|
Status |
Public on Mar 11, 2024 |
Title |
ChIP_CCI2 |
Sample type |
SRA |
|
|
Source name |
DRG
|
Organism |
Rattus norvegicus |
Characteristics |
group: CCI 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 |
ChIP-Seq |
Library source |
genomic |
Library selection |
ChIP |
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 |
SAMN30102651 |
SRA |
SRX16770459 |