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15 rows where devstage_curation = "Pharyngula" and tissue_curation = "Head"

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  • Head · 15 ✖

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devstage_curation 1

  • Pharyngula · 15 ✖
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
53640 53640 SRR10004189 SRX6742925 SRS5293748 SRP218844 PRJNA560923 Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA seq data of 33 hpf rbm24a / and wildtype embryo head explant GSE136003 Transcriptome Analysis This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant without xxx in splicing patterns. Overall design: It contains two groups: wildtype and rbm24a / . Wildtype was used as control   pubmed:32170011   R 1 GSM4039262   source name:head explant|dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB|genotype/variation: 8 bp deletion by TALEN in the 1st exon R 1 Base calling: Bcl2fastq v2.17.1.14 Data filtering step: Cutadapt（version 1.9.1） Allignment: Hisat2v2.0.1 default parameter Differential gene expression: DESeq2（V1.6.3） Gene expression: Htseq software V 0.6.1 Genome build: GRCz11 Supplementary files format and content: excel file gene expression level in FPKM Supplementary files format and content: excel file differentially expressed genes head explant the head region of 33 hpf embryos were cut and collected for RNA extraction Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al. 2017.   dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB|genotype/variation: 8 bp deletion by TALEN in the 1st exon GSM4039262 GSM4039262: R 1; Danio rerio; RNA Seq GSM4039262   1 Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al. 2017. GEO Accession:GSM4039262 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP218844     R1_combined_R1.fastq.gz R1_combined_R2.fastq.gz fastq fastq 7918195500.0 26393985.0 GSM4039262 r1 0:150 1:150 A:2130539253;C:1816469246;G:1847209333;T:2123238120;N:739548 150 150     2130539253 1816469246 1847209333 2123238120 739548 SRX6742925 SRS5293748 SRA945259 GEO School of Lifesciences, Shandong University 2 0.92358 0.92932 0.06139 0.0616 0.7218 0.73192 0.4833 0.48317 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2019-08-19 Pharyngula Embryo Head Nervous System
53641 53641 SRR10004188 SRX6742924 SRS5293747 SRP218844 PRJNA560923 Rbm24 functions as a critical translational regulator to pretect crystallin proteins accumulation for lens transparency. RNA seq data of 33 hpf rbm24a / and wildtype embryo head explant GSE136003 Transcriptome Analysis This experiment is aimed to compare the transcriptomes of rbm24a mutant and wildtype at 33 hpf. As Rbm24a is an RNA binding protein this comparation is suitable to obtain information on differential gene expression and alternative splicing. We found that the expression of most of the crystallin genes and many other lens specific genes are down regulated in rbm24a mutant without xxx in splicing patterns. Overall design: It contains two groups: wildtype and rbm24a / . Wildtype was used as control   pubmed:32170011   WT 1 GSM4039261   source name:head explant|dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB WT 1 Base calling: Bcl2fastq v2.17.1.14 Data filtering step: Cutadapt（version 1.9.1） Allignment: Hisat2v2.0.1 default parameter Differential gene expression: DESeq2（V1.6.3） Gene expression: Htseq software V 0.6.1 Genome build: GRCz11 Supplementary files format and content: excel file gene expression level in FPKM Supplementary files format and content: excel file differentially expressed genes head explant the head region of 33 hpf embryos were cut and collected for RNA extraction Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al. 2017.   