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10 rows where technology = "generic-scrnaseq-only" and tissue_curation_coarse = "Renal System"

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  • Renal System · 10 ✖

tissue_curation 1

technology 1

  • generic-scrnaseq-only · 10 ✖

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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
41902 41902 SRR5337748 SRX2635098 SRS2043910 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS6 GSM2534771   tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult YS6 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts Mesonephros DL   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534771 GSM2534771: YS6; Danio rerio; RNA Seq GSM2534771   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534771 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS6_R1.fastq.gz fastq 5434051896.0 43127396.0 GSM2534771 r1 0:126 A:1185876928;C:1354521221;G:1643633065;T:1249907593;N:113089 126       1185876928 1354521221 1643633065 1249907593 113089 SRX2635098 SRS2043910 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.97351   0.17501   0.85303   0.75625   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41903 41903 SRR5337747 SRX2635097 SRS2043909 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS5 GSM2534770   tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult YS5 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts DL segments   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534770 GSM2534770: YS5; Danio rerio; RNA Seq GSM2534770   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534770 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS5_R1.fastq(1).gz fastq 2297696058.0 18235683.0 GSM2534770 r1 0:126 A:648837532;C:505738661;G:568578688;T:574489076;N:52101 126       648837532 505738661 568578688 574489076 52101 SRX2635097 SRS2043909 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.94402   0.1927   0.77585   0.67728   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41904 41904 SRR5337746 SRX2635096 SRS2043908 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS4 GSM2534769   tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult YS4 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts Mesonephros DL   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534769 GSM2534769: YS4; Danio rerio; RNA Seq GSM2534769   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534769 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS4_R1.fastq.gz fastq 4570634754.0 36274879.0 GSM2534769 r1 0:126 A:1179398927;C:1024363944;G:1239125274;T:1127644877;N:101732 126       1179398927 1024363944 1239125274 1127644877 101732 SRX2635096 SRS2043908 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.93083   0.27465   0.78102   0.70638   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41905 41905 SRR5337745 SRX2635095 SRS2043907 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS3 GSM2534768   tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult YS3 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts DL segments   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534768 GSM2534768: YS3; Danio rerio; RNA Seq GSM2534768   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534768 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS3_R1.fastq.gz fastq 5648398686.0 44828561.0 GSM2534768 r1 0:126 A:1607436982;C:1222995706;G:1369036558;T:1448805498;N:123942 126       1607436982 1222995706 1369036558 1448805498 123942 SRX2635095 SRS2043907 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.93399   0.20266   0.78076   0.73978   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41906 41906 SRR5337744 SRX2635094 SRS2043906 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS2 GSM2534767   tissue:Mes1phros DL|transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult YS2 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts Mesonephros DL   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh |age:adult GSM2534767 GSM2534767: YS2; Danio rerio; RNA Seq GSM2534767   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534767 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS2_R1.fastq.gz fastq 4680679374.0 37148249.0 GSM2534767 r1 0:126 A:1320151433;C:986429614;G:1112497899;T:1261495719;N:104709 126       1320151433 986429614 1112497899 1261495719 104709 SRX2635094 SRS2043906 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.91952   0.24724   0.73884   0.63985   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
