{"database": "metadata", "table": "run_metadata", "rows": [[30079, "SRR27700031", "SRX23366855", "SRS20229172", "SRP485459", "PRJNA1068100", "Motile cilia modulate neuronal and astroglial activity in the zebrafish larval brain", "GSE254006", "Transcriptome Analysis", "The brain uses a specialized system to transport cerebrospinal fluid CSF  consisting of interconnected ventricles lined by motile ciliated ependymal cells. These cells act jointly with CSF secretion and cardiac pressure gradients to regulate CSF dynamics. To date  the link between cilia mediated CSF flow and brain function is poorly understood. Using zebrafish larvae as a model system  we identify that loss of ciliary motility does not alter progenitor proliferation  brain morphology  or spontaneous neural activity despite leading to an enlarged telencephalic ventricle. We observe altered neuronal responses to photic stimulations in the optic tectum and hindbrain and brain asymmetry defects in the habenula. Finally  we investigate astroglia since they contact CSF and regulate neuronal activity. Our analyses reveal a reduction in astroglial calcium signals during both spontaneous and light evoked activity. Our findings highlight a role of motile cilia in regulating brain physiology through the modulation of neural and astroglial networks. Overall design: To analyze the impact of cilia paralysis on gene expression  we performed RNA sequencing analysis of 4 dpf smh mutant and sibling control zebrafish larvae. We extracted total RNA from mutant selected based on their curly tail down phenotype and sibling controls mixture of heterozygous and wild type. RNAsequencing was performed on 4 different clutches.", null, "pubmed:39798091", null, "Smh control  clutch 4", "GSM8031708", null, "source name:whole larvae|tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment|geo loc name:missing|collection date:missing", "Smh control  clutch 4", "The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05 The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Assembly: GCF 000002035.6 GRCz11 Supplementary files format and content: excel file containing normalized and log transformed read counts: Normalized read counts smh.xlsx Supplementary files format and content: excel file containing differential expression: smhMUT vs smhCTRL mRNA diff expr CPM1.xlsx", "whole larvae", null, "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI\u2019s DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "tissue:whole larvae|genotype:mixture wt and +/ |treatment:no treatment", "GSM8031708", "GSM8031708: Smh control  clutch 4; Danio rerio; RNA Seq", "GSM8031708 r1", "GSM8031708", "1", "To isolate RNA for sequencing  30 larvae at 4 dpf were collected in a 1.5ml tube and placed on ice. To lyse the samples  500\u03bcL trizol was added and the euthanized larvae were homogenized through a 27 gauge needle until the mixture looked uniform. post adding another 500\u03bcL trizol  the samples were incubated for 5 minutes at room temperature. The larvae were then treated with 200\u03bcL chloroform  and the tube was rocked for 15secs to mix the contents. The tubes were incubated for 2 minutes at room temperature and then centrifuged for 15 minutes at 12000rpm at a temperature of 4\u00b0C. post centrifugation  the upper aqueous phase containing RNA was mixed with equal amounts of 100% ethanol and was then loaded onto an RNA spin column Qiagen and centrifuged for 30 seconds at 8000 rpm. The spin column was further incubated with 700\u03bcL of RW1 buffer and centrifuged for 30 seconds at 8000 rpm. The spin column tubes were then placed into a new collection tube and further treated to remove any DNA contamination by washing the tubes with 350\u03bcL of RW1 buffer followed by Dnase enzyme Qiagen in RDD buffer 10\u03bcL Dnase+ 70\u03bcL RDD buffer per tube for 45 minutes at room temperature. post incubation  350\u03bcL of RW1 buffer was added to the tubes and centrifuged for 15 seconds at 8000rpm. The tubes were then treated with 500\u03bcL RPE buffer and centrifuged for 30 seconds. This step was repeated twice  and the tubes were then centrifuged for 1 minute at 8000rpm to remove any residual buffer left in the column. For RNA extraction from the column  30\u03bcL nuclease free water was added and incubated for 2 minutes. The tubes were then centrifuged for 1 minute at 8000 rpm to elute the RNA. The concentration of the extracted RNA was quantified using Nanodrop and the quality was analyzed by bioanalyzer. The samples were then sequenced by BGI's DNBSEQTM Technology and bioinformatic analysis was performed by BGI. The filtering of sequencing data was done using SOAPnuke  v1.5.2  using the parameters Parameters  l 15  q 0.2  n 0.05. The Hierarchical Indexing for Spliced Alignment of Transcripts software HISAT2 v2.0.4 with parameters\uff1a  sensitive   no discordant   no mixed  I 1  X 1000  p 8   rna strandness RF was used for mapping RNA seq reads. We used Bowtie2 Version\uff1av2.2.5  Parameters\uff1a q   sensitive   dpad 0   gbar 99999999   mp 1 1   np 1   score min L 0  0.1  p 16  k 200 to map the clean reads to the reference gene sequence transcriptome  and then RSEM Version\uff1av1.2.8  Parameters\uff1a p 8   forward prob 0   paired end to calculate the gene expression level of each sample. The count matrix included genes that were selected based on their expression of average count per million of more than 1 across all samples. The resulting matrix was normalized  and log transformed using the voom algorithm from the limma package of Bioconductor Law et al.  2014; Ritchie et al.  2015. standard procedure performed by BGI", null, "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "BGISEQ", "MGISEQ-2000RS", null, "SRP485459", null, null, "SmhCTRL4_1.fq.gz SmhCTRL4_2.fq.gz", "fastq fastq", 4536141000.0, 22680705.0, "GSM8031708 r1", "0:100 1:100", "A:1196842043;C:1059535727;G:1071488375;T:1208274855;N:0", 100, 100, null, null, 1196842043, 1059535727, 1071488375, 1208274855, 0, "SRX23366855", "SRS20229172", "SRA1790727", "NTNU", "NTNU", 2, 0.94102, 0.95093, 0.09453, 0.09431, 0.66403, 0.6631, 0.49804, 0.49818, 100, 100, "B", "B", "biological fallback assumption", "bgi", "bgi", "unknown", "poly_a", "unknown", "bulk", "unknown", "unknown", null, "Unknown", "2024-01-23", "Larval", "Larval", "Whole Organism", "All anatomical structures"]], "columns": ["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"], "primary_keys": ["rowid"], "primary_key_values": ["30079"], "units": {}, "query_ms": 7.552777009550482}