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Series GSE201297 Query DataSets for GSE201297
Status Public on Oct 26, 2022
Title TE-derived small RNA analysis of human and chimpanzee iPS cells
Organisms Pan troglodytes; Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary Small RNA-seq were conducted for iPS cells of human-1 (409-B2/HPS0076), human-2 (Nips-B2/HPS0223), chimpanzee-1 (kiku/0138F-1), and chimpanzee-2 (mari/0274F-2). The human samples were mapped to the human genome (hg38) and the chimpanzee samples were mapped to the chimpanzee genome (panTro5). The mapped reads for individual TE copies (in the repeatmasker tables downloaded from UCSC genome browser) were counted, and those for the same subfamily were summed up. The counts were normalized by RPM (reads per million genome-mapped reads).
 
Overall design Two human and two chimpanzee iPS cell lines (all are females and 36 to 43 years old) were cultured in the same condition. RNAs were then extracted, and small RNA sequencing libraies were made for HiSeq sequencing in the 50-bp single-end mode.
 
Contributor(s) Ichiyanagi T, Hashimoto T, Imamura M, Ichiyanagi K
Citation(s) 36219870
Submission date Apr 22, 2022
Last update date Oct 27, 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
 
Platforms (2)
GPL18460 Illumina HiSeq 1500 (Homo sapiens)
GPL23655 Illumina HiSeq 1500 (Pan troglodytes)
Samples (4)
GSM6057989 small RNA-seq for human iPS cells #1
GSM6057990 small RNA-seq for human iPS cells #2
GSM6057991 small RNA-seq for chimpanzee iPS cells #1
This SubSeries is part of SuperSeries:
GSE201298 ChIP-seq and Transcriptome analysis of human and chimpanzee iPS cells
Relations
BioProject PRJNA830827

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE201297_RAW.tar 40.0 Kb (http)(custom) TAR (of TXT)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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