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9 rows where experiment.library_layout = "SINGLE", technology = "smartseq" and tissue_curation_coarse = "Renal System"

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tissue_curation_coarse 1

  • Renal System · 9 ✖

tissue_curation 1

technology 1

  • smartseq · 9 ✖

experiment.platform 1

experiment.library_strategy 1

experiment.library_source 1

experiment.library_selection 1

experiment.library_layout 1

  • SINGLE · 9 ✖

devstage_curation_coarse 1

devstage_curation 1

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
49049 49049 SRR7633485 SRX4497216 SRS3618216 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 pod 03 GSM3317057   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA G2 pod 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G2 mRNA GSM3317057 GSM3317057: G2 pod 03; Danio rerio; RNA Seq GSM3317057   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317057 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S9_trimmed.fastq.gz fastq 1265733350.0 25073196.0 GSM3317057 r1 0:50.48 1:0 A:351449147;C:285891495;G:278677300;T:349486454;N:228954 50 0     351449147 285891495 278677300 349486454 228954 SRX4497216 SRS3618216 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.88664   0.09978   0.70747   0.46307   50   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49050 49050 SRR7633484 SRX4497215 SRS3618215 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 pod 02 GSM3317056   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA G2 pod 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G2 mRNA GSM3317056 GSM3317056: G2 pod 02; Danio rerio; RNA Seq GSM3317056   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317056 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S8_trimmed.fastq.gz fastq 927703036.0 18397661.0 GSM3317056 r1 0:50.43 1:0 A:256098583;C:212027468;G:205646180;T:253765375;N:165430 50 0     256098583 212027468 205646180 253765375 165430 SRX4497215 SRS3618215 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.82269   0.09332   0.70676   0.47673   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49051 49051 SRR7633483 SRX4497214 SRS3618214 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G2 pod 01 GSM3317055   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G2 mRNA G2 pod 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G2 mRNA GSM3317055 GSM3317055: G2 pod 01; Danio rerio; RNA Seq GSM3317055   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317055 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S7_trimmed.fastq.gz fastq 1868917850.0 36965227.0 GSM3317055 r1 0:50.56 1:0 A:518334465;C:423085551;G:412301170;T:514857394;N:339270 50 0     518334465 423085551 412301170 514857394 339270 SRX4497214 SRS3618214 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.8967   0.11444   0.66793   0.47524   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49052 49052 SRR7633482 SRX4497213 SRS3618213 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 pod 03 GSM3317054   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA G0 pod 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G0 mRNA GSM3317054 GSM3317054: G0 pod 03; Danio rerio; RNA Seq GSM3317054   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317054 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S6_trimmed.fastq.gz fastq 1989842108.0 39354652.0 GSM3317054 r1 0:50.56 1:0 A:547820589;C:452831323;G:441782569;T:547047192;N:360435 50 0     547820589 452831323 441782569 547047192 360435 SRX4497213 SRS3618213 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.88797   0.1001   0.67016   0.46755   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49053 49053 SRR7633481 SRX4497212 SRS3618212 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 pod 02 GSM3317053   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA G0 pod 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G0 mRNA GSM3317053 GSM3317053: G0 pod 02; Danio rerio; RNA Seq GSM3317053   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317053 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S5_trimmed.fastq.gz fastq 1784099065.0 35295758.0 GSM3317053 r1 0:50.55 1:0 A:493338451;C:401706697;G:388876128;T:499853218;N:324571 50 0     493338451 401706697 388876128 499853218 324571 SRX4497212 SRS3618212 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.86757   0.09319   0.6733   0.46511   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49054 49054 SRR7633480 SRX4497211 SRS3618211 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   G0 pod 01 GSM3317052   tissue:zebrafish podocyte|line:pod:mCherry|treatment:human APOL1 G0 mRNA G0 pod 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:human