|
| Status |
Public on Aug 02, 2022 |
| Title |
JF26 |
| Sample type |
SRA |
| |
|
| Source name |
INK-ATTAC mouse, bred onto a C57BL/6 background
|
| Organism |
Mus musculus |
| Characteristics |
strain: INK-ATTAC mouse, bred onto a C57BL/6 background
tissue: bone
treatment age: old
treatment gropu: ap
|
| Treatment protocol |
INK-ATTAC mice (6-12 months=young) were compared to INK-ATTAC mice (20 months=old), treated with either Vehicle or 10 mg of AP20187 per kg body mass [drug/body mass]) twice weekly beginning at 20 months of age for a total of 4 months.
|
| Growth protocol |
INK-ATTAC transgenic mice were bred onto a C57BL/6 background
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
We obtained tibia diaphyses. The centrifuged bones were isolated using an Rneasy Micro Kit (Quiagen, Valenciy, CA) and treated with the Turbo DNA-freeTM Kit (Life Technologies, Grand Island, NY) to remove potential contaminationg DNA that may lead to false-positive amplification.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Sequenced on an Illumina HiSeq 2000 using TruSeq SBS sequencing software (version 3) and SCS data collection software (version 1.4.8)
Base calling was performed using Illumina RTA (version 1.12.4.2)
Paired-end reads from the raw RNAseq data were aligned using TopHat (version 2.0.6)
Quality control assessments were made using RSeQC software
Gene counts were generated using HTSeq software and gene annotation files were obtained from Illumina
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include count values for each Sample.
|
| |
|
| Submission date |
Mar 27, 2022 |
| Last update date |
Aug 02, 2022 |
| Contact name |
Sundeep Khosla |
| Organization name |
Mayo Clinic
|
| Department |
Endocrinology Research
|
| Street address |
200 1st St SW
|
| City |
Rochester |
| State/province |
MN |
| ZIP/Postal code |
55906 |
| Country |
USA |
| |
|
| Platform ID |
GPL13112 |
| Series (1) |
| GSE199493 |
A New Gene Set Identifies Senescent Cells and Predicts Senescence Associated Pathways Across Tissues |
|
| Relations |
| SRA |
SRX14535340 |
| BioSample |
SAMN26853336 |
