|
| Status |
Public on Mar 11, 2024 |
| Title |
ATAC_N3 |
| Sample type |
SRA |
| |
|
| Source name |
DRG
|
| Organism |
Rattus norvegicus |
| Characteristics |
group: naive
Sex: Female
strain: Sprague-Dawley
|
| Treatment protocol |
Chronic Constriction Injury and Naïve groups
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Dorsal root ganglion (L4-L6) harvested and homogenized
ATAC-seq with Illumina TDE1 enzyme after nuclei isolation
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Casava v1.8.2 used for base calling
Reads trimmed for adapter sequence
reads mapped to rn6 genome using Bowtie2
Assembly: rn6
Supplementary files format and content: Align reads shifted 4 nucleotides upstream for 5' and 5 nucleotides downstream for 3' end; insertion sites identified by trimming to the 5'end. Insertion site extended in both directions by 75bp; Reads downsampled; peaks called by MACS2; limma used to count reads for CCI versus Naive.
|
| |
|
| Submission date |
Aug 02, 2022 |
| Last update date |
Mar 11, 2024 |
| Contact name |
Kimberly E Stephens |
| E-mail(s) |
kestephens@uams.edu
|
| Phone |
501-364-3307
|
| Organization name |
University of Arkansas for Medical Sciences
|
| Department |
Pediatrics
|
| Street address |
13 Children's Way
|
| City |
Little Rock |
| State/province |
AR |
| ZIP/Postal code |
72202 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
| GSE210321 |
Identification of regulatory elements in primary sensory neurons involved in physical injury-induced neuropathic pain |
|
| Relations |
| BioSample |
SAMN31445151 |
| SRA |
SRX16770457 |
