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Status |
Public on Oct 26, 2022 |
Title |
small RNA-seq for chimpanzee iPS cells #2 |
Sample type |
SRA |
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Source name |
0274F-2
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Organism |
Pan troglodytes |
Characteristics |
cell line: 0274F-2 cell type: iPS cells Sex: female age: 39 origin of_ipscs: dermal fibroblasts
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Extracted molecule |
total RNA |
Extraction protocol |
Total cellular RNAs were isolated from ~1×106 cells by using Isogen (TOYOBO) and Direct-ZolTM RNA (ZYMO RESEARCH) according to manufactures’ instructions. After quality check by Agilent 2100 Bioanalyzer (Agilent Technologies), small RNA-seq libraries were prepared from approximately 0.5 μg of total RNA using NEBNext small RNA library kit (New England Biolabs). After library amplification by PCR, products were run on 6% polyacrylamide gel electrophoresis, and a gel region corresponding to DNA sizes with 15 to 40 bp insertion were cut for DNA extraction.
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Library strategy |
ncRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 1500 |
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Data processing |
Cutadapt (DOI:10.14806/ej.17.1.200) was used to remove the adapter sequences. the retained reads of 24 to 35 bp in length (corresponding to small RNAs of 24 to 35 nucleotides, which is the range for typical piRNAs) were mapped to the respective reference genomes (hg38 or panTro5) by Hisat2 (Kim et al. 2019) allowing multiple hits. Reads originated from TE regions in the repeatmasker track were counted and normalized as RPM. If a read was mapped to multiple candidate regions, all regions were used for read counting, using a weighted number, 1/n, where n is the number of mapped regions. Assembly: hg38/panTro5 Supplementary files format and content: tab-separated files with TE names and RPM values (total, sense hits, and antisense hits)
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Submission date |
Apr 22, 2022 |
Last update date |
Oct 26, 2022 |
Contact name |
Kenji Ichiyanagi |
E-mail(s) |
ichiyana@agr.nagoya-u.ac.jp
|
Phone |
+81-52-789-4066
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Organization name |
Nagoya University
|
Department |
Graduate School of Bioagricultural Sciences
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Lab |
Laboratory of Genome and Epigenome Dynamics
|
Street address |
Furo-cho, Chikusa-ku
|
City |
Nagoya |
ZIP/Postal code |
464-8601 |
Country |
Japan |
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Platform ID |
GPL23655 |
Series (2) |
GSE201297 |
TE-derived small RNA analysis of human and chimpanzee iPS cells |
GSE201298 |
ChIP-seq and Transcriptome analysis of human and chimpanzee iPS cells |
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Relations |
BioSample |
SAMN27738462 |
SRA |
SRX14967153 |