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Sample GSM4338385 Query DataSets for GSM4338385
Status Public on Apr 06, 2020
Title Lemur-(6-4)PP-rep2
Sample type SRA
 
Source name primary mouse lemur fibroblasts
Organism Microcebus murinus
Characteristics tissue: mouse lemur fibroblasts
treatment: UV irradiation
time point (after treatment): 5 minutes
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 genomic DNA
Extraction protocol Samples are pooled, lysed, and immunoprecipitated with anti-TFIIH antibodies p62 (Santa Cruz Biotechnology, sc292) and p89 (XPB, Santa Cruz Biotechnology, sc293).
Ligated to adapters and processed for sequencing.
 
Library strategy OTHER
Library source genomic
Library selection other
Instrument model Illumina HiSeq 4000
 
Description UV irradiated cell line derived from primary mouse lemur fibroblasts
Data processing Library strategy: XR-Seq
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 SAMN14180205
SRA SRX7798780

Supplementary file Size Download File type/resource
GSM4338385_Lemur645m2_TAGCTT_S155_L007_R1_001_cutadapt_sorted.bed.gz 414.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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