|
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 |