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Series GSE83945 Query DataSets for GSE83945
Status Public on Mar 20, 2018
Title Genome-wide profiling of mature piRNAs in human Neuroblastoma (NB) cell lines
Organism Homo sapiens
Experiment type Non-coding RNA profiling by high throughput sequencing
Summary To elucidate potential role of piRNAs in Neuroblastoma (NB), we performed the genome wide profiling in two human NB cell lines, IMR-32 and SH-SY-5Y by adopting high-throughput RNA sequencing (RNA-Seq) and unveil their possible functions in neoplastic pathways. The RNA sequencing results revealed both known and novel piRNAs in both the cell lines. We observed a total 630 annotated mature piRNAs, distributed across chromosomes and mitochondria which were mapped to various genomic locations such as introns, protein coding regions, repeats, pseudogenes, ncRNAs etc. This is the first study reporting the extensive catalogue of human NB piRNAs which will provide a useful resource to dissect complex neoplastic events that are possibly mediated by piRNAs in neuroblastoma. Moreover, these piRNAs could be used as probable small RNA biomarkers for the Neuroblastoma.
Overall design 1 µg of total RNA isolated from above two cell lines was used as the starting material for library preparation as prescribed by Illumina Truseq small RNA library protocol. The small RNA libraries (size range 16 nts - 40 nts) were sequenced on Illumina NextSeq 500. Upon de-multiplexing, reads are obtained and then analyzed after QC to predict both known and novel piRNAs.
Contributor(s) Roy J, Mallick B
Citation(s) 29516567
Submission date Jul 01, 2016
Last update date May 15, 2019
Contact name Dr. Bibekanand Mallick
Organization name National Institute of Technology
Department Department of Life Science
Lab RNAi & Functional Genomics Lab.
Street address NIT Rourkela
City Rourkela
State/province Odisha
ZIP/Postal code 769008
Country India
Platforms (1)
GPL18573 Illumina NextSeq 500 (Homo sapiens)
Samples (2)
GSM2222674 IMR32
GSM2222675 SH-SY-5Y
BioProject PRJNA327500
SRA SRP077720

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
GSE83945_RAW.tar 20.0 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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