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Sample GSM8170425 Query DataSets for GSM8170425
Status Public on Apr 02, 2024
Title XR-seq xpc-1 mutant C. elegans mixed stages CPD 1h rep 1
Sample type SRA
 
Source name Mixed stages
Organism Caenorhabditis elegans
Characteristics tissue: Mixed stages
genotype: xpc-1
treatment: UV irradiation induced CPD
Growth protocol The C. elegans wild-type (N2 ancestral), csb-1 (RB1801) and xpc-1 (TG2226) strains were obtained from the Caenorhabditis Genetics Center and were cultured under standard conditions at room temperature on nematode growth media (NGM) agar plates with E. coli strain OP50.
Extracted molecule other
Extraction protocol For XR-seq, supernatants were incubated with 5μL RNase A and then 5μL Proteinase K, purified, and then immunoprecipitated with either anti-CPD antibodies.
For XR-seq, immunoprecipitations were ligated to the adaptors, purified with the antibody used in the first purification, and DNA damage was reversed by CPD photolyase. After PCR amplification, the library was sequenced.
 
Library strategy OTHER
Library source other
Library selection other
Instrument model NextSeq 2000
 
Data processing For XR-seq, cutadapt was used to trim reads with adaptor sequence TGGAATTCTCGGGTGCCAAGGAACTCCAGTNNNNNNACGATCTCGTATGCCGTCTTCTGCTTG at the 3′-end and to discard untrimmed reads. Bowtie 2 was used for read alignment to the ce11 reference genome, followed by filtering, sorting, deduplication, and indexing. Post-alignment filtering steps were adopted using Rsamtools. We only keep reads that: (i) have mapping quality greater than 20; (ii) are from chromosome I, II, III, IV, V, and X; and (iii) are of length 19-24 bp. For plotting strand-based average repair profiles of the genes, we selected 7061 genes longer than 1 kilobase pair, situated at least 500 base pairs away from neighboring genes. Each gene was evenly divided into 100 bins from the Transcription Start Site (TSS) to the Transcription End Site (TES), and 25 bins (2 kbp) upstream of TSS, 25 bins (2 kbp) downstream of TES. Bed files of the reads were intersected to the 150 bin-divided-gene list by Bedtools intersect with the following commands -d -wa -F 0.5 -S or -s for TS and NTS, respectively22. We present the descriptive properties of our data in Supplementary Table 1. For RNA-seq, reads were aligned using STAR, followed by a filtering step to remove unmapped reads, reads with unmapped mates, reads that do not pass quality controls, reads that are unpaired, and reads that are not properly paired. We only kept the first read from the mate pair to ensure independent measures. Read counts for each gene were obtained using FeatureCounts.
Assembly: ce11
Supplementary files format and content: bed
Library strategy: XR-seq
 
Submission date Mar 26, 2024
Last update date Apr 02, 2024
Contact name Yuchao Jiang
E-mail(s) yuchaojiang@tamu.edu
Organization name Texas A&M University
Street address 3143 TAMU
City College Station
State/province TX
ZIP/Postal code 77843
Country USA
 
Platform ID GPL32326
Series (1)
GSE262486 Genome-wide CPD repair maps of Caenorhabditis elegans
Relations
BioSample SAMN40620148
SRA SRX24066114

Supplementary file Size Download File type/resource
GSM8170425_XR_seq_XPC_C_elegans_mixed_CPD_1h_rep1.bed.gz 51.2 Mb (ftp)(http) BED
SRA Run SelectorHelp
Raw data are available in SRA

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