run_metadata: 28969
This data as json
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| 28969 | SRR26862028 | SRX22556950 | SRS19565491 | SRP472550 | PRJNA1041773 | Transcriptome profiles of liver from 7dpf zebrafish larvae from control sec31anju221 and double mutation of sec31anju221 and UPR effectors by Next Generation Sequencing | GSE248098 | Transcriptome Analysis | We found that zebrafish larvae bearing a homozygous hypomorphic mutation in the sec31a gene sec31anju221 exhibited hepatic steatosis accompanied with activation of unfolded protein response UPR. As systematic efforts to investigate how different branches of UPR impact on the hepatic metabolic maladaptation critical effectors of the UPR xbp1 atf4a/4b atf6 srebf1 and srebf2 were separately knock outed on sec31anju221 background. In order to access the changes on transcriptome landscape livers were dissected from the 7 dpf zebrafish larvae and low input RNA seq was applied. Overall design: Livers from 7dpf zebrafish larvae were dissected with forceps and dissociated cells with 0.25% trypsin treatment. The libraries were constructed with NEBNext® Single Cell/Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 and sequenced on Illumina Novaseq platform. | pubmed:39139065 | xbp1 / ;sec31anju221 7dpf liver rep1 | GSM7905868 | source name:liver|tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin|geo loc name:missing|collection date:missing | xbp1 / ;sec31anju221 7dpf liver rep1 | Illumina bcl2fastq2 v 2.20.0.422 software was used for base calling. Sequenced reads were trimmed for adaptor sequence and masked for low complexity or low quality sequence. Read quality was checked for each sample by using FastQC v 0.11.9. High quality reads were alligned to GRCz11 whole genome using HISAT2 V2.1.0 with default parameters. Mapping results with MAPQ>15 were kept for further analysis by samtools 1.10. Raw counts of sequencing reads were generated by using FeatureCounts v1.6.0. Assembly: GRCz11 Supplementary files format and content: Tab delimited text files include raw counts for each sample | liver | At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries. | tissue:liver|genotype:xbp1 / ;sec31anju221|treatment:Digested with 2.5percent trypsin | GSM7905868 | GSM7905868: xbp1 / ;sec31anju221 7dpf liver rep1; Danio rerio; RNA Seq | GSM7905868 r1 | GSM7905868 | 1 | At 7dpf zebrafish larvea livers were dissected with forceps and dissociated into single cells with 0.25% trypsin treatment. NEBNext Single Cell Low Input RNA Library Prep Kit for Illumina NEB Cat No.6420 was used with all 7dpf liver cell for the construction of sequencing libraries. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina NovaSeq 6000 | SRP472550 | xbp1_sec31a_7dpf_liver_1_R1.fastq.gz xbp1_sec31a_7dpf_liver_1_R2.fastq.gz | fastq fastq | 6187152900.0 | 20623843.0 | GSM7905868 r1 | 0:150 1:150 | A:1877304250;C:1115136591;G:1381366555;T:1812912124;N:433380 | 150 | 150 | 1877304250 | 1115136591 | 1381366555 | 1812912124 | 433380 | SRX22556950 | SRS19565491 | SRA1753371 | Xin Lou Lab, Medical School, Nanjing University | Xin Lou Lab, Medical School, Nanjing University | 2 | 0.77014 | 0.76961 | 0.43869 | 0.43265 | 0.77863 | 0.78293 | 0.54465 | 0.54127 | 150 | 150 | B | B | biological fallback assumption | illumina | novaseq_era | unknown | cdna_unspecified | nebnext | bulk | unknown | unknown | China | 2023-11-17 | Larval | Larval | Liver | Liver and Biliary System |