run_metadata: 29954
This data as json
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| 29954 | SRR27592979 | SRX23261701 | SRS20163666 | SRP484215 | PRJNA1065838 | Diencephalic and Neuropeptidergic Dysfunction in Zebrafish with Autism Risk Mutations | GSE253405 | Transcriptome Analysis | Hundreds of human mutations are linked to autism and related disorders yet the functions of many of these mutated genes during vertebrate neural development are unclear. We generated 28 zebrafish mutants with presumptive protein truncating mutations or patient specific missense variants corresponding to autism risk alleles in 17 human genes. We observed baseline and stimulus driven behavioral changes at larval stages as well as social behavior differences in lines tested as juveniles. Imaging whole brain activity revealed a near identical activity map for mutations in the unrelated genes kmt5b and hdlbpa defined by increased activity mainly in the diencephalon. Truncating 7 of the 17 risk genes resulted in substantial brain size differences. Using RNA sequencing we further defined molecular drivers of the observed phenotypes identifying targetable disruptions in neuropeptide signaling neuronal maturation and cell proliferation. This multi modal screen has nominated brain regions cell types and molecular pathways that may contribute to autism susceptibility. Overall design: Dissected heads of larval zebrafish and brains of adult zebrafish mutants in genes that increase risk for autism which were generated using CRISPR/Cas9 mutagenesis. | deaf1 c207y 2 dpf rep6 | GSM8020161 | source name:head with eyes 2 5 heads combined|tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous|geo loc name:missing|collection date:missing | deaf1 c207y 2 dpf rep6 | Single end reads were aligned to GRCz11 release 104 using the Lawson Lab Zebrafish Transcriptome Annotation version 4.3.2 with STAR aligner 2.7.3a GCC 6.4.0 2.28. https://www.umassmed.edu/lawson lab/reagents/zebrafish transcriptome/ The raw counts files from STAR in this record were normalized using the rlog method in DESeq2 for subsequent published analysis. Assembly: GRCz11 Supplementary files format and content: Raw counts files from STAR; expected input for DESeq2. | head with eyes 2 5 heads combined | RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096. | tissue:head with eyes 2 5 heads combined|genotype:deaf1 c207y homozygous | GSM8020161 | GSM8020161: deaf1 c207y 2 dpf rep6; Danio rerio; RNA Seq | GSM8020161 r1 | GSM8020161 | 1 | RNA was extracted using the MicroElute Total RNA Kit Omega Bio Tek R6834 02 with a 15 min incubation with Dnase I. Libraries were constructed using an in house protocol based on SMART Seq2 followed by Nextera XT Library Preparation FC 131 1096. | RNA-Seq | TRANSCRIPTOMIC | cDNA | SINGLE | ILLUMINA | Illumina NovaSeq 6000 | SRP484215 | loader:fastq load.py | deaf1-c207y-2dpf-hom_A6_S6_R1_001.fastq.gz | fastq | 2545549965.0 | 25203465.0 | GSM8020161 r1 | 0:101 | A:689302325;C:596907356;G:578571204;T:680690103;N:78977 | 101 | 689302325 | 596907356 | 578571204 | 680690103 | 78977 | SRX23261701 | SRS20163666 | SRA1787174 | UMass Chan Medical School | UMass Chan Medical School | B | usable mapping rate | illumina | novaseq_era | unknown | cdna_unspecified | nextera | sc | single_cell_plate | smartseq | United States | 2024-01-16 | Hatching | Embryo | Multi-tissue | Multi-system |