dev stage:33 hpf|tissue:head region cut before otic vesicle|strain:AB GSM4039261 GSM4039261: WT 1; Danio rerio; RNA Seq GSM4039261   1 Trizol and isopropanol precipitation The mRNA libraries were constructed by TruSeq RNA Library Preparation Kit and 100 bp paired end sequencing was performed on Illumina HiSeq 2000. The data obtained from three independent samples were aligned and analysed as described Shao et al. 2017. GEO Accession:GSM4039261 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP218844     WT1_combined_R1.fastq.gz WT1_combined_R2.fastq.gz fastq fastq 6916773600.0 23055912.0 GSM4039261 r1 0:150 1:150 A:1871554357;C:1578397354;G:1603789627;T:1862359143;N:673119 150 150     1871554357 1578397354 1603789627 1862359143 673119 SRX6742924 SRS5293747 SRA945259 GEO School of Lifesciences, Shandong University 2 0.92052 0.92653 0.07178 0.07144 0.72076 0.73312 0.46318 0.48078 150 150 B B biological fallback assumption illumina hiseq_era unknown cdna_unspecified trueseq bulk unknown unknown   China 2019-08-19 Pharyngula Embryo Head Nervous System
59313 59313 SRR11855605 SRX8405706 SRS6718147 SRP264942 PRJNA635369 Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing GSE151273 Transcriptome Analysis Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 / zebrafish were generated by deep sequence in three independent biological replicates.   pubmed:33476374   AB Head mt 3 GSM4570141   source name:Head|strain:AB|tissue:Head|age:36 hpf / AB Head mt 3 Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels Trapnell Cole et al. 2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample Head   Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system   strain:AB|tissue:Head|age:36 hpf / GSM4570141 GSM4570141: AB Head mt 3; Danio rerio; RNA Seq GSM4570141   1 Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system GEO Accession:GSM4570141 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP264942     mt3_2.fastq.gz mt3_1.fastq.gz fastq fastq 13313574600.0 44378582.0 GSM4570141 r1 0:150 1:150 A:3477543422;C:3199199156;G:3207403563;T:3429195541;N:232918 150 150     3477543422 3199199156 3207403563 3429195541 232918 SRX8405706 SRS6718147 SRA1080304 GEO Huazhong University of Science and Technology 2 0.94266 0.94401 0.08928 0.08979 0.69191 0.69179 0.45995 0.46233 150 150 B B biological fallback assumption illumina hiseq_era 5prime poly_a nebnext bulk unknown unknown   China 2020-05-27 Pharyngula Embryo Head Nervous System
59314 59314 SRR11855604 SRX8405705 SRS6718146 SRP264942 PRJNA635369 Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing GSE151273 Transcriptome Analysis Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 / zebrafish were generated by deep sequence in three independent biological replicates.   pubmed:33476374   AB Head sib3 GSM4570140   source name:Head|strain:AB|tissue:Head|age:36 hpf type AB Head sib3 Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels Trapnell Cole et al. 2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample Head   Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system   strain:AB|tissue:Head|age:36 hpf type GSM4570140 GSM4570140: AB Head sib3; Danio rerio; RNA Seq GSM4570140   1 Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system GEO Accession:GSM4570140 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP264942     sib3_2.fastq.gz sib3_1.fastq.gz fastq fastq 13010052000.0 43366840.0 GSM4570140 r1 0:150 1:150 A:3375957983;C:3149320854;G:3162958825;T:3321576463;N:237875 150 150     3375957983 3149320854 3162958825 3321576463 237875 SRX8405705 SRS6718146 SRA1080304 GEO Huazhong University of Science and Technology 2 0.95142 0.95014 0.06943 0.06912 0.69049 0.69065 0.45158 0.46064 150 150 B B biological fallback assumption illumina hiseq_era 5prime poly_a nebnext bulk unknown unknown   China 2020-05-27 Pharyngula Embryo Head Nervous System
