GSM5318593: EpiCs tcf21+/+ 96 hpf [Epi-WT_1]; Danio rerio; RNA-Seq - SRA

SRX10902995: GSM5318593: EpiCs tcf21+/+ 96 hpf [Epi-WT_1]; Danio rerio; RNA-Seq
1 ILLUMINA (NextSeq 500) run: 52.8M spots, 3.9G bases, 1.9Gb downloads

Submitted by: NCBI (GEO)

Study: Identification of Tcf21 downstream genes in the epicardial cells and cardiomyocytes by transcriptomic analysis

PRJNA730305 • SRP319994 • All experiments • All runs

show Abstracthide Abstract

Purpose: Studying the epicardium-myocardium crosstalk in the zebrafish larval heart. To do so, we aimed to identify, with RNA-seq, the genes dysregulated following the loss of the epicardial marker gene tcf21 in sorted epicardial cells and cardiomyocytes. Results: We first analyzed the transcriptome of epicardial and myocardial WT cells and identified cell-type specific/enriched genes. Then, we identified several differential expressed genes in tcf21 mutants, including several ligand-receptor couples known to mediate the epicardium-myocardium crosstalk. Overall design: Hearts were manually extracted from 96 hpf Tg(myl7:mcherry), TgBAC(tcf21:nls-EGFP) tcf21+/+ and tcf21-/- zebrafish larvae. Hearts were dissociated into single-cell suspensions and FACS was performed to sort epicardial and myocardial cells based on the fluorescence signal.

Sample: EpiCs tcf21+/+ 96 hpf [Epi-WT_1]

SAMN19227703 • SRS8995270 • All experiments • All runs

Organism: Danio rerio

Library:

Instrument: NextSeq 500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Construction protocol: Hearts from 96 hpf Tg(myl7:mcherry), TgBAC(tcf21:nls-EGFP) tcf21+/+ and tcf21-/- zebrafish larvae were manually dissected using forceps. Hearts were dissociated into single-cell suspensions and FACS was performed to sort cardiomyocytes and epicardial cells. Approximately 6000-1000 cells per replicate were used, and total RNA was isolated using the miRNeasy micro kit (Qiagen), combined with on-column DNase digestion. 4 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 and fragmented by Ultrasonication by E220 machine (Covaris). Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Clontech).

Experiment attributes:

GEO Accession: GSM5318593

Links:

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 52.8M spots, 3.9G bases, 1.9Gb

Run	# of Spots	# of Bases	Size	Published
SRR14559689	52,785,328	3.9G	1.9Gb	2022-11-10

ID:: 14500456

SRA

Sequence Read Archive

Result Filters

Send to:

Supplemental Content

Related information

Search details

Recent activity