 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 01, 2022 |
| Title |
Injury Sciatic nerve JUN ChIP-seq 2 |
| Sample type |
SRA |
| |
|
| Source name |
sciatic nerve
|
| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague Dawley
developmental stage: P28
Sex: Male
fraction: ChIP DNA
antibody: JUN
treatment: Injury
|
| Treatment protocol |
Sciatic nerves of adult Sprague-Dawley rats were cut following the surgery protocol described previously (Hung et al., 2015). The nerve tissue distal to the transection awas isolated at 8 d post-transection.
|
| Growth protocol |
Male Sprague Dawley rats (Harlan Laboratory) were housed with a normal light/dark cycles and ad libitum access to rat chow and water.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Freshly dissected rat sciatic nerve was used for ChIP-seq using the MNase protocol described previously (Ma et al., 2018) with 4μg of JUN antibody (Santa Cruz SC-1694, RRID:AB_631263).
Libraries were prepared from ChIP DNA, and respective inputs, using the Illumina TruSeq ChIP Sample Preparation Kit.
Two biological replicates were performed, and samples with respective inputs were sequenced on a Illumina HiSeq 2500 instrument at the UW Biotechnology Center.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Illumina Pipeline Casava 1.8.2
Reads were mapped to the reference genome rn5 using Bowtie2 (Langmead and Salzberg, 2012; Langmead et al., 2009) to produce BAM files, and the files from the two biological replicates were combined for further analysis.
BAM files were filtered for mapped reads using BamTools (Barnett et al., 2011; Quinlan and Hall, 2010) and peaks were called using MACS2 (Feng et al., 2012; Liu, 2014; Zhang et al., 2008).
BedTools bamCoverage generated bedgraphs of ChIP-seq samples.
Genome_build: Rn5
Supplementary_files_format_and_content: bedgraph and peak bed files
|
| |
|
| Submission date |
Dec 14, 2021 |
| Last update date |
Mar 01, 2022 |
| Contact name |
John Svaren |
| E-mail(s) |
jpsvaren@wisc.edu
|
| Organization name |
University of Wisconsin
|
| Department |
Comparative Biosciences
|
| Lab |
Waisman Center
|
| Street address |
1500 Highland Ave.
|
| City |
Madison |
| State/province |
WI |
| ZIP/Postal code |
53705 |
| Country |
USA |
| |
|
| Platform ID |
GPL18694 |
| Series (1) |
|
| Relations |
| BioSample |
SAMN24021601 |
| SRA |
SRX13437598 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
