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Sample GSM4338381 Query DataSets for GSM4338381
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

Supplementary file Size Download File type/resource
GSM4338381_Lemur2_cutadapt_sorted.bed.gz 182.9 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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