|
Status |
Public on Jun 19, 2024 |
Title |
Old Biological Rep 2, Passage 2, input |
Sample type |
SRA |
|
|
Source name |
dermal fibroblasts
|
Organism |
Homo sapiens |
Characteristics |
cell type: dermal fibroblasts chip antibody: none age: 97 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 OLD_P2_Merged_fe.bw O2P2_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 |
SAMN39514948 |
SRA |
SRX23335284 |