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| Status |
Public on Jun 25, 2024 |
| Title |
SMCHD1 CHIP pull down |
| Sample type |
SRA |
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| Source name |
Immortalized non-FSHD human myoblast cell line WS234 (donor 15VBic)
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| Organism |
Homo sapiens |
| Characteristics |
chip antibody: SMCHD1 antibody (Abcam #ab31865)
cell tpye: human myoblast cell line WS234 (donor 15VBic, female non-FSHD sample)
cell line: WS234
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| Treatment protocol |
Proliferating myoblasts were fixed in 1% (v/v) formaldehyde for 20 minutes at RT and quenched with 125 mM glycine for 10 minutes at RT.
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| Growth protocol |
Cells were cultured in LHCN medium on 0.1% (w/v) gelatin coated plates at 37oC in 5% CO2 incubator.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were rinsed with PBS, collected using cell scrapers, centrifuged at 500 x g for 5 minutes and resuspended in swelling buffer (50 mM Tris pH 8, 2.5 mM EDTA and 30% (v/v) glycerol). Cells were then incubated for 30 minutes in swelling buffer at 4oC, sonicated using Bioruptor (Diagenode) for 2 cycles (HI power, cycles of 30 sec on / 1 min off). Nuclei were spun down at 1000 x g for 5 mins at 4oC, resuspended in sonication buffer (50 mM Hepes pH 7.9, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-deoxycholate and 1% SDS), and sonicated for 13 cycles using the same settings as the previous step. 7.5 ug of SMCHD1 antibody (Abcam # ab31865) was added to 250 ug of precleared chromatin and incubated for 3 hours at RT.
Library was constructed using KAPA HyperPrep Kit (Roche #07962363001).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
The reads were aligned to the human hg38 genome using bowtie2 (v2.3.5.1).
Peak calling: MACS2 using a q value cutoff = 0.05
Genome_build: hg38
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| Submission date |
Dec 13, 2021 |
| Last update date |
Jun 25, 2024 |
| Contact name |
Jeffrey Dilworth |
| E-mail(s) |
fdilworth@wisc.edu
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| Phone |
6082653758
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| Organization name |
University of Wisconsin
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| Street address |
1111 Highland Ave
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| City |
Madison |
| State/province |
Wisconsin |
| ZIP/Postal code |
53705 |
| Country |
USA |
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| Platform ID |
GPL20301 |
| Series (2) |
| GSE190829 |
SMCHD1 activates the expression of genes required for the expansion of human myoblasts (ChIP-seq) |
| GSE190830 |
SMCHD1 activates the expression of genes required for the expansion of human myoblasts |
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| Relations |
| BioSample |
SAMN24011167 |
| SRA |
SRX13401713 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5732678_SMCHD1-ChIP_peaks.narrowPeak.gz |
355.6 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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