run_metadata: 34708
This data as json
| 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 |
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| 34708 | SRR32217642 | SRX27557942 | SRS23971743 | SRP561365 | PRJNA1218818 | p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP 18hpf] | GSE288667 | Transcriptome Analysis | p53 is a transcription factor that plays a critical role in cancer prevention. However the mechanisms by which p53 exerts its tumor suppressive function is still unclear. While PUMA/BBC3 and NOXA/PMAIP1 are known to be important in p53 dependent apoptosis and p21/CDKN1A is crucial for p53 dependent cell cycle arrest we demonstrate that zebrafish lacking puma noxa and p21 do not show a predisposition to cancer. This suggests that additional p53 transcriptional targets are sufficient for its tumor suppressive function. Contrary to the prevailing belief that p21 is the key regulator of p53 dependent cell cycle arrest we provide evidence that p53 can still induce cell cycle arrest in the absence of p21 following DNA damage or loss of mdm2 p53 activation in the absence of stress. This implies the involvement of other p53 transcriptional targets in mediating p53 dependent cell cycle arrest. Since p53 tumor suppression is conserved across multiple vertebrate species we conducted a cross species comparative analysis of p53 dependent transcriptional profiles to identify a conserved set of 136 p53 upregulated transcripts. Our analysis stresses the importance of ortholog to paralog analysis across species since in many cases the paralog but not ortholog in differing species is p53 dependent. Additionally we performed a CRISPR/Cas9 G0 “crispant” screen in a genetic background lacking mdm2 puma noxa and p21 to identify key components involved in p53 dependent cell cycle arrest. Our findings revealed that ccng1 fbxw7 and foxo3b play an important role in this process. Overall design: RNA sequencing was performed on zebrafish quadruple knockouts of mdm2 puma noxa and p21 at 18 hpf Sibling controls from the same batch including mdm2+/ or mdm2+/+; puma / ; noxa / ; and p21 / embryos were also harvested to extract RNA for comparison. | pubmed:40487439 | Zebrafish Normal PNP 18hpf 2 | GSM8772778 | source name:30 hpf embryos|tissue:30 hpf embryos|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / |geo loc name:missing|collection date:missing | Zebrafish Normal PNP 18hpf 2 | Raw sequencing reads were aligned to the Danio rerio GRCz11 genome assemblies using STAR version 2.7.3a GCC 6.4.0 2.28 with default setting. Following alignment raw read counts were generated using HTSeq version 0.12.3 foss 2018b Python 3.6.6. The corresponding gene annotation files used in HTSeq were Danio rerio.GRCz11.102.chr.gtf for zebrafish samples. Differentially expressed genes DEGs were identified using DESeq2 version 1.42.1 in R version 4.3.3. Normalized counts were obtained using RSEM version 1.3.3 Assembly: GRCz11 Supplementary files format and content: tab delimited text file includes TPM values for each samples | 30 hpf embryos | Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer’s instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences. | The fertilization windown was set to 15 minutes. All embryos were cleaned approximately 6 hpf with approximately 30 embryos pooled in each Petri dish. | tissue:30 hpf embryos|genotype:mdm2+/ or mdm2+/+; puma / ; noxa / ; p21 / | GSM8772778 | GSM8772778: Zebrafish Normal PNP 18hpf 2; Danio rerio; RNA Seq | GSM8772778 r1 | GSM8772778 | 1 | Total RNA was extracted using QIAGEN RNeasy Plus Mini Kit QIAGEN #74134 according to the manufacturer's instructions. 500 ng of total RNA was used for the construction of sequencing libraries. RNA libraries were prepared using the Illumina RNA kit with PolyA selection. Sequencing was performed on the Illumina HiSeq platform generating 2x150 bp paired end reads and was conducted by Genewiz from Azenta Life Sciences. | RNA-Seq | TRANSCRIPTOMIC | cDNA | PAIRED | ILLUMINA | Illumina HiSeq 2500 | SRP561365 | PNP-18hpf-R2-LCM9117_L3_R1_001 PNP-18hpf-R2-LCM9117_L3_R2_001 | fastq fastq | 11448228300.0 | 38160761.0 | GSM8772778 r1 | 0:150 1:150 | A:2869273191;C:2853873509;G:2871650417;T:2853336221;N:94962 | 150 | 150 | 2869273191 | 2853873509 | 2871650417 | 2853336221 | 94962 | SRX27557942 | SRS23971743 | SRA2069215 | University of Alabama at Birmingham | University of Alabama at Birmingham | B | B | biological fallback assumption | illumina | hiseq_era | unknown | poly_a | unknown | bulk | unknown | unknown | United States | 2025-02-03 | Multi-stage | Embryo | Embryo Imprecise | All anatomical structures |