mutant PBS injected WT M. marinum infected mutant M. marinum infected. | pubmed:39916610 | Mut Inf 5 [210019 22 Mut Inf 39 s22 S233] | GSM5704995 | source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | Mut Inf 5 [210019 22 Mut Inf 39 s22 S233] | Automatic adapter trimming Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx | Mut Inf kidney | 9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish treated with identical protocol were used as controls. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | GSM5704995 | GSM5704995: Mut Inf 5 [210019 22 Mut Inf 39 s22 S233]; Danio rerio; RNA Seq | GSM5704995 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM5704995 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP348087 | loader:fastq load.py | 210019_22_Mut_Inf_39_s22_S233_L004_R1_001.fastq.gz 210019_22_Mut_Inf_39_s22_S233_L004_R2_001.fastq.gz | fastq fastq | 6574444328.0 | 33467850.0 | GSM5704995 r1 | 0:98.20 1:98.24 | A:1646588277;C:1641744576;G:1664107413;T:1614615584;N:7388478 | 98 | 98 | 1646588277 | 1641744576 | 1664107413 | 1614615584 | 7388478 | SRX13237922 | SRS11162466 | SRA1335306 | GEO | Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center | 2 | 0.95384 | 0.95827 | 0.10707 | 0.10445 | 0.80752 | 0.80507 | 0.63725 | 0.59647 | 100 | 98 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Finland | 2021-11-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||
| 67065 | 67065 | SRR17048181 | SRX13237921 | SRS11162465 | SRP348087 | PRJNA783915 | RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection | GSE189627 | Transcriptome Analysis | Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected mutant PBS injected WT M. marinum infected mutant M. marinum infected. | pubmed:39916610 | Mut Inf 4 [210019 21 Mut Inf 38 s21 S232] | GSM5704994 | source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | Mut Inf 4 [210019 21 Mut Inf 38 s21 S232] | Automatic adapter trimming Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx | Mut Inf kidney | 9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish treated with identical protocol were used as controls. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | GSM5704994 | GSM5704994: Mut Inf 4 [210019 21 Mut Inf 38 s21 S232]; Danio rerio; RNA Seq | GSM5704994 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM5704994 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP348087 | loader:fastq load.py | 210019_21_Mut_Inf_38_s21_S232_L004_R1_001.fastq.gz 210019_21_Mut_Inf_38_s21_S232_L004_R2_001.fastq.gz | fastq fastq | 7220864595.0 | 36751167.0 | GSM5704994 r1 | 0:98.20 1:98.28 | A:1710142182;C:1905627574;G:1926351728;T:1672025400;N:6717711 | 98 | 98 | 1710142182 | 1905627574 | 1926351728 | 1672025400 | 6717711 | SRX13237921 | SRS11162465 | SRA1335306 | GEO | Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center | 2 | 0.96396 | 0.9651 | 0.11474 | 0.11004 | 0.82763 | 0.82781 | 0.67982 | 0.65505 | 100 | 100 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Finland | 2021-11-26 | Multi-stage | Multi-stage | Kidney | Renal System | |||||||||
| 67066 | 67066 | SRR17048180 | SRX13237920 | SRS11162464 | SRP348087 | PRJNA783915 | RNA seq analysis from the kidney of pycard mutant adult zebrafish in Mycobacterium marinum infection | GSE189627 | Transcriptome Analysis | Zebrafish / Mycobacterium marinum model is useful in modeling human tuberculosis as zebrafish recapitulate several aspects of the disease. We generated a mutant line for the inflammasome adaptor gene pycard to study the loss of inflammasome signaling in adult zebrafish M. marinum infection. We discovered a number of immunity related genes up or downregulated in mutant pycard zebrafish in comparison to WT control siblings. The RNA seq was conducted using a low dose infection approximately 30 CFU at 4 weeks post infection from the kidney of adult male fish. Mock injected controls received PBS instead of bacteria. Overall design: Identification of the up and downregulated genes in Mycobacterium marinum infection in pycard mutant adult zebrafish. 24 samples were analyzed from three to nine biological replicates in each group. Wild type WT sibling fish were used as a control. The groups were WT PBS injected mutant PBS injected WT M. marinum infected mutant M. marinum infected. | pubmed:39916610 | Mut Inf 3 [210019 20 Mut Inf 36 s20 S231] | GSM5704993 | source name:Mut Inf kidney|treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | Mut Inf 3 [210019 20 Mut Inf 36 s20 S231] | Automatic adapter trimming Base calling bcl2fastq2 conversion software NovaSeq 6000 Alignment using STAR aligner version 2.5.3a and Ensembl reference genome GRCz11 Quantification of genewise read counts using featureCounts version 1.6.2 and Ensembl reference gene set release GRCz11.104 Generation of DESeq2 normalized counts