Small RNA-Seq of Xenopus laevis stage 15 animal caps induced to form ... - SRA

SRX3557389: Small RNA-Seq of Xenopus laevis stage 15 animal caps induced to form ectoderm tissue
1 ILLUMINA (Illumina HiSeq 2500) run: 39.3M spots, 2G bases, 1.3Gb downloads

Design: Total RNA was extracted using the miRCURY RNA isolation kit (Exiqon) according to manufacturer s instructions. RNA concentration and integrity was measured on the NanoDrop 8000 Spectrophotometer (Thermo Fisher Scientific). All 12 libraries (three replicates of four tissue types) were constructed using 1.5 g of RNA which was ligated to 3 and 5 HD adapters. Ligated RNA products were reverse transcribed to cDNA and amplified by PCR. The cDNA products were selected and purified by 8% polyacrylamide gel electrophoresis and ethanol precipitation. Libraries were sequenced at the Earlham Institute, Norwich Research Park, on the HiSeq 2500 Ultra High Throughput Sequencing System (Illumina).

Submitted by: UEA

Study: microRNAs associated with early neural crest development in Xenopus laevis

PRJNA429716 • SRP128993 • All experiments • All runs

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To uncover novel small RNAs in NC development we used high definition adapters and next generation sequencing of libraries derived from ectodermal explants of Xenopus laevis embryos induced to form neural and NC tissue. Ectodermal and blastula stage tissues were also sequenced. We show that miR-427 is highly abundant in all four tissue types though in an isoform specific manner and we define a set of 11 miRNAs that are enriched in the NC. In addition, we show miR-301a and miR-338 are highly expressed in both the NC and blastula suggesting a role for these miRNAs in maintaining the stem cell-like phenotype of NC cells.

Sample: Model organism or animal sample from Xenopus laevis laevis

SAMN08358022 • SRS2830687 • All experiments • All runs

Organism: Xenopus laevis laevis

Library:

Name: Ectoderm3

Instrument: Illumina HiSeq 2500

Strategy: RNA-Seq

Source: TRANSCRIPTOMIC

Selection: size fractionation

Layout: SINGLE

Runs: 1 run, 39.3M spots, 2G bases, 1.3Gb

Run	# of Spots	# of Bases	Size	Published
SRR6467431	39,291,438	2G	1.3Gb	2018-01-12

ID:: 4940405

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