|
| Status |
Public on Apr 06, 2020 |
| Title |
Lemur-rna-rep2 |
| Sample type |
SRA |
| |
|
| Source name |
primary mouse lemur fibroblasts
|
| Organism |
Microcebus murinus |
| Characteristics |
tissue: mouse lemur fibroblasts
treatment: None
time point (after treatment): NA
replicate: 2
|
| Treatment protocol |
Cells grown to ~80% confluency in 15-cm plates were harvested 1 h and 5 minutes after irradiation with 20 J/m2 of UV.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from one 10 cm plate of exponentially growing NHF1 or Lemur cells using Trizol (Invitrogen) and the RNeasy Mini Kit (Qiagen) following the manufacturer's instructions.
The library preparation and strand-specific paired-end sequencing (2 × 150 bp) on a HiSeq 4000 platform (Illumina) was performed by Novogene Co., Ltd.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
Cell line derived from primary mouse lemur fibroblasts
|
| Data processing |
3' adapter sequences trimmed using Cutadapt (Martin 2011) for XR-Seq reads
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Bowtie2 version 2.3.4.1 (Langmead and Salzber 2012) with default parameters for XR-Seq reads.
Reads were aligned to hg19 human genome and Mmur_3.0 mouse lemur genome with Star version 2.6.1a (Dobin et al. 2012) with default parameters for RNA-Seq reads.
Aligned reads transformed to bed format, and sorted to remove duplicate reads
Genome_build: hg19 for human genome and Mmur_3.0 for mouse lemur
Supplementary_files_format_and_content: bed files containing regions and read counts
|
| |
|
| Submission date |
Feb 25, 2020 |
| Last update date |
Apr 07, 2020 |
| Contact name |
Ogun Adebali |
| E-mail(s) |
oadebali@sabanciuniv.edu
|
| Organization name |
Sabanci University
|
| Department |
Mol. Bio. Genetics & Bioeng.
|
| Lab |
Adebali Lab
|
| Street address |
Orta Mahalle, Üniversite Caddesi No:27 Tuzla, Sabancı Üniversitesi
|
| City |
Istanbul |
| ZIP/Postal code |
34956 |
| Country |
Turkey |
| |
|
| Platform ID |
GPL28199 |
| Series (1) |
| GSE145883 |
Comparative analysis of genome-wide UV repair events in two primates show different rates but similar distribution. |
|
| Relations |
| BioSample |
SAMN14180209 |
| SRA |
SRX7798776 |
