run_metadata: 62467

This data as json

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62467	SRR13191909	SRX9626277	SRS7827448	SRP295659	PRJNA682370	Identification of Snai1b targets in zebrafish heart by transcriptomic analysis	GSE162604	Transcriptome Analysis	Purpose: identifying with RNA seq genes targets of Snai1b during zebrafish cardiac development. Results: we identified several differential expressed genes in particular cytoskeletal genes. In particular the intermediate filament gene desmin b is upregulated. Overall design: Hearts were manually dissected at 48 hpf from snai1b mutants and wild type		pubmed:34152269		Hearts wt 2	GSM4955125		source name:Heart\|developmental stage:48 hpf\|tissue:Heart\|genotype:wild type	Hearts wt 2	The resulting raw reads were assessed for quality adapter content and duplication rates with FastQC. Trimmomatic version 0.39 was used to trim reads with a quality drop below a mean of Q20 in a window of 10 nucleotides . Only reads between 30 and 150 nucleotides were used in subsequent analyses. Trimmed and filtered reads were aligned versus the Ensembl Zebrafish genome version DanRer11 GRCz11.92 using STAR 2.6.1d with the parameter “outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10% The number of reads aligning to genes was counted with featureCounts 1.6.5 tool from the Subread package Liao et al. 2014. Only reads mapping at least partially inside exons were admitted and aggregated per gene while reads overlapping multiple genes or aligning to multiple regions were excluded from further analyses. Differentially expressed genes were identified using DESeq2 version 1.18.1. The Ensembl annotation was enriched with UniProt data release 06.06.2014 based on Ensembl gene identifiers Genome build: DanRer11 Supplementary files format and content: library size normalized counts	Heart		48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.		developmental stage:48 hpf\|tissue:Heart\|genotype:wild type	GSM4955125	GSM4955125: Hearts wt 2; Danio rerio; RNA Seq	GSM4955125		1	48 hpf Tgmyl7:BFP CAAX snai1b+/+ and snai1b / hearts were manually dissected using forceps. Approximately 20 hearts per replicate were pooled and total RNA was isolated using the miRNeasy micro kit combined with on column DNase digestion. Approximately 10 ng of total RNA was used as input for SMART Seq® v4 Ultra® Low Input RNA Kit Takara Clontech for cDNA pre amplification. Obtained full length cDNA was checked on LabChip GX Touch 24 and fragmented by Ultrasonication by E220 machine Covaris. Final Library Preparation was performed by Low Input Library Prep Kit v2 Takara Clontech.	GEO Accession:GSM4955125	RNA-Seq	TRANSCRIPTOMIC	cDNA	SINGLE	ILLUMINA	NextSeq 500		SRP295659			Felix_AG_3_R1.fastq.gz	fastq	2312289944.0	32497996.0	GSM4955125 r1	0:71.15 1:0	A:646717753;C:512859953;G:511898920;T:640804094;N:9224	71	0			646717753	512859953	511898920	640804094	9224	SRX9626277	SRS7827448	SRA1166534	GEO	MPI for heart and lung research	1	0.93649		0.1068		0.72914		0.44928		74		B		usable mapping rate	illumina	nextseq	full_length	cdna_unspecified	unknown	sc	single_cell_plate	smartseq		Germany	2020-12-03	Hatching	Embryo	Heart	Cardiovascular System