|
| Status |
Public on Jul 22, 2024 |
| Title |
WI38-ER:RASG12V, 144hrs post-treament with 4-OHT, H3K4me, 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
cut&tag antibody_target: H3K4me1(Epicypher: 13–0057)
time: 144hrs
|
| Treatment protocol |
Nuclei from 100,000-200,000 cells per target per indicated timepoint were extracted and processed using the CUTANA CUT&Tag kit (Epicypher:14–1102) according to manufacturer's instructions. For the corresponding histone modications the following antibodies were used: H3K4me1(Epicypher: 13–0057), H3K27me3 (Epicypher: 13–005), H3K27ac(Active Motif: 39,133) and rabbit IgG as a negative control(Epicypher: 13–0042), according to the manufacturer’s instructions.
|
| 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 extraction and PCR amplification was performed and processed on Concavalin A bead immobilized nuclei using the CUTANA CUT&Tag kit (Epicypher:14–1102) according to manufacturer's instructions.
Libraries and library clean up per target per sample was performed according to CUTANA CUT&Tag kit (epicypher:14-1102) manufacturer's instructions (PCR amplification: 16 cycles). Library quality was assessed using an Agilent Tapestation 4200.
|
| |
|
| Library strategy |
OTHER |
| 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)
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
Library strategy: CUT&Tag
|
| |
|
| 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) |
| GSE271460 |
Transcription factor network dynamics during the commitment to oncogene-induced senescence [CUT&Tag] |
|
| Relations |
| BioSample |
SAMN42288923 |
| SRA |
SRX25202726 |
