run_metadata: 34181
This data as json
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| 34181 | SRR31377620 | SRX26751129 | SRS23239742 | SRP545865 | PRJNA1187491 | CCSER1 transcriptomic analysis reveals a role in neurodevelopmental phenotypes and alcohol response. | GSE282155 | Transcriptome Analysis | CCSER1 a gene with limited prior knowledge in neurological conditions has emerged as a potential tumor suppressor and regulator of neurodevelopment. Our analysis reveals that CCSER1 downregulation correlates with down regulation of DNA repair and DNA replication pathways and up regulation of neurodevelopmental pathways including calcium signaling and neuroactive ligand receptor interaction in CCSER1 deficient zebrafish. These findings suggest a potential role for CCSER1 in neurodevelopmental processes and its impact on adult behavior as evidenced by altered alcohol preference in zebrafish models. Further investigation is needed to elucidate the precise molecular mechanisms underlying CCSER1 function and its contribution to human diseases such as addiction and neurodevelopmental disorders. Overall design: We generated CRISPR/Cas 9 mutants in the gene CCSER1 CCSER1 P471 or CCSER1 M and CCSER1 S48Y* or CCSER1 S. For analysis of trancriptomic changes in adult zebrafish whole bodies and brains homozygous mutants were raised to maturity. WT controls were siblings from the heterozygous incross. RNA seq analysis performed on whole brains and of whole body without xxx brain. Sample QC and sequencing was outsourced. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument. | WT 1. | GSM8636981 | source name:whole brain|tissue:whole brain|genotype:WT|geo loc name:missing|collection date:missing | WT 1. | Raw reads were first processed by Novogene AIT to remove adapter poly N sequences and reads with low quality from raw data. All downstream analyses were based on the clean data with a Phred score of 39 indicating a 99.9% base call accuracy Further analysis was performed in PartekTM FlowTM Explore Spatial Multiomics Data using PartekTM FlowTM software v11.0. Reads were aligned to GRCz11 genome assembly by STAR aligner default parameters and subsequently filtered to a minimum mapping quality score of > 30. Assembly: GRCz10 genome assembly by STAR aligned Supplementary files format and content: STAR aligned | whole brain | The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument. | tissue:whole brain|genotype:WT | GSM8636981 | GSM8636981: WT 1.; Danio rerio; RNA Seq | GSM8636981 r1 | GSM8636981 | 1 | The quality of each sample was verified by gel electrophoresis and bio analyser. Samples that passed QC were sent for sequencing by Novogene AIT. An mRNA cDNA library made up of Paired end sequencing reads of 150 bp in length was generated on the Illumina HiSeq instrument. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 1000 | SRP545865 | RZW013_HS006-PE-R00645_L005_R1_unaligned_001.fastq.gz RZW013_HS006-PE-R00645_L005_R2_unaligned_001.fastq.gz | fastq fastq | 3675466840.0 | 12170420.0 | GSM8636981 r1 | 0:151 1:151 | A:1024674488;C:812714996;G:831919969;T:1005797546;N:359841 | 151 | 151 | 1024674488 | 812714996 | 831919969 | 1005797546 | 359841 | SRX26751129 | SRS23239742 | SRA2016812 | ASM Lab, Physiology, NUS | ASM Lab, Physiology, NUS | B | B | biological fallback assumption | illumina | hiseq_era | unknown | cdna_unspecified | unknown | bulk | unknown | unknown | Singapore | 2024-11-18 | Undetermined | Adult | Brain | Nervous System |