59315 59315 SRR11855603 SRX8405704 SRS6718145 SRP264942 PRJNA635369 Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing GSE151273 Transcriptome Analysis Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 / zebrafish were generated by deep sequence in three independent biological replicates.   pubmed:33476374   AB Head mt 2 GSM4570139   source name:Head|strain:AB|tissue:Head|age:36 hpf / AB Head mt 2 Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels Trapnell Cole et al. 2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample Head   Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system   strain:AB|tissue:Head|age:36 hpf / GSM4570139 GSM4570139: AB Head mt 2; Danio rerio; RNA Seq GSM4570139   1 Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system GEO Accession:GSM4570139 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP264942     mt2_1.fastq.gz mt2_2.fastq.gz fastq fastq 13374951000.0 44583170.0 GSM4570139 r1 0:150 1:150 A:3463556768;C:3233594067;G:3255830360;T:3421731102;N:238703 150 150     3463556768 3233594067 3255830360 3421731102 238703 SRX8405704 SRS6718145 SRA1080304 GEO Huazhong University of Science and Technology 2 0.94607 0.94512 0.08117 0.08079 0.698 0.69875 0.45364 0.45399 150 150 B B biological fallback assumption illumina hiseq_era 5prime poly_a nebnext bulk unknown unknown   China 2020-05-27 Pharyngula Embryo Head Nervous System
59316 59316 SRR11855602 SRX8405703 SRS6718144 SRP264942 PRJNA635369 Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing GSE151273 Transcriptome Analysis Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 / zebrafish were generated by deep sequence in three independent biological replicates.   pubmed:33476374   AB Head sib2 GSM4570138   source name:Head|strain:AB|tissue:Head|age:36 hpf type AB Head sib2 Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels Trapnell Cole et al. 2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample Head   Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system   strain:AB|tissue:Head|age:36 hpf type GSM4570138 GSM4570138: AB Head sib2; Danio rerio; RNA Seq GSM4570138   1 Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system GEO Accession:GSM4570138 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP264942     sib2_1.fastq.gz sib2_2.fastq.gz fastq fastq 12076874100.0 40256247.0 GSM4570138 r1 0:150 1:150 A:3116319895;C:2937698203;G:2949917740;T:3072719174;N:219088 150 150     3116319895 2937698203 2949917740 3072719174 219088 SRX8405703 SRS6718144 SRA1080304 GEO Huazhong University of Science and Technology 2 0.95283 0.95237 0.06658 0.06623 0.69292 0.69365 0.44936 0.45234 150 150 B B biological fallback assumption illumina hiseq_era 5prime poly_a nebnext bulk unknown unknown   China 2020-05-27 Pharyngula Embryo Head Nervous System
59317 59317 SRR11855601 SRX8405702 SRS6718143 SRP264942 PRJNA635369 Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing GSE151273 Transcriptome Analysis Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 / zebrafish were generated by deep sequence in three independent biological replicates.   pubmed:33476374   AB Head mt 1 GSM4570137   source name:Head|strain:AB|tissue:Head|age:36 hpf / AB Head mt 1 Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels Trapnell Cole et al. 2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample Head   Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system   strain:AB|tissue:Head|age:36 hpf / GSM4570137 GSM4570137: AB Head mt 1; Danio rerio; RNA Seq GSM4570137   1 Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system GEO Accession:GSM4570137 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP264942     mt1_1.fastq.gz mt1_2.fastq.gz fastq fastq 12961323900.0 43204413.0 GSM4570137 r1 0:150 1:150 A:3332696255;C:3164828320;G:3171695699;T:3291860380;N:243246 150 150     3332696255 3164828320 3171695699 3291860380 243246 SRX8405702 SRS6718143 SRA1080304 GEO Huazhong University of Science and Technology 2 0.95246 0.94862 0.06807 0.06741 0.71634 0.71585 0.45271 0.44523 150 150 B B biological fallback assumption illumina hiseq_era 5prime poly_a nebnext bulk unknown unknown   China 2020-05-27 Pharyngula Embryo Head Nervous System
