 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Sep 24, 2022 |
| Title |
embryo, 120min, biol rep2 |
| Sample type |
SRA |
| |
|
| Source name |
embryo
|
| Organism |
Oscheius tipulae |
| Characteristics |
strain: CEW1
tissue: embryo
time after_harvest: 120min
developmental stage: embryos were developed for embryo, 120min, biol rep2 after harvest (a typical harvest is between the 2-4 cell stages)
treatment: FseI
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Egg-laying worms were washed off plates and passed through a 70-µm mesh. This step allows existing eggs to fall through the mesh, leaving the mature worms on the top. These worms were then bleached with sodium hypochlorite solution (Sigma Cat# 425044-250ML, 0.5 M NaOH, 3% bleach) to collect embryos (largely 2-4 cell stage, Fig. S1). Early embryos were further developed in Virgin S Basal (VSB) medium (100 mM NaCl, 5.7 mM K2HPO4, 44.1 mM KH2PO4) at 25°C to reach to the desired embryonic stages
An adapted END-seq protocol was used (Canela et al. 2016, Wong et al. 2021). Briefly, embryos were embedded in agarose plugs to protect the DNA from exogenous breaks. Some plugs were digested with the restriction enzyme AsiSI (NEB, catalog # R0630) or FseI (NEB, catalog # R0588) to generate DSBs as an internal control. DSBs were blunted with exonuclease VII (NEB, catalog # R0630) and exonuclease T (NEB, catalog # M0625). Blunt ends were A-tailed and capped with END-seq adaptor 1, a biotinylated hairpin adaptor. DNA was liberated from the plugs and sheared to ~200-300 bp with a Covaris M220 focused-ultrasonicator (130 L tube, peak power 50, duty 16, cycles/burst 200 for 420 seconds). DNA fragments containing END-seq adaptor 1 were isolated with Dynabeads™ MyOne™ Streptavidin C1 (Invitrogen, catalog # 65001). The other ends broken by sonication were repaired and A-tailed with END-seq adaptor 2. Hairpins were digested with USER (NEB, catalog # M5505), and the DNA was amplified with Illumina TruSeq primers and barcodes.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
endRep5_32c_FseI
|
| Data processing |
Reads (R1 files only) were mapped to the genome with Bowtie2 v2.4.2
Mapped reads were processed with SAMtools v1.14
The 5’ position of each read was mapped, and its strand was determined with BEDTools v2.30.0 genomecov
For comparison between libraries reads were normalized to 1 million genome-mapped reads
Reads (R1 and R2 files) with two sequential telomeric sequences (TTAGGCTTAGGC) were obtained with grep v3.8. Reads were converted to the G-rich strand (TTAGGC)
Cutadapt v3.7 (-j 0 -m 20 -b TTAGGCTTAGGC) was used to trim the telomeric sequences
Reads were mapped to the genome and processed as previously described except 3' ends of the read were mapped
Assembly: Oscheius tipulae ASM1342590v1
Supplementary files format and content: bigWig file containing the 5' end of reads
Supplementary files format and content: bigWig file containing telomere additon site
Library strategy: END-seq
|
| |
|
| Submission date |
Sep 21, 2022 |
| Last update date |
Sep 24, 2022 |
| Contact name |
Jianbin Wang |
| E-mail(s) |
jianbin.wang@utk.edu
|
| Phone |
865-974-4085
|
| Organization name |
University of Tennessee Knoxville
|
| Department |
Biochemistry & Cellular and Molecular Biology
|
| Lab |
420C
|
| Street address |
1311 Cumberland Avenue
|
| City |
Knoxville |
| State/province |
TN |
| ZIP/Postal code |
37996 |
| Country |
USA |
| |
|
| Platform ID |
GPL32681 |
| Series (2) |
| GSE213884 |
The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination [END-seq] |
| GSE213886 |
The Nematode Oscheius tipulae as A Genetic Model for Programmed DNA Elimination |
|
| Relations |
| BioSample |
SAMN30952751 |
| SRA |
SRX17660931 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6595804_END_120min_rep2_FseI_ends.fwd.bw |
4.9 Mb |
(ftp)(http) |
BW |
| GSM6595804_END_120min_rep2_FseI_ends.rev.bw |
4.9 Mb |
(ftp)(http) |
BW |
| GSM6595804_END_120min_rep2_FseI_telomere_fwd.bw |
63.0 Kb |
(ftp)(http) |
BW |
| GSM6595804_END_120min_rep2_FseI_telomere_rev.bw |
63.8 Kb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