41907 41907 SRR5337743 SRX2635093 SRS2043905 SRP101756 PRJNA378882 Transcriptome of the distal late segment of the zebrafish mesonephros GSE96519 Transcriptome Analysis We aimed to gain insights into the evolutionary origin of genetic mechanisms of NaCl handling. To this aim we obtained transcription profilings in the zebrafish distal late DL segment the equvalent segment of the mammalian distal convoluted tubules that play a critical role in NaCl homeostasis. Overall design: We compared the transcriptomes from DL segments and the rest of the mesonephros isolated from transgenic zebrafish expressing mCherry in the DL segments.   pubmed:28656378   YS1 GSM2534766   tissue:DL segments|transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult YS1 none provided by the submitter Genome build: n/a Supplementary files format and content: raw counts DL segments   DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN.   transgene:Tgslc12a3:mCherry|genotype:mCh+|age:adult GSM2534766 GSM2534766: YS1; Danio rerio; RNA Seq GSM2534766   1 DL segments were manually micro dissected from Tgslc12a3:mCherry and RNAs were extracted using the RNA extraction kit Machery Nagel. Apaptor ligated cDNA libraries were constructed using Ovation Single Cell RNA seq System NuGEN. GEO Accession:GSM2534766 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP101756     20150717.A-YS1_R1.fastq.gz fastq 7000703892.0 55561142.0 GSM2534766 r1 0:126 A:1521231890;C:1760818628;G:2148863730;T:1569634203;N:155441 126       1521231890 1760818628 2148863730 1569634203 155441 SRX2635093 SRS2043905 SRA544882 GEO Drummond, Nephrology, Massachusetts General Hospital 1 0.96016   0.1982   0.86261   0.75572   126   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc_generic single_cell_generic generic-scrnaseq-only   United States 2017-03-12 Adult Adult Kidney Renal System
76328 76328 SRR24835114 SRX20599525 SRS17899571 SRP441312 PRJNA980571 Targeting TNF/IL 17/MAPK Pathway in hE2A PBX1 Leukemia: effects of OUL35 KJ Pyr 9 and CID44216842 GSE234222 Transcriptome Analysis t1;19q23;p13 is one of the most common translocation genes in childhood acute lymphoblastic leukemia ALL and is also present in acute myeloid leukemia AML and mixed phenotype acute leukemia MPAL. This translocation results in the formation of the oncogenic E2A PBX1 fusion protein which contains a trans activating domain from E2A and a DNA binding homologous domain from PBX1. Despite its clear oncogenic potential the pathogenesis of E2A PBX1 fusion protein is not fully understood especially in leukemias other than ALL and effective targeted clinical therapies have not been developed. To address this we established a stable and heritable zebrafish line expressing human E2A PBX1 hE2A PBX1 for high throughput drug screening. Blood phenotype analysis showed that hE2A PBX1 expression induced myeloid hyperplasia by increasing myeloid differentiation propensity of hematopoietic stem cells HSPCs and myeloid proliferation in larvae and progressed to AML in adults. Mechanistic studies revealed that hE2A PBX1 activated the TNF/IL 17/MAPK signaling pathway in blood cells and induced myeloid hyperplasia by up regulating the expression of the runx1. Interestingly through high throughput drug screening three small molecules targeting the TNF/IL 17/MAPK signaling pathway were identified including OUL35 KJ Pyr 9 and CID44216842 which not only alleviated the hE2A PBX1 induced myeloid hyperplasia in zebrafish but also inhibited the growth and oncogenicity of human pre B ALL cells with E2A PBX1. Overall this study provides a novel hE2A PBX1 transgenic zebrafish leukemia model and identifies potential targeted therapeutic drugs which may offer new insights into the treatment of E2A PBX1 leukemia and improve the quality of life of leukemia patients. Overall design: Kidney marrow of the wild type Tghsp70:E2A PBX1 EGFP zebrafish post 3 month heat shock were isolated separately. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.   pubmed:38385270   WT KM 1 GSM7457552   source name:kidney marrow|development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:wt|geo loc name:missing|collection date:missing WT KM 1 To get high quality clean reads reads were further filtered by fastp version 0.18.0. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1 the better the repeatability between two parallel experiments. Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables gene expression into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas. RNA differential expression analysis was performed by DESeq2 software between two different groups and by edgeR between two samples. The genes/transcripts with the parameter of false discovery rate FDR below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts. We performed gene set enrichment analysis using software GSEA and MSigDB to identify whether a set of genes in specific GO terms\KEGG pathways\Reactome pathways\DO terms sh… kidney marrow   Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:wt GSM7457552 GSM7457552: WT KM 1; Danio rerio; RNA Seq GSM7457552 r1 GSM7457552 1 Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP441312   loader:fastq load.py WT-KM-1_1.fq.gz WT-KM-1_2.fq.gz fastq fastq 6487394100.0 21624647.0 GSM7457552 r1 0:150 1:150 A:1774895118;C:1466110386;G:1480006819;T:1766263784;N:117993 150 150     1774895118 1466110386 1480006819 1766263784 117993 SRX20599525 SRS17899571 SRA1650345 Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology 2 0.92675 0.92431 0.10444 0.10427 0.725 0.72468 0.5002 0.49957 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext sc_generic single_cell_generic generic-scrnaseq-only   China 2023-06-06 Adult Adult Kidney Renal System