59318 59318 SRR11855600 SRX8405701 SRS6718142 SRP264942 PRJNA635369 Prpf31 is essential for the survival and differentiation of retinal progenitor cells by modulating alternative splicing GSE151273 Transcriptome Analysis Dysfunction of splicing factors often result in abnormal cell differentiation and apoptosis especially in neural tissues. Mutations in pre mRNAs processing factor 31 PRPF31 cause autosomal dominant retinitis pigmentosa a progressive retinal degeneration disease. The transcriptome wide splicing events specifically regulated by PRPF31 and their biological roles in the development and maintenance of retina are still unclear. Here we showed that the differentiation and viability of retinal progenitor cells RPCs are severely perturbed in prpf31 knockout zebrafish when compared with other tissues at an early embryonic stage. At the cellular level significant mitotic arrest and DNA damage were observed. These defects could be rescued by the wild type human PRPF31 rather than the disease associated mutants. Further bioinformatic analysis and experimental verification uncovered that Prpf31 deletion predominantly causes the skipping of exons with a weak five prime splicing site. Moreover genes necessary for DNA repair and mitotic progression are most enriched among the differentially spliced events which may explain the cellular and tissular defects in prpf31 mutant retinas. This is the first time that Prpf31 is demonstrated to be essential for the survival and differentiation of RPCs during retinal neurogenesis by specifically modulating the alternative splicing of genes involved in DNA repair and mitosis. Overall design: Head mRNA profiles of 36 hpf sibling wild type and prpf31 / zebrafish were generated by deep sequence in three independent biological replicates.   pubmed:33476374   AB Head sib1 GSM4570136   source name:Head|strain:AB|tissue:Head|age:36 hpf type AB Head sib1 Illumina Casava1.8 software used for basecalling. RNA seq reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence then mapped to GRCz11 genome assembly using HISAT version 2.0.4. HTSeq v0.9.1 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels Trapnell Cole et al. 2010 Genome build: GRCz11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample Supplementary files format and content: tab delimited text files with raw gene counts for every gene and every sample Head   Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of 3’ ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system   strain:AB|tissue:Head|age:36 hpf type GSM4570136 GSM4570136: AB Head sib1; Danio rerio; RNA Seq GSM4570136   1 Zebrafish embryos at 36 hpf were used for total RNA extraction. The tails were cut off and used for genotyping. Heads were dissected from wt siblings or prpf31 knockout embryos using 21G needles and put together to extract RNA using the TRIzol Reagent Life Technologies. 35 heads were used for each RNA sample A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. Briefly mRNA was purified from total RNA using poly T oligo attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in NEBNext First Strand Synthesis Reaction Buffer（5X） . First strand cDNA was synthesized using random hexamer primer and M MuLV Reverse Transcriptase（RNase H ） . Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. post adenylation of three prime ends of DNA fragments NEBNext Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 250300 bp in length the library fragments were purified with AMPure XP system Beckman Coulter Beverly USA. Then 3 µl USER Enzyme NEB USA was used with size selected adaptor ligated cDNA at 37°C for 15 min followed by 5 min at 95 °C before PCR. Then PCR was performed with Phusion High Fidelity DNA polymerase Universal PCR primers and Index X Primer. At last PCR products were purified AMPure XP system and library quality was assessed on the Agilent Bioanalyzer 2100 system GEO Accession:GSM4570136 RNA-Seq TRANSCRIPTOMIC cDNA PAIRED ILLUMINA Illumina HiSeq 2000   SRP264942     sib1_1.fastq.gz sib1_2.fastq.gz fastq fastq 11694742200.0 38982474.0 GSM4570136 r1 0:150 1:150 A:3017467040;C:2846786828;G:2857204470;T:2973074374;N:209488 150 150     3017467040 2846786828 2857204470 2973074374 209488 SRX8405701 SRS6718142 SRA1080304 GEO Huazhong University of Science and Technology 2 0.95096 0.95068 0.07163 0.07124 0.6939 0.69351 0.46447 0.46482 150 150 B B biological fallback assumption illumina hiseq_era 5prime poly_a nebnext bulk unknown unknown   China 2020-05-27 Pharyngula Embryo Head Nervous System
