|
| Status |
Public on Jul 22, 2024 |
| Title |
WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, Biol. Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
WI38 (ATCC,CCL-75 )
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: WI38 (ATCC,CCL-75 )
cell type: normal lung fibroblasts
genotype: cells were retrovirally transduced with ER:RAS construct for inducible expression of oncogenic HRASG12V upon treatment with 4OHT
treatment: 4-OHT
time: 144hrs
|
| Treatment protocol |
Nuclei from WI38-ER:RAS(G12V) cells were extracted at indicated time-points post stimulation with 400 nM 4-hydroxy-tamoxifen (4-OHT) by incubating cells in nuclear extraction buffer (containing 10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630) and immediately centrifuging at 500 × g at 4 °C for 5 min. The supernatant was carefully removed by pipetting, and the transposition was performed by resuspending nuclei in 50 µl of Transposition Mix containing 1× TD Buffer (Illumina, San Diego, CA) and 2.5 µl Tn5 (Illumina) for 30 min at 37 °C.
|
| Growth protocol |
WI38 normal human lung fibroblasts (CCL-75, ATCC) were cultured in a DMEM (D629, Sigma) medium supplemented with 10% fetal bovine serum (#25-514, GenClone) at 37°C in a 5% CO2 and 2% O2 atmosphere.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was extracted using a Qiagen MinElute kit.
Libraries were produced by PCR amplification (7 cycles) of tagmented DNA using the NEBNext Ultra II High-Fidelity 2× PCR Master Mix (#M0544, NEB). Library quality was assessed using an Agilent Tapestation 4200.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X |
| |
|
| Data processing |
fastq files were quality checked with multiqc
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option in paired-end mode
fastq files were trimmed with trimmomatic te moreve adapters and aligned using bowtie 2 with the local option in paired-end mode
Enriched regions were identified using macs v.2.2.7.1 (macs2 callpeak --nomodel --shiftsize --shift-control--gsize hs -p 1e-3). The identified peaks were subsequently processed using the irreproducibility discovery rate (IDR) pipeline, generating time point-specific reproducible peak sets at each time point. Reproducible peaks were collapsed into master peaksets per histone modification analyzed.
Signal visualization tracks were generated with deeptools using the RPGC approach to obtain 1X coverage after merging time point replicates into a single bam file.
Assembly: GRCh38-hg38
Supplementary files format and content: BigWig and narrowPeak
|
| |
|
| Submission date |
Jul 03, 2024 |
| Last update date |
Jul 22, 2024 |
| Contact name |
Ricardo Iván Martínez Zamudio |
| E-mail(s) |
rm1238@rwjms.rutgers.edu
|
| Organization name |
Rutgers Biomedical and Health Sciences | Rutgers-Robert Wood Johnson Medical School
|
| Department |
Pharmacology
|
| Lab |
Martínez Zamudio Lab
|
| Street address |
675 Hoes Lane West
|
| City |
Piscataway |
| State/province |
New Jersey |
| ZIP/Postal code |
08854 |
| Country |
USA |
| |
|
| Platform ID |
GPL34281 |
| Series (1) |
| GSE271459 |
Transcription factor network dynamics during the commitment to oncogene-induced senescence [ATAC-Seq] |
|
| Relations |
| BioSample |
SAMN42288750 |
| SRA |
SRX25201444 |