using R version 3.6.1 and DESeq2 version 1.24.0 Genome build: GRCz11 Supplementary files format and content: Genewise read counts for each sample featureCounts .txt and protein coding gene filtered DESeq2 normalized count matrix .xlsx | Mut Inf kidney | 9 mpf to 10 mpf zebrafish were infected with approximately 30 cfu of ATCC 927 strain Mycobacterium marinum and the RNA was collected at 4 weeks post infection. PBS injected fish treated with identical protocol were used as controls. | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer’s instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | The zebrafish were maintained according to the standard protocols. | treatment:M. marinum infection|genotype:pycard / mutant|disease state:low dose 4 wpi|tissue:Zebrafish kidney | GSM5704993 | GSM5704993: Mut Inf 3 [210019 20 Mut Inf 36 s20 S231]; Danio rerio; RNA Seq | GSM5704993 | 1 | Total RNA was extracted from the adult zebrafish kidneys using the Qiagen RNeasy Mini Plus Kit ID: 74136 according to the manufacturer's instructions. RNA libraries were prepared for sequencing using standard Illumina protocols. | GEO Accession:GSM5704993 | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP348087 | loader:fastq load.py | 210019_20_Mut_Inf_36_s20_S231_L004_R1_001.fastq.gz 210019_20_Mut_Inf_36_s20_S231_L004_R2_001.fastq.gz | fastq fastq | 6906529169.0 | 35214335.0 | GSM5704993 r1 | 0:98.01 1:98.12 | A:1647670645;C:1800519104;G:1830091985;T:1613290370;N:14957065 | 98 | 98 | 1647670645 | 1800519104 | 1830091985 | 1613290370 | 14957065 | SRX13237920 | SRS11162464 | SRA1335306 | GEO | Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center | 2 | 0.96372 | 0.96513 | 0.11777 | 0.11299 | 0.82919 | 0.82806 | 0.67879 | 0.67604 | 100 | 100 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Finland | 2021-11-26 | Multi-stage | Multi-stage | Kidney | Renal System |
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CREATE TABLE run_metadata("run.accession" VARCHAR, "experiment.accession" VARCHAR, "sample.accession" VARCHAR, "study.accession" VARCHAR, bioproject VARCHAR, "study.title" VARCHAR, "study.alias" VARCHAR, "study.type" VARCHAR, "study.abstract" VARCHAR, "study.attributes" VARCHAR, "study.PMIDs" VARCHAR, "sample.description" VARCHAR, "sample.title" VARCHAR, "sample.alias" VARCHAR, "sample.centername" VARCHAR, "sample.attributes" VARCHAR, "GEOsample.title" VARCHAR, "GEOsample.dataprocessing" VARCHAR, "GEOsample.source" VARCHAR, "GEOsample.treatmentprotocol" VARCHAR, "GEOsample.extractprotocol" VARCHAR, "GEOsample.growthprotocol" VARCHAR, "GEOsample.characteristics" VARCHAR, "GEOsample.accession" VARCHAR, "experiment.title" VARCHAR, "experiment.alias" VARCHAR, "experiment.library_name" VARCHAR, "experiment.design_description" VARCHAR, "experiment.library_construction_protocol" VARCHAR, "experiment.attributes" VARCHAR, "experiment.library_strategy" VARCHAR, "experiment.library_source" VARCHAR, "experiment.library_selection" VARCHAR, "experiment.library_layout" VARCHAR, "experiment.platform" VARCHAR, "experiment.instrument_model" VARCHAR, "experiment.spot_descriptor" VARCHAR, "experiment.study_ref" VARCHAR, "run.title" VARCHAR, "run.attributes" VARCHAR, "run.filename" VARCHAR, "run.semantic_name" VARCHAR, "run.total_bases" DOUBLE, "run.total_spots" DOUBLE, "run.alias" VARCHAR, "run.read_lengths" VARCHAR, "run.base_counts" VARCHAR, "run.r1_length" BIGINT, "run.r2_length" BIGINT, "run.r3_length" BIGINT, "run.r4_length" BIGINT, "run.Acount" BIGINT, "run.Ccount" BIGINT, "run.Gcount" BIGINT, "run.Tcount" BIGINT, "run.Ncount" BIGINT, "run.experiment" VARCHAR, "run.pool_member" VARCHAR, "submission.accession" VARCHAR, "submission.srasource" VARCHAR, "submission.bioprojectsource" VARCHAR, "seqdetective.n_mates" BIGINT, "seqdetective.mapping_rate.mate1" DOUBLE, "seqdetective.mapping_rate.mate2" DOUBLE, "seqdetective.nofeature_rate.mate1" DOUBLE, "seqdetective.nofeature_rate.mate2" DOUBLE, "seqdetective.sparsity.mate1" DOUBLE, "seqdetective.sparsity.mate2" DOUBLE, "seqdetective.pos_strand_rate.mate1" DOUBLE, "seqdetective.pos_strand_rate.mate2" DOUBLE, "seqdetective.readlen.mate1" BIGINT, "seqdetective.readlen.mate2" BIGINT, "seqdetective.judgement.mate1" VARCHAR, "seqdetective.judgement.mate2" VARCHAR, "seqdetective.judgement.reason" VARCHAR, platform_family VARCHAR, instrument_generation VARCHAR, read_bias VARCHAR, selection_class VARCHAR, prep_kit VARCHAR, sc_or_bulk VARCHAR, tech_class VARCHAR, technology VARCHAR, tech_variant VARCHAR, "submission.bioprojectsource.country" VARCHAR, earliest_date DATE, devstage_curation VARCHAR, devstage_curation_coarse VARCHAR, tissue_curation VARCHAR, tissue_curation_coarse VARCHAR);;
CREATE INDEX idx_run_bioproject ON run_metadata(bioproject);;
CREATE INDEX idx_run_run_accession ON run_metadata("run.accession");;