GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM4257271 Query DataSets for GSM4257271
Status Public on Aug 12, 2021
Title Clock_bioRep1
Sample type SRA
Source name gastrocnemius muscles_Clock
Organism Mus musculus
Characteristics strain: C57BL/6J
Sex: male
time: ZT2
tissue: gastrocnemius muscles
chip antibody: Clock (Abcam, Ab3517, GR3243020-1)
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 Clock-1_S84_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
Organization name University of Florida
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.
BioSample SAMN13781256
SRA SRX7525068

Supplementary file Size Download File type/resource
GSM4257271_Clock.ucsc.bigWig 1.3 Gb (ftp)(http) BIGWIG
GSM4257271_Clock_peaks.txt.gz 621.3 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap