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| Status |
Public on Oct 30, 2024 |
| Title |
WT L1 48 hrs (6-4)PP Damage-seq Rep2 |
| Sample type |
SRA |
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| Source name |
whole-organism
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| Organism |
Caenorhabditis elegans |
| Characteristics |
cell type: whole-organism
genotype: N2
treatment: UVB 4000 j/m2
antibody: anti-(6-4)PP
time after_uvb: 48 hours
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| Treatment protocol |
UVB 4000 J/m2
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| Growth protocol |
L1 worms were grown on NGM plates and fed with E. coli bacteria
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
L1 stage worms were irradiated with 4 kJ/m2 UVB at collected in M9 buffer at indicated repair times. Worms were washed 3 times with M9 buffer and then, genomic DNAs were isolated with QIamp DNA Mini Kit/tissue protocol. Ultrasonic fragmented genomic DNAs were purified using an equal volume of HighPrep PCR beads (MagBio). Purified DNA (~1 µg) was used for end-repair and dA-tailing and adaptor ligation (NEBNext Ultra II DNA Library Prep Kit) following manufacturer’s instructions. Damage-containing DNA fragments were purified with either anti-(6-4)PP (Cosmo Bio, cat. no. CAC-NM-DND-002) or Anti-CPD (Cosmo Bio, cat. no. CAC-NM-DND-001).
The purified DNA was primer extended in the presence of 30 pmol Bio3U (biotin elongation primer, 5′-bio-AGAGTG/dU/GACTGGAGTTCAGACGTGTGCTCTTCCGATCT-3′) using NEBNext Q5 Hot Start HiFi PCR Master Mix. Next, undamaged DNA strands were captured by 20 pmol (2 µL) of SH oligo (SH, Subtractive hybridization, 5′-bio-NNGACTGGTTCCAATTGAAAGTGCTCTTCCG-SpC-3′), DNAs were purified using phenol-chloroform extraction and ethanol precipitation. The DNA was then ligated to a second adaptor ligation using T4 DNA ligase HC (Thermo) at 16 °C overnight. After quality check, the DNA samples were purified with HighPrep PCR beads, and ligated DNAs were PCR amplified by NEBNext Ultra II PCR Master Mix with NEBNext Multiplex Oligos for Illumina (New England Biolabs). The PCR libraries were purified with HighPrep PCR beads. Libraries were sequenced by an Illumina NextSeq2000P2 with 50-bp.
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| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| Data processing |
Damage-seq reads were trimmed to remove adaptor sequences by Cutadapt, paired-end reads were aligned with Bowtie with parameters ‐‐nomaqround, ‐‐phred33-quals, -m 4, -X 1000, ‐‐seed123. For each sample, duplicated reads were reduced to a single read. Damage sites were identified as the two nucleotides upstream of each fragment. Using custom scripts, reads were trimmed to the first 4 nucleotides from the 5’ end and slopped 6 nucleotides upstream to generate 10 nucleotide-long genomic regions with the damaged nucleotide in the middle.
Assembly: Caenorhabditis elegans (ce11)
Supplementary files format and content: stranded bedGraph
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| Submission date |
Oct 25, 2024 |
| Last update date |
Oct 30, 2024 |
| Contact name |
Cansu Kose |
| E-mail(s) |
cansuk@live.unc.edu
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| Organization name |
UNC-Chapel Hill
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| Department |
Biochemistry and Biophysics
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| Lab |
Sancar Lab
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| Street address |
120 Mason Farm Rd.
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27599 |
| Country |
USA |
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| Platform ID |
GPL32326 |
| Series (1) |
| GSE280347 |
(6-4)PP and CPD Damage-seq data for L1 stage wildtype, csb-1 and xpc-1 C.elegans |
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| Relations |
| BioSample |
SAMN44459234 |
| SRA |
SRX26506042 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8595187_R2WTL16448h_minus_sorted.bedGraph.gz |
44.9 Mb |
(ftp)(http) |
BEDGRAPH |
| GSM8595187_R2WTL16448h_plus_sorted.bedGraph.gz |
43.8 Mb |
(ftp)(http) |
BEDGRAPH |
SRA Run Selector |
| Raw data are available in SRA |
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