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Sample GSM5861418 Query DataSets for GSM5861418
Status Public on Sep 07, 2022
Title RNAseq_GM10253A_1
Sample type SRA
 
Source name Somatic cell hybrid
Organisms Homo sapiens; Cricetulus griseus
Characteristics cell type: GM10253A
treatment: untreated
Treatment protocol Normally growing cells
Growth protocol Human/Hamster hybrid cell lines GM10253A and HybNeo3 were grown in RPMI 1640 with L-Glutamine, 10% FCS and penicillin and streptomycin. Human parenral lymphoblastoid cell line was grown in RPMI 1640 with L-Glutamine, 20% FCS and penicillin and streptomycin.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from cells using RNeasy mini kit (Qiagen) with on-column DNase I digestion (RNAse-Free DNase Set, Qiagen). Ribosomal RNA was depleted using Illumina® Ribo-Zero Plus rRNA Depletion Kit (Illumina, 20040526) following the manufacturer’s instructions.
Libraries for RNA-seq were prepared and indexed using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (NEB #E7645L) and NEBNext Singleplex Oligos for Illumina (NEB #E7335, E7500) following the manufacturer’s instructions. Single-end RNA-seq of 50-bp read length was performed on Illumina Hi-Seq 2000.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Chinese hamster/human hybrid retaining human chromosome #3
GM10253A_RNAseq_norm.bdg
Data processing RNA-seq reads were aligned to the human reference genome (hg19) using TopHat v2 and processed with Samtools v1.6 and the deepTools “bamCoverage” tool with RPKM normalisation across Human chromsome 3 and with a 200bp bin size.
Genome_build: hg19
Supplementary_files_format_and_content: bedGraph files of combined replicates for human chromosome 3 only, with RPKM normalisation and binsize of 200bp.
 
Submission date Feb 04, 2022
Last update date Sep 07, 2022
Contact name Catherine Naughton
E-mail(s) Catherine.Naughton@ed.ac.uk
Organization name University of Edinburgh
Department MRC Human Genetics Unit
Lab Nick Gilbert Lab
Street address Crewe Road
City Edinburgh
ZIP/Postal code EH4 2XU
Country United Kingdom
 
Platform ID GPL31911
Series (2)
GSE195886 Human centromere repositioning activates transcription and opens chromatin fibre structure
GSE196160 Human centromere repositioning activates transcription and opens chromatin fibre structure [RNAseq]
Relations
BioSample SAMN25653799
SRA SRX14045836

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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