76329 76329 SRR24835115 SRX20599524 SRS17899572 SRP441312 PRJNA980571 Targeting TNF/IL 17/MAPK Pathway in hE2A PBX1 Leukemia: effects of OUL35 KJ Pyr 9 and CID44216842 GSE234222 Transcriptome Analysis t1;19q23;p13 is one of the most common translocation genes in childhood acute lymphoblastic leukemia ALL and is also present in acute myeloid leukemia AML and mixed phenotype acute leukemia MPAL. This translocation results in the formation of the oncogenic E2A PBX1 fusion protein which contains a trans activating domain from E2A and a DNA binding homologous domain from PBX1. Despite its clear oncogenic potential the pathogenesis of E2A PBX1 fusion protein is not fully understood especially in leukemias other than ALL and effective targeted clinical therapies have not been developed. To address this we established a stable and heritable zebrafish line expressing human E2A PBX1 hE2A PBX1 for high throughput drug screening. Blood phenotype analysis showed that hE2A PBX1 expression induced myeloid hyperplasia by increasing myeloid differentiation propensity of hematopoietic stem cells HSPCs and myeloid proliferation in larvae and progressed to AML in adults. Mechanistic studies revealed that hE2A PBX1 activated the TNF/IL 17/MAPK signaling pathway in blood cells and induced myeloid hyperplasia by up regulating the expression of the runx1. Interestingly through high throughput drug screening three small molecules targeting the TNF/IL 17/MAPK signaling pathway were identified including OUL35 KJ Pyr 9 and CID44216842 which not only alleviated the hE2A PBX1 induced myeloid hyperplasia in zebrafish but also inhibited the growth and oncogenicity of human pre B ALL cells with E2A PBX1. Overall this study provides a novel hE2A PBX1 transgenic zebrafish leukemia model and identifies potential targeted therapeutic drugs which may offer new insights into the treatment of E2A PBX1 leukemia and improve the quality of life of leukemia patients. Overall design: Kidney marrow of the wild type Tghsp70:E2A PBX1 EGFP zebrafish post 3 month heat shock were isolated separately. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.   pubmed:38385270   WT KM 2 GSM7457553   source name:kidney marrow|development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:wt|geo loc name:missing|collection date:missing WT KM 2 To get high quality clean reads reads were further filtered by fastp version 0.18.0. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1 the better the repeatability between two parallel experiments. Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables gene expression into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas. RNA differential expression analysis was performed by DESeq2 software between two different groups and by edgeR between two samples. The genes/transcripts with the parameter of false discovery rate FDR below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts. We performed gene set enrichment analysis using software GSEA and MSigDB to identify whether a set of genes in specific GO terms\KEGG pathways\Reactome pathways\DO terms sh… kidney marrow   Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:wt GSM7457553 GSM7457553: WT KM 2; Danio rerio; RNA Seq GSM7457553 r1 GSM7457553 1 Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP441312   loader:fastq load.py WT-KM-2_1.fq.gz WT-KM-2_2.fq.gz fastq fastq 5742019800.0 19140066.0 GSM7457553 r1 0:150 1:150 A:1578475745;C:1289996320;G:1303093237;T:1570360797;N:93701 150 150     1578475745 1289996320 1303093237 1570360797 93701 SRX20599524 SRS17899572 SRA1650345 Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology 2 0.92391 0.91943 0.11727 0.11584 0.72981 0.73168 0.48805 0.48399 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext sc_generic single_cell_generic generic-scrnaseq-only   China 2023-06-06 Adult Adult Kidney Renal System
