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Sample GSM5829477

Query DataSets for GSM5829477

Status

Public on Jan 24, 2022

Title

experiment1-Fed-10dpf

Sample type

SRA

Source name

tadpoles

Organism

Xenopus laevis

Characteristics

group: Fed
developmental stage: 10dpf

Extracted molecule

total RNA

Extraction protocol

Fed and unfed tadpoles at 10 and 16 dpf were anesthetized, and the GI tubes were isolated using a thin razor and forceps. A total of 20–26 intestinal tubes from each stage were collected and homogenized in TRIzol LS reagent (#10296010; Thermo Fisher Scientific). RNA was purified using RNA Clean & Concentrator-5 (R1014; Zymo Research, Irvine, CA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina NextSeq 500

Data processing

Quality filtering of reads was performed using Sickle v1.33, and filtered reads were mapped to the reference genes (Xenopus laevis, http://www.xenbase.org/other/static-xenbase/ftpDatafiles.jsp) using hisat2.
The mapped reads were counted using the featureCounts.
Genome_build: Xenopus laevis, http://www.xenbase.org/other/static-xenbase/ftpDatafiles.jsp
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

Submission date

Jan 21, 2022

Last update date

Jan 24, 2022

Contact name

Asako Shindo

E-mail(s)

shindo@kumamoto-u.ac.jp

Organization name

Kumamoto University

Street address

2-2-1 Honjo, Chuo-ku