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| Status |
Public on May 15, 2024 |
| Title |
Deaf1, Input, replicate1 |
| Sample type |
SRA |
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| Source name |
C2C12
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| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: Mouse myoblasts
chip antibody: none
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| Growth protocol |
C2C12 were cultured in DMEM media with 10% FBS and 1x pen/strep under 37C at 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with 1% formaldehyde for 10 mins. After quenching and cell lysis, chromatin was sheared using Bioruptor sonicator
Native ChIP-seq
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
BGISEQ-500 |
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| Data processing |
Quality control was performed using fastqc v0.11.8.
ChIP-seq reads were aligned to the UCSC mm10 genome using version bwa 0.7.17-r1198-dirty.
Duplicates and unmapped reads were flagged with samblaster version 0.1.24, and removed with sambamba version 0.7.0.
Peaks were called using macs2 v2.1.2 with the significance cut-off q-value <= 0.1.
Peaks were merged and filtered using the idr R package. Only highly reproducible peaks with IDR between 0 and 0.05 (inclusive) were kept.
Assembly: mm10
Supplementary files format and content: narrowPeak file includes peak calls from macs2
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| Submission date |
Jul 11, 2023 |
| Last update date |
May 15, 2024 |
| Contact name |
NATHAN HARMSTON |
| E-mail(s) |
harmstonn@cardiff.ac.uk
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| Organization name |
Cardiff University
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| Street address |
Museum Avenue
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| City |
Cardiff |
| ZIP/Postal code |
CF10 3AX |
| Country |
United Kingdom |
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| Platform ID |
GPL23479 |
| Series (1) |
| GSE237088 |
FOXO-regulated Deaf1 controls muscle regeneration through autophagy |
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| Relations |
| BioSample |
SAMN36407702 |
| SRA |
SRX20983603 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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