|
| Status |
Public on Aug 12, 2021 |
| Title |
Bmal1_bioRep2 |
| Sample type |
SRA |
| |
|
| Source name |
gastrocnemius muscles_Bmal1
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6J
Sex: male
time: ZT2
tissue: gastrocnemius muscles
chip antibody: Bmal1 (Sigma, SAB4300614, 951421415)
|
| Treatment protocol |
for CLOCK Ab ChIPseq,muscle samples were sequentially treated with EGS and formaldehyde. For BMAL1 Ab ChIPseq, muscle samples were treated with formaldehyde.
|
| Growth protocol |
12 wks old C57BL/6J mice - Gastrocnemius muscles were collected.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
muscle nuclei were isolated by homogenization and and centrifugation. ChIP DNA was recovered after sonication and centrifugation.
ChIPseq library was prepared by using NEBNext Ultra DNA library prep kit for Illumina.
A 2 X 100 run was conducted on HiSeq 3000 Illumina sequencing system
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Bmal1-2_S83_L006
|
| Data processing |
quality of the fastq files were assessed by fastqQC, and the data quality was great
fastq files were aligned to mm10 using bowtie2
biological replicates of the resulting sam files were merged
homer was use for peak calling, using input as background
bigwig files were generated for UCSC genomebrowswer visualization purpose
Genome_build: mm10
Supplementary_files_format_and_content: peak.txt contains identified peaks; bigWig contains binary data to display ChIP-Seq data in Genome Browswer
|
| |
|
| Submission date |
Jan 08, 2020 |
| Last update date |
Aug 12, 2021 |
| Contact name |
Karyn A Esser |
| E-mail(s) |
kaesser@ufl.edu
|
| Organization name |
University of Florida
|
| Department |
PHYSIOLOGY & FUNCTIONAL GENOMICS
|
| Lab |
Esser's lab
|
| Street address |
1345 Center Drive
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32610 |
| Country |
USA |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE143334 |
Genome-wide binding of Bmal1 and Clock in adult mouse skeletal muscle. |
|
| Relations |
| BioSample |
SAMN13781257 |
| SRA |
SRX7525067 |
