|
| Status |
Public on Jun 19, 2024 |
| Title |
Neonatal Biological Rep 1, Passage 2, input |
| Sample type |
SRA |
| |
|
| Source name |
foreskin fibroblasts
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: foreskin fibroblasts
chip antibody: none
age: 0
passage number: 2
|
| Growth protocol |
All fibroblasts were thawed in passage 2 (P2) and maintained in Human Dermal Fibroblast Media (#116-500, Cell Applications). Media was refreshed every other day and fibroblasts were passaged using Tryple Select (12563011,Gibco) when culture dishes were >80% confluent.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP experiments were performed on chromatin extracts according to the manufacturer's protocol (ChIP-IT High sensitivity, Active Motif, Cat.n. 53040) and chromatin sheared using the Bioruptor system (Bioruptor Plus, diagenode, Cat.n. B01020001) between 30-45 cycles (each cycle 30 sec ON/ 30 sec OFF high voltage).
ChIP-Seq library preparation and sequencing reactions were conducted at Novogene Corporation Inc (Sacramento, CA, USA).
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Input/Control
NEO_P2_Merged_fe.bw
N1P2_peaks.narrowPeak
|
| Data processing |
Trimming (Trimgalore)
mapping (Bowtie2)
Callpeak ran on merged replicates for each tissue/passage (MACS2) using Inp (control) and IP to find fold enrichment. CD4 samples have no Inp file, online ENCODE file ENCFF918OQM.bam was used instead.
bigwig file called (bedGraphToBigWig)
Assembly: hg38
Supplementary files format and content: bigwig file containing fold enrichment signal track for either neonatal P2 merged, old P2 merged or CD4 samples (all donors) merged
|
| |
|
| Submission date |
Jan 20, 2024 |
| Last update date |
Jun 19, 2024 |
| Contact name |
Vittorio Sebastiano |
| E-mail(s) |
vsebast@stanford.edu
|
| Organization name |
Stanford University
|
| Department |
OB-GYN/Reproductive, Perinatal and Stem Cell Biology Research
|
| Lab |
Sebastiano Lab
|
| Street address |
265 Campus Drive
|
| City |
Stanford |
| State/province |
California |
| ZIP/Postal code |
94305-5454 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE253773 |
PRC2-AgeIndex: a universal biomarker of aging and rejuvenation [ChIP-seq] |
| GSE253987 |
PRC2-AgeIndex: a universal biomarker of aging and rejuvenation |
|
| Relations |
| BioSample |
SAMN39514951 |
| SRA |
SRX23335281 |
