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Sample GSM6057992 Query DataSets for GSM6057992
Status Public on Oct 26, 2022
Title small RNA-seq for chimpanzee iPS cells #2
Sample type SRA
 
Source name 0274F-2
Organism Pan troglodytes
Characteristics cell line: 0274F-2
cell type: iPS cells
Sex: female
age: 39
origin of_ipscs: dermal fibroblasts
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.
 
Library strategy ncRNA-Seq
Library source transcriptomic
Library selection size fractionation
Instrument model Illumina HiSeq 1500
 
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)
 
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
Organization name Nagoya University
Department Graduate School of Bioagricultural Sciences
Lab Laboratory of Genome and Epigenome Dynamics
Street address Furo-cho, Chikusa-ku
City Nagoya
ZIP/Postal code 464-8601
Country Japan
 
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
Relations
BioSample SAMN27738462
SRA SRX14967153

Supplementary file Size Download File type/resource
GSM6057992_smallRNA_rpm_chimpanzee-2.txt.gz 6.7 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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