76330 76330 SRR24835116 SRX20599523 SRS17899570 SRP441312 PRJNA980571 Targeting TNF/IL 17/MAPK Pathway in hE2A PBX1 Leukemia: effects of OUL35 KJ Pyr 9 and CID44216842 GSE234222 Transcriptome Analysis t1;19q23;p13 is one of the most common translocation genes in childhood acute lymphoblastic leukemia ALL and is also present in acute myeloid leukemia AML and mixed phenotype acute leukemia MPAL. This translocation results in the formation of the oncogenic E2A PBX1 fusion protein which contains a trans activating domain from E2A and a DNA binding homologous domain from PBX1. Despite its clear oncogenic potential the pathogenesis of E2A PBX1 fusion protein is not fully understood especially in leukemias other than ALL and effective targeted clinical therapies have not been developed. To address this we established a stable and heritable zebrafish line expressing human E2A PBX1 hE2A PBX1 for high throughput drug screening. Blood phenotype analysis showed that hE2A PBX1 expression induced myeloid hyperplasia by increasing myeloid differentiation propensity of hematopoietic stem cells HSPCs and myeloid proliferation in larvae and progressed to AML in adults. Mechanistic studies revealed that hE2A PBX1 activated the TNF/IL 17/MAPK signaling pathway in blood cells and induced myeloid hyperplasia by up regulating the expression of the runx1. Interestingly through high throughput drug screening three small molecules targeting the TNF/IL 17/MAPK signaling pathway were identified including OUL35 KJ Pyr 9 and CID44216842 which not only alleviated the hE2A PBX1 induced myeloid hyperplasia in zebrafish but also inhibited the growth and oncogenicity of human pre B ALL cells with E2A PBX1. Overall this study provides a novel hE2A PBX1 transgenic zebrafish leukemia model and identifies potential targeted therapeutic drugs which may offer new insights into the treatment of E2A PBX1 leukemia and improve the quality of life of leukemia patients. Overall design: Kidney marrow of the wild type Tghsp70:E2A PBX1 EGFP zebrafish post 3 month heat shock were isolated separately. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.   pubmed:38385270   E2A PBX1 KM 1 GSM7457554   source name:kidney marrow|development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:Tghsp70:E2A PBX1 EGFP|geo loc name:missing|collection date:missing E2A PBX1 KM 1 To get high quality clean reads reads were further filtered by fastp version 0.18.0. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1 the better the repeatability between two parallel experiments. Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables gene expression into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas. RNA differential expression analysis was performed by DESeq2 software between two different groups and by edgeR between two samples. The genes/transcripts with the parameter of false discovery rate FDR below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts. We performed gene set enrichment analysis using software GSEA and MSigDB to identify whether a set of genes in specific GO terms\KEGG pathways\Reactome pathways\DO terms sh… kidney marrow   Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:Tghsp70:E2A PBX1 EGFP GSM7457554 GSM7457554: E2A PBX1 KM 1; Danio rerio; RNA Seq GSM7457554 r1 GSM7457554 1 Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP441312   loader:fastq load.py E2A-PBX1-KM-1_1.fq.gz E2A-PBX1-KM-1_2.fq.gz fastq fastq 6392366700.0 21307889.0 GSM7457554 r1 0:150 1:150 A:1755784364;C:1435584469;G:1449269156;T:1751607576;N:121135 150 150     1755784364 1435584469 1449269156 1751607576 121135 SRX20599523 SRS17899570 SRA1650345 Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology 2 0.92945 0.92734 0.1176 0.11766 0.72279 0.72352 0.48053 0.48034 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext sc_generic single_cell_generic generic-scrnaseq-only   China 2023-06-06 Adult Adult Kidney Renal System
76331 76331 SRR24835117 SRX20599522 SRS17899569 SRP441312 PRJNA980571 Targeting TNF/IL 17/MAPK Pathway in hE2A PBX1 Leukemia: effects of OUL35 KJ Pyr 9 and CID44216842 GSE234222 Transcriptome Analysis t1;19q23;p13 is one of the most common translocation genes in childhood acute lymphoblastic leukemia ALL and is also present in acute myeloid leukemia AML and mixed phenotype acute leukemia MPAL. This translocation results in the formation of the oncogenic E2A PBX1 fusion protein which contains a trans activating domain from E2A and a DNA binding homologous domain from PBX1. Despite its clear oncogenic potential the pathogenesis of E2A PBX1 fusion protein is not fully understood especially in leukemias other than ALL and effective targeted clinical therapies have not been developed. To address this we established a stable and heritable zebrafish line expressing human E2A PBX1 hE2A PBX1 for high throughput drug screening. Blood phenotype analysis showed that hE2A PBX1 expression induced myeloid hyperplasia by increasing myeloid differentiation propensity of hematopoietic stem cells HSPCs and myeloid proliferation in larvae and progressed to AML in adults. Mechanistic studies revealed that hE2A PBX1 activated the TNF/IL 17/MAPK signaling pathway in blood cells and induced myeloid hyperplasia by up regulating the expression of the runx1. Interestingly through high throughput drug screening three small molecules targeting the TNF/IL 17/MAPK signaling pathway were identified including OUL35 KJ Pyr 9 and CID44216842 which not only alleviated the hE2A PBX1 induced myeloid hyperplasia in zebrafish but also inhibited the growth and oncogenicity of human pre B ALL cells with E2A PBX1. Overall this study provides a novel hE2A PBX1 transgenic zebrafish leukemia model and identifies potential targeted therapeutic drugs which may offer new insights into the treatment of E2A PBX1 leukemia and improve the quality of life of leukemia patients. Overall design: Kidney marrow of the wild type Tghsp70:E2A PBX1 EGFP zebrafish post 3 month heat shock were isolated separately. Blood cells were collected from these tissues by pipetting and filtering and analyzed using scRNAseq.   