69472 69472 SRR18712321 SRX14812930 SRS12569573 SRP369458 PRJNA825495 Regulation of retina microexons by srrm3 in zebrafish PRJNA825495 Other To investigate the role of srrm3 as a regulator of retina microexons RetMICs we have sequenced heads from WT animals at 24 hpf and enucleated eyes from 48 hpf 60 hpf and 72 hpf larvae WT and KO for srrm3.         Head 24hpf WT b   strain:WT|dev stage:24 hpf|sex:NA|tissue:Head|BioSampleModel:Model organism or animal                 Heads from 24 hpf larvae WT for the eMIC domain of srrm3. Head 24hpf WT Head 24hpf WT WT and srrm3 mutant zebrafish were grown at 28C 14h light/10h dark cycle. Extract protocol: 24 hpf WT fish heads were removed and pulled for RNA extraction using RNA RNeasy Mini kit QIAGEN. Larvae eyes were removed and from twenty to sixty eyes per genotype were pulled for RNA extraction using RNA RNeasy Micro kit QIAGENLibrary preparation: RNA libraries were prepared for sequencing using standard Illumina protocols; polyA selected stranded RNA seq     RNA-Seq TRANSCRIPTOMIC RANDOM PAIRED ILLUMINA Illumina HiSeq 2500   SRP369458     Head_24hpf_WT_b_R1-125.fq.gz Head_24hpf_WT_b_R2-125.fq.gz fastq fastq 16050157000.0 64200628.0 Head 24hpf WT b R1 125.fq.gz 0:125 1:125 A:4076433263;C:3955246853;G:3964617037;T:4044497256;N:9362591 125 125     4076433263 3955246853 3964617037 4044497256 9362591 SRX14812930 SRS12569573 SRA1402039 Centre for Genomic Regulation|Systems Biology Centre for Genomic Regulation|Systems Biology 2 0.97774 0.97918 0.03623 0.03592 0.71035 0.71474 0.46304 0.46994 125 125 B B biological fallback assumption illumina hiseq_era unknown random_priming trueseq bulk unknown unknown   Spain 2022-04-11 Pharyngula Embryo Head Nervous System
70954 70954 SRR21006674 SRX17023411 SRS14607347 SRP390914 PRJNA868349 Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [RNA seq] GSE210940 Other Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish parent bioproject:PRJNA868347 pubmed:37460694   miRNA 128 WT 26HPF HWT2 GSM6443146   source name:head|cell line:kdrl:GFP+|cell type:endothelial cells|genotype:WT|tissue:head|time:26HPF|geo loc name:missing|collection date:missing miRNA 128 WT 26HPF HWT2 Sequence reads were trimmed for adaptor sequence/low quality sequence using BBDUK Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR Read count extraction was performed using HTSEQ Differential gene expression was performed using Deseq2 Assembly: GRCz10 /GRCh38 Supplementary files format and content: tab delimited text files include read counts for each Sample head   RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   cell line:kdrl:GFP+|cell type:endothelial cells|genotype:WT|tissue:head|time:26HPF GSM6443146 GSM6443146: miRNA 128 WT 26HPF HWT2; Danio rerio; RNA Seq GSM6443146 r1 GSM6443146 1 RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390914     26WTH3_S47_L002_R1_001.fastq.gz fastq 293662860.0 3863985.0 GSM6443146 r1 0:76 1:0 A:88773317;C:65249979;G:70156873;T:69476812;N:5879 76 0     88773317 65249979 70156873 69476812 5879 SRX17023411 SRS14607347 SRA1472938 Nicoli Lab, Genetics/Internal Medicine, Yale University Nicoli Lab, Genetics/Internal Medicine, Yale University 1 0.83214   0.26114   0.83422   0.6553   76   B   usable mapping rate illumina hiseq_era 3prime small_rna lexogen bulk unknown unknown   United States 2022-08-10 Pharyngula Embryo Head Nervous System
