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Status |
Public on Jan 24, 2022 |
Title |
experiment1-Unfed-10dpf |
Sample type |
SRA |
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Source name |
tadpoles
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Organism |
Xenopus laevis |
Characteristics |
group: unfed developmental stage: 13dpf
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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
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
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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
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Submission date |
Jan 21, 2022 |
Last update date |
Jan 24, 2022 |
Contact name |
Asako Shindo |
E-mail(s) |
shindo@kumamoto-u.ac.jp
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Organization name |
Kumamoto University
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Street address |
2-2-1 Honjo, Chuo-ku
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City |
Kumamoto |
ZIP/Postal code |
860-0811 |
Country |
Japan |
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Platform ID |
GPL21248 |
Series (1) |
GSE194146 |
RNA-seq Analysis of intestinal tubes from the Unfed and Fed Xenopus laevis tadpoles |
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Relations |
BioSample |
SAMN25153995 |
SRA |
SRX13853417 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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