pubmed:38385270   E2A PBX1 KM 2 GSM7457555   source name:kidney marrow|development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:Tghsp70:E2A PBX1 EGFP|geo loc name:missing|collection date:missing E2A PBX1 KM 2 To get high quality clean reads reads were further filtered by fastp version 0.18.0. Short reads alignment tool Bowtie2 version 2.2.8 was used for mapping reads to ribosome RNA rRNA database. The rRNA mapped reads then will be removed. The remaining clean reads were further used in assembly and gene abundance calculation.An index of the reference genome was built and paired end clean reads were mapped to the reference genome using HISAT2. 2.4 and other parameters set as a default. The mapped reads of each sample were assembled by using StringTie v1.3.1 in a reference based approach. For each transcription region a FPKM fragment per kilobase of transcript per million mapped reads value was calculated to quantify its expression abundance and variations using RSEM software. Correlation analysis was performed by R. Correlation of two parallel experiments provides the evaluation of the reliability of experimental results as well as operational stability. The correlation coefficient between two replicas was calculated to evaluate repeatability between samples. The closer the correlation coefficient gets to 1 the better the repeatability between two parallel experiments. Principal component analysis PCA was performed with R package gmodels http://www.r project.org/ in this experience. PCA is a statistical procedure that converts hundreds of thousands of correlated variables gene expression into a set of values of linearly uncorrelated variables called principal components. PCA is largely used to reveal the structure/relationship of the samples/datas. RNA differential expression analysis was performed by DESeq2 software between two different groups and by edgeR between two samples. The genes/transcripts with the parameter of false discovery rate FDR below 0.05 and absolute fold change≥2 were considered differentially expressed genes/transcripts. We performed gene set enrichment analysis using software GSEA and MSigDB to identify whether a set of genes in specific GO terms\KEGG pathways\Reactome pathways\DO terms sh… kidney marrow   Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer’s protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   development stage:6 mpf|tissue:kidney marrow|cell type:blood cells|genotype:Tghsp70:E2A PBX1 EGFP GSM7457555 GSM7457555: E2A PBX1 KM 2; Danio rerio; RNA Seq GSM7457555 r1 GSM7457555 1 Kidney marrows were isolated from 6 mpf fish placed in PBS with 5% fetal bovine serum triturated by pipet and filtered through a 40 μm cell strainer. Total RNA was extracted using a Trizol reagent kit Invitrogen Carlsbad CA USA according to the manufacturer's protocol. RNA quality was assessed on an Agilent 2100 Bioanalyzer Agilent Technologies Palo Alto CA USA and checked using RNase free agarose gel electrophoresis post total RNA was extracted eukaryotic mRNA was enriched by OligodTbeads.Then the enriched mRNA was fragmented into short fragments using fragmentation buffer and reversly transcribed into cDNA by using NEBNext Ultra RNA Library Prep Kit for IlluminaNEB #7530 New England Biolabs Ipswich MA USA. The purified double stranded cDNA fragments were end repaired A base was added and ligated to Illumina sequencing adapters. The ligation reaction was purified with the AMPure XP Beads1.0X. And polymerase chain reaction PCR amplified. The resulting cDNA library was sequenced using Illumina Novaseq6000 by Gene Denovo Biotechnology Co. Guangzhou China.   RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina NovaSeq 6000   SRP441312   loader:fastq load.py E2A-PBX1-KM-2_2.fq.gz E2A-PBX1-KM-2_1.fq.gz fastq fastq 6481440000.0 21604800.0 GSM7457555 r1 0:150 1:150 A:1773856613;C:1460702707;G:1475415238;T:1771402610;N:62832 150 150     1773856613 1460702707 1475415238 1771402610 62832 SRX20599522 SRS17899569 SRA1650345 Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology Division of Cell, Developmental and Integrative Biology, School of Medicine, South China University of Technology 2 0.93286 0.9293 0.11326 0.11315 0.7274 0.7292 0.49505 0.48961 150 150 B B biological fallback assumption illumina novaseq_era unknown poly_a nebnext sc_generic single_cell_generic generic-scrnaseq-only   China 2023-06-06 Adult Adult 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");;