70955 70955 SRR21006675 SRX17023410 SRS14607346 SRP390914 PRJNA868349 Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [RNA seq] GSE210940 Other Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish parent bioproject:PRJNA868347 pubmed:37460694   miRNA 128 WT 26HPF HWT1 GSM6443145   source name:head|cell line:kdrl:GFP+|cell type:endothelial cells|genotype:WT|tissue:head|time:26HPF|geo loc name:missing|collection date:missing miRNA 128 WT 26HPF HWT1 Sequence reads were trimmed for adaptor sequence/low quality sequence using BBDUK Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR Read count extraction was performed using HTSEQ Differential gene expression was performed using Deseq2 Assembly: GRCz10 /GRCh38 Supplementary files format and content: tab delimited text files include read counts for each Sample head   RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   cell line:kdrl:GFP+|cell type:endothelial cells|genotype:WT|tissue:head|time:26HPF GSM6443145 GSM6443145: miRNA 128 WT 26HPF HWT1; Danio rerio; RNA Seq GSM6443145 r1 GSM6443145 1 RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390914     26WTH2_S46_L002_R1_001.fastq.gz fastq 283439720.0 3729470.0 GSM6443145 r1 0:76 1:0 A:88271336;C:60494399;G:65947843;T:68720414;N:5728 76 0     88271336 60494399 65947843 68720414 5728 SRX17023410 SRS14607346 SRA1472938 Nicoli Lab, Genetics/Internal Medicine, Yale University Nicoli Lab, Genetics/Internal Medicine, Yale University 1 0.82341   0.21988   0.83179   0.65713   76   B   usable mapping rate illumina hiseq_era 3prime small_rna lexogen bulk unknown unknown   United States 2022-08-10 Pharyngula Embryo Head Nervous System
70956 70956 SRR21006676 SRX17023409 SRS14607345 SRP390914 PRJNA868349 Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [RNA seq] GSE210940 Other Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish parent bioproject:PRJNA868347 pubmed:37460694   miRNA 128 mutant 26HPF HMT4 GSM6443144   source name:head|cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF|geo loc name:missing|collection date:missing miRNA 128 mutant 26HPF HMT4 Sequence reads were trimmed for adaptor sequence/low quality sequence using BBDUK Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR Read count extraction was performed using HTSEQ Differential gene expression was performed using Deseq2 Assembly: GRCz10 /GRCh38 Supplementary files format and content: tab delimited text files include read counts for each Sample head   RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF GSM6443144 GSM6443144: miRNA 128 mutant 26HPF HMT4; Danio rerio; RNA Seq GSM6443144 r1 GSM6443144 1 RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390914     26128H4_S42_L002_R1_001.fastq.gz fastq 214038648.0 2816298.0 GSM6443144 r1 0:76 1:0 A:66311060;C:43807945;G:47240963;T:56674434;N:4246 76 0     66311060 43807945 47240963 56674434 4246 SRX17023409 SRS14607345 SRA1472938 Nicoli Lab, Genetics/Internal Medicine, Yale University Nicoli Lab, Genetics/Internal Medicine, Yale University 1 0.83728   0.15836   0.81278   0.67399   76   B   usable mapping rate illumina hiseq_era 3prime small_rna lexogen bulk unknown unknown   United States 2022-08-10 Pharyngula Embryo Head Nervous System
70957 70957 SRR21006677 SRX17023408 SRS14607344 SRP390914 PRJNA868349 Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [RNA seq] GSE210940 Other Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish parent bioproject:PRJNA868347 pubmed:37460694   miRNA 128 mutant 26HPF HMT3 GSM6443143   source name:head|cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF|geo loc name:missing|collection date:missing miRNA 128 mutant 26HPF HMT3 Sequence reads were trimmed for adaptor sequence/low quality sequence using BBDUK Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR Read count extraction was performed using HTSEQ Differential gene expression was performed using Deseq2 Assembly: GRCz10 /GRCh38 Supplementary files format and content: tab delimited text files include read counts for each Sample head   RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF GSM6443143 GSM6443143: miRNA 128 mutant 26HPF HMT3; Danio rerio; RNA Seq GSM6443143 r1 GSM6443143 1 RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390914     26128H3_S41_L002_R1_001.fastq.gz fastq 205876552.0 2708902.0 GSM6443143 r1 0:76 1:0 A:62770921;C:42144301;G:45222985;T:55734166;N:4179 76 0     62770921 42144301 45222985 55734166 4179 SRX17023408 SRS14607344 SRA1472938 Nicoli Lab, Genetics/Internal Medicine, Yale University Nicoli Lab, Genetics/Internal Medicine, Yale University 1 0.85109   0.14682   0.81   0.66403   76   B   usable mapping rate illumina hiseq_era 3prime small_rna lexogen bulk unknown unknown   United States 2022-08-10 Pharyngula Embryo Head Nervous System
