{"database": "metadata", "table": "run_metadata", "rows": [[56082, "SRR10868203", "SRX7538226", "SRS5976890", "SRP241164", "PRJNA600413", "Withdrawal from chronic alcohol exposure leads to tissue specific recovery of the zebrafish transcriptome", "GSE143416", "Transcriptome Analysis", "Alcohol consumption can lead to a wide range of systemic disorders brought about by transcriptional changes. Recent studies have shown altered behavioral and expression changes in zebrafish on exposure to alcohol. We have identified changes associated with transcriptome profiles in response to chronic alcohol exposure and extent of recovery upon withdrawal. Our results indicate a tissue specific response where the brain responds positively to withdrawal when compared to liver. We identified two distinct classes of genes in response to withdrawal from alcohol exposure \u2013 one group recovered the pre exposure expression profile while the other set of genes retained altered expression profiles despite withdrawing from alcohol whose altered expression profiles remained changed even post withdrawal. We also examined gender specific responses to alcohol. Male fish appear to be more susceptible to changes induced by alcohol indicated by a higher percent of genes appearing to change their expression profiles when compared to females. Female fish appear to show a better recovery as compared to males as a sizable number of genes appear to have their expression levels recovered upon the introduction of withdrawal. Overall  our work identifies pathways / genes perturbed by exposure to alcohol and demonstrates the extent of tissue specific transcriptional changes and takes into account the variability of gender in assessing the effect of chronic alcoholism and withdrawal. Overall design: Methods: Brain and liver tissue from six groups of zebrafish Danio rerio  shortfin 'AB' strain of both sexes i.e  Male control  Female control  Male alcohol exposed  Female alcohol exposed  Male withdrawal and Female withdrawal were pooled in respective groups and their mRNA profiles were generated using Illumina HiSeq 2000. There were 14 samples from brain tissue i.e two replicates of male control  three replicates of female control  two replicates of Male alcohol exposed  two replicates of Female alcohol exposed  three replicates of Male withdrawal and two replicates of Female withdrawal group. There were 12 samples of liver tissues i.e two replicates for each of the six groups. The sequence reads were quality checked using FastQC  mapped to reference genome danRer10 using STAR  abundance estimates of transcripts calculated using RSEM and differential expression was performed using EBSeq.", null, "pubmed:33163595", null, "WDMB rep2", "GSM4259023", null, "source name:Withdrawal Male Brain 2|strain:short fin  'AB' strain|condition:Withdrawal|Sex:male|tissue:Brain", "WDMB rep2", "Base calling was performed using bcl2fastq of Illumina Quality control was performed on the FASTQ read files using FastQC v0.11.7. The reads were aligned to the reference genome using STAR 2.5.2 with the parameters STAR   runThreadN 16   runMode alignReads   readFilesCommand zcat   outSAMstrandField intronMotif   outSAMtype BAM SortedByCoordinate   quantMode TranscriptomeSAM Abundance estimates were calculated using RSEM 1.3.1 using the parameters  rsem calculate expression   bam   no bam output  p Differential expression across the three conditions were performed using EBSeq module from RSEM 1.3.1 Genome build: danRer10 Supplementary files format and content: Files containing TPM values for both tissues", "Withdrawal Male Brain 2", "For the chronic alcohol exposure program fish were transferred every postnoon into a new tank containing 0.5% ethanol and maintained in the same tank for the next 24 h.Experimental conditions of automated light/dark cycle 14/10 h temperature of 28C  water salinity of 3 g of sea salt per liter  and aeration by air bubbling were maintained. This way fish were exposed to 0.5% ethanol for 9 weeks. Fish in the control group were also transferred each postnoon to a new tank but without xxx in the medium. From the 5th week of alcohol treatment to the 9th week fish were bred to measure fecundity. Fish in the four groups were bred in four different combinations   both partners control only male alcohol exposed  only female alcohol exposed  and both sexes alcohol exposed. Because alcohol exposed fish were very vulnerable to handling stress and did not lay eggs if handled just before breeding  we kept male and female fish in the same breeding tank a night before the breeding. The next morning  breeding was stimulated by white light and eggs were collected post 1 h. Eggs were counted manually and maintained further to look for developmental defects.", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer\u2019s protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "Zebrafish were maintained at CSIR CCMB zebrafish facility as per standard practices.One hundred twenty na\u00efve wild type short fin \u2018AB\u2019strainD. rerio60 males  60 females were separated into four groups representing male control male alcohol exposed female control and female alcohol exposed groups.Thus  each group was composed of 30 fish  exclusively either male or female  maintained in a 20 L water tank.", "strain:short fin  'AB' strain|condition:Withdrawal|Sex:Male|tissue:Brain", "GSM4259023", "GSM4259023: WDMB rep2; Danio rerio; RNA Seq", "GSM4259023", null, "1", "Brain and liver tissue isolation was performed by anaesthetizing the zebrafish by treatment with Tricaine Sigma  USA. Utmost care was taken while dissecting out the tissue to ward off contamination to obtain a pure sample for each tissue type. Harvested tissues were immediately submerged in RNALater 200\u2009\u03bcl in total volume; Sigma for storage in RNase free microcentrifuge tubes Ambion. Tissues were later stored at  80 \u00b0C. Total RNA was prepared using NucleoSpin\u00ae RNA kit Macherey Nagel  REF # 740955.50 as mentioned by the manufacturer's protocol. Tissues were separated from RNALater and were homogenized in the lysis buffer from RNA kit using a hand held microtube homogenizer. On column DNase digestion was performed to eliminate genomic DNA contamination.RNAs were eluted from the column using RNase and DNase free water Sigma. post purification  the quantity and quality of RNA was determined using NanoDrop spectrophotometer and 1% RNA Agarose gel electrophoresis  respectively. All RNA samples were stored at  80 \u00b0C. TruSeq RNA Library Prep Kit v2 LT Non stranded kit was used to prepare libraries for sequencing as per manufacturer's instructions.", "GEO Accession:GSM4259023", "RNA-Seq", "TRANSCRIPTOMIC", "cDNA", "PAIRED", "ILLUMINA", "Illumina HiSeq 2000", null, "SRP241164", null, null, "WDMB2_R1.fastq.gz WDMB2_R2.fastq.gz", "fastq fastq", 7911217000.0, 39556085.0, "GSM4259023 r1", "0:100 1:100", "A:2166287949;C:1800275915;G:1804637340;T:2135900682;N:4115114", 100, 100, null, null, 2166287949, 1800275915, 1804637340, 2135900682, 4115114, "SRX7538226", "SRS5976890", "SRA1023469", "GEO", "CSIR Centre for Cellular and Molecular biology", 2, 0.93471, 0.93064, 0.12564, 0.12609, 0.68592, 0.6912, 0.52362, 0.52186, 100, 100, "B", "B", "biological fallback assumption", "illumina", "hiseq_era", "unknown", "cdna_unspecified", "trueseq", "bulk", "unknown", "unknown", null, "India", "2020-01-10", "Juvenile", "Juvenile", "Brain", "Nervous System"]], "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": ["56082"], "units": {}, "query_ms": 11.154680003528483}