run_metadata: 65803

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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
65803	SRR15626565	SRX11923632	SRS9937150	SRP334272	PRJNA758088	Next Generation Sequencing of zebrafish spinal cord transcriptomes before xxx post injury	GSE182868	Transcriptome Analysis	The goals of this study is to compare transcriptome profiles RNA seq of zebrafish spinal cord before xxx post injury. The five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted and cDNA libraries N=4 5 were subjected to Illumina sequencing. Differential expression analysis was performed using DESeq2. The resulting P values were adjusted using the Benjamini and Hochberg's approach for controlling the false discovery rate.We mapped about 40 80 million sequence reads per sample to the zebrafish genome and identified 37 603 transcripts in the injured and uninjured zebrafish spinal cord. Our study represents the detailed analysis of zebrafish spinal cord transcriptomes before xxx post injury. Overall design: For RNA sequencing of zebrafish spinal cord tissue the five segments rostral and five segments caudal to the lesion site were collected from three adult fish at one two four and six xxx post injury. Corresponding segments were also collected from uninjured animals. Total RNA was extracted using Trizol regent Invitrogen and cDNA libraries N=4 5 were subjected to Illumina sequencing according to the manufacturer's protocol.	parent bioproject:PRJNA758278	pubmed:34876587		W4 C4	GSM5538894		source name:spinal cord\|strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	W4 C4	Raw data raw reads of fastq format were firstly processed through in house perl scripts. In this step clean data clean reads were obtained by removing reads containing adapter reads containing ploy N and low quality reads from raw data. At the same time Q20 Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5. featureCounts v1.5.0 p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced considers the effect of sequencing depth and gene length for the reads count at the same time and is currently the most commonly used method for estimating gene expression levels. Genome build: danRer11 Supplementary files format and content: tab delimited text files include FPKM values for each Sample.	spinal cord		Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer’s recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols		strain:AB\|tissue:5 spinal segment caudal to the injury site\|disease state:4 xxx post injury	GSM5538894	GSM5538894: W4 C4; Danio rerio; RNA Seq	GSM5538894		1	Spinal cord segments were isolated flash frozen on dry ice and RNA was harvested using Trizol reagent. A total amount of 3 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® NEB USA following manufacturer's recommendations and index codes were added to attribute sequences to each sample. RNA libraries were prepared for sequencing using standard Illumina protocols	GEO Accession:GSM5538894	RNA-Seq	TRANSCRIPTOMIC	cDNA	PAIRED	ILLUMINA	Illumina HiSeq 2000		SRP334272		loader:fastq load.py	W4_C4_1.fq.gz W4_C4_2.fq.gz	fastq fastq	12129480900.0	40431603.0	GSM5538894 r1	0:150 1:150	A:3451519288;C:2515952240;G:2531389661;T:3629453781;N:1165930	150	150			3451519288	2515952240	2531389661	3629453781	1165930	SRX11923632	SRS9937150	SRA1284220	GEO	Neuroscience, School of Medcine, Tongji University, 42508444-9	2	0.90598	0.90619	0.11287	0.10949	0.74184	0.75049	0.52714	0.51794	150	150	B	B	biological fallback assumption	illumina	hiseq_era	unknown	cdna_unspecified	nebnext	bulk	bulk	bulk		China	2021-08-26	Undetermined	Adult	Spinal Cord	Nervous System