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Series GSE98005 Query DataSets for GSE98005
Status Public on May 21, 2018
Title Oxidation treated small RNA-seq for studying roles of chicken piRNAs in germ cell development
Organism Gallus gallus
Experiment type Non-coding RNA profiling by high throughput sequencing
Expression profiling by high throughput sequencing
Summary We adapted oxidation treatment for the identification of methylated small RNAs, which is an identifiable feature for piRNAs in animal kingdom. Upon obtaining piRNA candidates at blastodermal cells, E7 cultured primordial germ cells (PGCs), E11 gonads, and E14 gonads, we are able to compare and contrast PIWI/piRNA pathway regulation in different germ cell development stages, that include pre-migratory PGCs, PGCs, pro-spermatogonia, and spermatogonia. We found dramatic changes in piRNA features. include length distribution, secondary piRNA features, and genomic association between blastodermal cell piRNAs and embryonic gonadal piRNAs. Such observation reflect stage-dependent transcriptions in piRNA clusters and also imply stage-depndent transcriptional regulation.
 
Overall design Small RNA isolated from chicken blastodermal cells, cultured E7 primordial germ cells, E11 male gonads, and E14 male gonads. Periodate oxidation treatments are performed prior small RNA library construction. Total RNA isolated from chicken blastodermal cells, E11 male gonads, and E14 male gonads.
 
Contributor(s) Tseng Y, Chang K, Lin S
Citation(s) 29859049
Submission date Apr 20, 2017
Last update date Jul 25, 2021
Contact name Shau-Ping Lin
E-mail(s) shaupinglin@ntu.edu.tw
Organization name National Taiwan University
Department Institute of Biotechnology
Street address No. 81, Chang-Xing St.
City Taipei City
ZIP/Postal code 10672
Country Taiwan
 
Platforms (2)
GPL16133 Illumina HiSeq 2000 (Gallus gallus)
GPL19064 Illumina MiSeq (Gallus gallus)
Samples (14)
GSM2585323 BC rep1
GSM2585324 BC rep2
GSM2585325 E11G rep1
Relations
BioProject PRJNA383649
SRA SRP104389

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
GSE98005_A234.cuffnorm.genes.expressions.txt.gz 1.5 Mb (ftp)(http) TXT
GSE98005_RAW.tar 810.0 Kb (http)(custom) TAR (of TXT)
GSE98005_RAW.tar.gz 250.1 Kb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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