|
| Status |
Public on May 31, 2023 |
| Title |
Input biol rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Adult skeletal muscle
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Adult skeletal muscle
tissue type: Gastrocnemius and quadriceps
chip antibody: None
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei were fixed with 4% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sheared on a Bioruptor Pico (Diagenode) for 10 cycles (30 sec on/ 30 sec off for each cycle) at 4°C
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Preparation Kit complemented with NEBNext Multiplex Oligos for Illumina from NEB. 10 ng of DNA was used as starting material for input samples and 1 ng for ip samples. Libraries were amplified using 15 cycles for ip samples and 12 cycles for input on the thermocycler. Post amplification libraries were size selected at 250-450bp in length using SPRISelect beads from Beckman Coulter. Libraries were validated using the Agilent D1000 ScreenTape.
|
| |
|
| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalls were performed using bcl2fastq v2.17 for Novaseq output.
After quality control using FastQC tool, reads were trimed for adapter sequence and were aligned to mm10 reference genome using bowtie2 (Version 2.3.2) with default settings.
Picard (Version 2.10.3) was then used to remove duplicated reads.
HOMER software was used for .bigWig generation.
HOMER software was used for peak calling. For Maf ChIPseq, default setting was used except with -style factor, for H3K27ac ChIPseq, fdr was set to 1e-3 and -style histone was used.
For heatmap generation, merge .bed file for each condition were generated and the summit .bed used as input for ngs.plot.r R package.
Assembly: GRCm38 - mm10
Supplementary files format and content: bigWig, .bed format peaks called by HOMER (except for Input sample)
|
| |
|
| Submission date |
Aug 18, 2022 |
| Last update date |
May 31, 2023 |
| Contact name |
kenian chen |
| E-mail(s) |
chenkn007@gmail.com
|
| Organization name |
UTsouthwestern
|
| Department |
Population and Data Science
|
| Lab |
Quantitative Biological Research Center
|
| Street address |
5323 Harry Hines Boulevard
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE211541 |
Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution [ChIP-seq] |
| GSE211545 |
Opposing transcriptional circuits governing skeletal muscle development and maturation revealed at single nuclear resolution. |
|
| Relations |
| BioSample |
SAMN30385718 |
| SRA |
SRX17133646 |