APOL1 G0 mRNA GSM3317052 GSM3317052: G0 pod 01; Danio rerio; RNA Seq GSM3317052   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317052 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S4_trimmed.fastq.gz fastq 1294942611.0 25649695.0 GSM3317052 r1 0:50.49 1:0 A:358939215;C:292943376;G:284204779;T:358621256;N:233985 50 0     358939215 292943376 284204779 358621256 233985 SRX4497211 SRS3618211 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89677   0.09742   0.66695   0.46036   49   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49055 49055 SRR7633479 SRX4497210 SRS3618210 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control pod 03 GSM3317051   tissue:zebrafish podocyte|line:pod:mCherry|treatment:control control pod 03 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:control GSM3317051 GSM3317051: control pod 03; Danio rerio; RNA Seq GSM3317051   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317051 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S3_trimmed.fastq.gz fastq 1864996530.0 36896407.0 GSM3317051 r1 0:50.55 1:0 A:514542102;C:423583183;G:412707586;T:513826127;N:337532 50 0     514542102 423583183 412707586 513826127 337532 SRX4497210 SRS3618210 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89167   0.10091   0.67773   0.48093   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49056 49056 SRR7633478 SRX4497209 SRS3618209 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control pod 02 GSM3317050   tissue:zebrafish podocyte|line:pod:mCherry|treatment:control control pod 02 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:control GSM3317050 GSM3317050: control pod 02; Danio rerio; RNA Seq GSM3317050   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317050 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S2_trimmed.fastq.gz fastq 1405360276.0 27811908.0 GSM3317050 r1 0:50.53 1:0 A:388467227;C:319138771;G:310773160;T:386727396;N:253722 50 0     388467227 319138771 310773160 386727396 253722 SRX4497209 SRS3618209 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.898   0.10269   0.66967   0.45546   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval Kidney Renal System
49057 49057 SRR7633477 SRX4497208 SRS3618208 SRP155992 PRJNA483985 Transcriptomic analysis of isolated zebrafish podocytes and endothelial cells exposed to human APOL1 mRNA GSE118000 Transcriptome Analysis We injected zebrafish embryos with human APOL1 mRNA dissociated embryos at xxx days of age and purified podocytes and endothelial cells with fluorescence activated cell sorting. post sorting mRNA was extracted from purified cells and used to generate cDNA libraries which were sequenced on an Illumina HiSeq 2500. Overall design: Examination of two cell types exposed to one of 3 mRNA treatments sham APOL1 G0 APOL1 G2   pubmed:31158233   control pod 01 GSM3317049   tissue:zebrafish podocyte|line:pod:mCherry|treatment:control control pod 01 Quality control analysis of each sequenced library was performed using fastQC version 0.11.7 Removal of primer adapters was performed with Trim Galore version 0.4.0 Trimmed sequencing reads were aligned and mapped using to the D. rerio genome release GRCm38 using the STAR version 2.6.0c reads were filtered sorted and indexed with Samtools version 1.3 Uniquely mapped reads were used to generate counts for each annotated gene using HTSeq 0.10.0 read counts were analyzed with DESeq2 Genome build: GRCm38 Supplementary files format and content: .count files contain raw unnormalized read counts for input to DESeq2 zebrafish podocyte Zebrafsih were injected with 1nL of either APOL1 mRNA 150pg/nL or phenol red RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech Zebrafish were injected immediately post fertilization single cell stage and enbryos were harvested 4 dpf line:pod:mCherry|treatment:control GSM3317049 GSM3317049: control pod 01; Danio rerio; RNA Seq GSM3317049   1 RNA was extracted from purified cells using a Qiagen RNeasy micro kit cDNA libraries were prepared using the SMARTSeq v.4 Ultra Low Input RNA Kit Clonetech GEO Accession:GSM3317049 RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP155992     BA_S1_trimmed.fastq.gz fastq 931525657.0 18454172.0 GSM3317049 r1 0:50.48 1:0 A:259125695;C:210068089;G:204402139;T:257763012;N:166722 50 0     259125695 210068089 204402139 257763012 166722 SRX4497208 SRS3618208 SRA749599 GEO Duke Molecular Physiology Institute, Duke University Medical Center 1 0.89072   0.10423   0.67107   0.46057   51   B   usable mapping rate illumina hiseq_era unknown cdna_unspecified unknown sc single_cell_plate smartseq   United States 2018-08-01 Larval Larval 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");;