run_metadata: 69686

This data as json

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69686	SRR19135486	SRX15203072	SRS12941936	SRP374105	PRJNA836108	Single cell sequencing data of zebrafish spinal cord injury	GSE202429	Transcriptome Analysis	post spinal cord injury in adult zebrafish the spinal cord was taken out for single cell data sequencing Overall design: The spinal cord of adult zebrafish was taken for single cell sequencing				sci 1 day	GSM6122391		tissue:Wild type zebrafish\|age:4 month\|geo loc name:missing\|collection date:missing	sci 1 day	The Cell Ranger software was obtained from 10x Genomics website https://support.10xgenomics.com/single cell gene expression/software/downloads/latest Alignment filtering barcode counting and UMI counting were performed with cellranger count module to generate feature barcode matrix and determine clusters. Dimensionality reduction was performed using PCA and the first ten principle compoments were used to generate clusters by K means algorithm and graph based algorithm respectively. Assembly: GRCz11 Supplementary files format and content: Matrix table with raw gene count for every gene and every sample	Wild type zebrafish		single cells were suspended in PBS containing 0.04% BSA According to the manufacture’s introduction Single cell RNA seq libraries were constructed using Single Cell 3’ Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		age:4 month	GSM6122391	GSM6122391: sci 1 day; Danio rerio; RNA Seq	GSM6122391 r1	GSM6122391	1	single cells were suspended in PBS containing 0.04% BSA According to the manufacture's introduction Single cell RNA seq libraries were constructed using Single Cell three prime Library andGel Bead Kit V3. The libraries were finally sequenced using an Illumina Novaseq6000 sequencer with a sequencing depth of at least 100 000 reads per cell with pair end 150 bp PE150 reading strategy		RNA-Seq	TRANSCRIPTOMIC SINGLE CELL	cDNA	PAIRED	ILLUMINA	Illumina NovaSeq 6000		SRP374105			200326B_SCI_1d_S1_L002_R1_001.fastq.gz 200326B_SCI_1d_S1_L002_R2_001.fastq.gz	fastq fastq	50002460700.0	166674869.0	GSM6122391 r2	0:150 1:150	A:20017686965;C:8776481027;G:8531485975;T:12675453459;N:1353274	150	150			20017686965	8776481027	8531485975	12675453459	1353274	SRX15203072	SRS12941936	SRA1416672	?????????, ????, ????	神经再生重点实验室, 神经再生, 南通大学	2	0.0	0.82772	0.0	0.41128	1.0	0.75526		0.57912	150	150	T	B	mate1 technical by mapping diff	illumina	novaseq_era	unknown	cdna_unspecified	unknown	sc	single_cell_droplet	10x		China	2022-05-07	Adult	Adult	Undetermined	Undetermined