70958 70958 SRR21006678 SRX17023407 SRS14607343 SRP390914 PRJNA868349 Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [RNA seq] GSE210940 Other Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish parent bioproject:PRJNA868347 pubmed:37460694   miRNA 128 mutant 26HPF HMT2 GSM6443142   source name:head|cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF|geo loc name:missing|collection date:missing miRNA 128 mutant 26HPF HMT2 Sequence reads were trimmed for adaptor sequence/low quality sequence using BBDUK Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR Read count extraction was performed using HTSEQ Differential gene expression was performed using Deseq2 Assembly: GRCz10 /GRCh38 Supplementary files format and content: tab delimited text files include read counts for each Sample head   RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF GSM6443142 GSM6443142: miRNA 128 mutant 26HPF HMT2; Danio rerio; RNA Seq GSM6443142 r1 GSM6443142 1 RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390914     26128H2_S40_L002_R1_001.fastq.gz fastq 218090056.0 2869606.0 GSM6443142 r1 0:76 1:0 A:65896736;C:44617231;G:47882052;T:59689601;N:4436 76 0     65896736 44617231 47882052 59689601 4436 SRX17023407 SRS14607343 SRA1472938 Nicoli Lab, Genetics/Internal Medicine, Yale University Nicoli Lab, Genetics/Internal Medicine, Yale University 1 0.85882   0.14403   0.80894   0.65974   76   B   usable mapping rate illumina hiseq_era 3prime small_rna lexogen bulk unknown unknown   United States 2022-08-10 Pharyngula Embryo Head Nervous System
70959 70959 SRR21006679 SRX17023406 SRS14607342 SRP390914 PRJNA868349 Hematopoietic stem and progenitor cell heterogeneity is inherited from the embryonic hemogenic endothelium [RNA seq] GSE210940 Other Investigate the role of miR128 in the EHT process and the formation of nHSPCs Overall design: Comparative gene expression analysis of RNA seq data for WT and MT samples for miRNA128 in Human and Fish parent bioproject:PRJNA868347 pubmed:37460694   miRNA 128 mutant 26HPF HMT1 GSM6443141   source name:head|cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF|geo loc name:missing|collection date:missing miRNA 128 mutant 26HPF HMT1 Sequence reads were trimmed for adaptor sequence/low quality sequence using BBDUK Trimmed sequence reads were mapped to GRCz10 /GRCh38 using STAR Read count extraction was performed using HTSEQ Differential gene expression was performed using Deseq2 Assembly: GRCz10 /GRCh38 Supplementary files format and content: tab delimited text files include read counts for each Sample head   RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   cell line:kdrl:GFP+|cell type:endothelial cells|genotype:miRNA 128 mutant|tissue:head|time:26HPF GSM6443141 GSM6443141: miRNA 128 mutant 26HPF HMT1; Danio rerio; RNA Seq GSM6443141 r1 GSM6443141 1 RNA was isolated with the Lexogen SPLIT RNA Extraction Kit and 10ng were used to prepare libraries. RNA libraries for RNA seq were prepared using Lexogen QuantSeq 3′ mRNA Seq kit following manufacturer's protocols.   RNA-Seq TRANSCRIPTOMIC cDNA SINGLE ILLUMINA Illumina HiSeq 2500   SRP390914     26128H1_S39_L002_R1_001.fastq.gz fastq 232440984.0 3058434.0 GSM6443141 r1 0:76 1:0 A:73894818;C:46790741;G:49817876;T:61932852;N:4697 76 0     73894818 46790741 49817876 61932852 4697 SRX17023406 SRS14607342 SRA1472938 Nicoli Lab, Genetics/Internal Medicine, Yale University Nicoli Lab, Genetics/Internal Medicine, Yale University 1 0.82145   0.1448   0.81501   0.65955   76   B   usable mapping rate illumina hiseq_era 3prime small_rna lexogen bulk unknown unknown   United States 2022-08-10 Pharyngula Embryo Head Nervous 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");;