GSM3452128: FACS sorted sample 1; Danio rerio; RNA-Seq - SRA

SRX4956942: GSM3452128: FACS sorted sample 1; Danio rerio; RNA-Seq
4 ILLUMINA (Illumina HiSeq 2500) runs: 56.8M spots, 11.3G bases, 4.4Gb downloads

Submitted by: NCBI (GEO)

Study: Profiling the endothelial translatome in vivo using 'AngioTag' zebrafish

PRJNA501871 • SRP167240 • All experiments • All runs

show Abstracthide Abstract

We profiled the gene expression patterns of undisturbed endothelial cells in living animals using a novel 'AngioTag' zebrafish transgenic line that permits isolation of actively translating mRNAs from endothelial cells in their native environment. This transgenic line uses the endothelial cell-specific kdrl promoter to drive expression of an epitope tagged Rpl10a 60S ribosomal subunit protein, allowing for Translating Ribosome Affinity Purification (TRAP) of actively translating endothelial cell mRNAs. We also collected the whole embryo translatome using the TRAP protocol and a ubiquitously expressed tagged Rpl10a, and the endothelial transcritome by collecting the GFP+ endothelial cells that had the kdrl promoter driving GFP. Overall design: Examination of 24hpf zebrafish whole embryo translatome, 24hpf zebrafish endothelial translatome, and 24hpf zebrafish endothelial transciptome

Sample: FACS sorted sample 1

SAMN10347852 • SRS3997451 • All experiments • All runs

Organism: Danio rerio

Library:

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: cDNA

Layout: PAIRED

Construction protocol: Whole embryo and endothelial translatomes were collected using HA antibody and the translating ribosome affinity purification protocol, the endothelial transcriptome was collected through GFP+ FACs sorted endothelial cells RNA concentration and quality were measured on a Qubit (Thermo Fisher) and on an Agilent 2100 BioAnalyzer + RNA Pico Chip (Agilent), respectively. 500 ng RNA was polyA selected or rRNA depleted using Ribo-Zero rRNA Removal Kit (Illumina) and libraries were constructed using TruSeq Stranded mRNA Library Prep Kits (Illumina).

Experiment attributes:

GEO Accession: GSM3452128

Links:

NCBI link: NCBI Entrez (gds)

Runs: 4 runs, 56.8M spots, 11.3G bases, 4.4Gb

Run	# of Spots	# of Bases	Size	Published
SRR8135938	18,575,932	3.7G	1.5Gb	2019-03-29
SRR8135939	18,521,477	3.7G	1.4Gb	2019-03-29
SRR8135940	9,763,694	2G	772Mb	2019-03-29
SRR8135941	9,898,557	2G	785.1Mb	2019-03-29

ID:: 6685118

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