run_metadata: 34690

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
34690	SRR32217624	SRX27557936	SRS23971737	SRP561364	PRJNA1218816	p21 ccng1 foxo3b and fbxw7 contribute to p53 dependent cell cycle arrest [MPNP timecross]	GSE288666	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 of un genotyped progeny from mdm2+/ ; pnp / intercrosses at various developmental stages 8 10 12 14 16 hpf as the mutant group N=50 embryos for each group referred to as MPNP. While this approach generated a dilution of RNA transcripts since only approxmiately ¼ of the embryos were mpnp / it nonetheless allowed us to glimpse at the dynamics of p53 target gene induction in mpnp / animals. Same stage progeny from pnp / intercrosses were harvested to extract RNA for comparison referred to as PNP.		pubmed:40487439		Zebrafish MPNP 16hpf 2	GSM8772772		source name:16 hpf embryos\|tissue:16 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 / \|geo loc name:missing\|collection date:missing	Zebrafish MPNP 16hpf 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	16 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:16 hpf embryos\|genotype:mdm2 / or mdm2+/+ mdm2+/ ; puma / ; noxa / ; p21 /	GSM8772772	GSM8772772: Zebrafish MPNP 16hpf 2; Danio rerio; RNA Seq	GSM8772772 r1	GSM8772772	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		SRP561364			MPNP-16hpf-R2_R1_001.fastq.gz MPNP-16hpf-R2_R2_001.fastq.gz	fastq fastq	14701359300.0	49004531.0	GSM8772772 r1	0:150 1:150	A:3947459353;C:3409168557;G:3472564779;T:3870403810;N:1762801	150	150			3947459353	3409168557	3472564779	3870403810	1762801	SRX27557936	SRS23971737	SRA2069214	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