|
| Status |
Public on Sep 07, 2022 |
| Title |
RNAseq_HybNeo3_2 |
| Sample type |
SRA |
| |
|
| Source name |
Somatic cell hybrid
|
| Organisms |
Homo sapiens; Cricetulus griseus |
| Characteristics |
cell type: HybNeo3
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 the following human chromosomes ; 4, 6, 8, 11, 13, 18 ,X and a 3 carrying a neocentromere (Neo3).
HybNeo3_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) |
[email protected]
|
| 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 |
SAMN25653796 |
| SRA |
SRX14045839 |
