|
| Status |
Public on Dec 05, 2023 |
| Title |
WT SKN-1GFP with antibody rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole Animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole Animal
genotype: WT
antibody: Chromotek, Cat. gta , Lot 90513001MA
|
| Growth protocol |
C. elegans were raised on 6 cm nematode growth media (NGM) plates supplemented with streptomycin and seeded with OP50. All worm strains were grown at 20°C and unstarved for at least three generations before being used.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Worm pellets were ground via mortar and pestle and resuspended with 1.1% formaldehyde to crosslink proteins.
Purified DNA fragments were then used as input for sequencing library preparation using the Diagenode MicroPlex Library prep kit V2.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Description |
SP02IP2
|
| Data processing |
Quality trimming and Adapter sequences were trimmed from raw paired end reads using Trim Galore package v 0.6.4.
Reads were mapped to the C. elegans reference genome using bwa v 0.7.17.
BAM files were sorted with Samtools v 1.10. BAM files were sorted to contain only uniquely mapped reads using Sambamba v 0.6.8.
Peak calls were made using MACS2 v2.2.7.1
Assembly: ce10
Supplementary files format and content: narrowPeak
|
| |
|
| Submission date |
Oct 27, 2023 |
| Last update date |
Dec 05, 2023 |
| Contact name |
Chris Turner |
| E-mail(s) |
cdturner@usc.edu
|
| Organization name |
University of Southern California
|
| Street address |
3715 McClintock Ave
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90089 |
| Country |
USA |
| |
|
| Platform ID |
GPL22765 |
| Series (2) |
| GSE246466 |
A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI [ChIP-seq] |
| GSE246467 |
A dicer-related helicase opposes the age-related pathology from SKN-1 activation in ASI neurons. |
|
| Relations |
| BioSample |
SAMN38022755 |
| SRA |
SRX22254198 |
