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| Status |
Public on May 03, 2021 |
| Title |
C2C12_H3K27me3 |
| Sample type |
SRA |
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| Source name |
C2C12_WT
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| Organism |
Mus musculus |
| Characteristics |
cell line: C2C12
cell type: skeletal muscle cell line
genotype: WT
chip antibody: H3K27me3, Cell Signalling, 9733, Lot 8
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| Treatment protocol |
none
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| Growth protocol |
C2C12 control and C2C12 Hira KO cell lines were collected when grown in high serum medium at low density (proliferating conditions)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were subjected to nuclei isolation, chromatin fragmentation using Micrococcal Nuclease and nucleosome purification by Hydroxyapatite. Immunoprecipitation was performed overnight at 4°C with 6μg of chromatin and 5μg of antibody previously incubated with Protein-A- (for H3K27ac, H3K4me3, H3K27me3 antibodies) or Protein-G-coated (for H3.3 antibody) magnetic beads.
Library was prepared using KAPA Hyper Prep Kits with PCR Library Amplification/Illumina series (Roche, 07962363001) with IDT for Illumina TruSeq DNA-RNA UD 96 Indexes (UDI) (Illumina, 2023784) and quantified by RT-qPCR using NEBNext Library Quant Kit for Illumina (NEB, E7640AA). Sequencing was carried out on paired-end 50bp of Illumina HiSeq4000.
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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 |
FASTQ groomer tool (https://usegalaxy.org)
BOWTIE2 v2.3.4.2 (https://usegalaxy.org)
MACS2 v2.1.1.2 using paired-end BAM files with the cutoff q-value 5-e2 and the broad region calling off, the input was used as control (https://usegalaxy.org)
ChIPseeker v1.18.0 (https://usegalaxy.org)
Genome_build: mm10
Supplementary_files_format_and_content: MACS2 resulting bedgraph file was converted to bigwig format using the wig/bedgraph-to-bigwig converter v1.1.1 (https://usegalaxy.org)
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| Submission date |
Nov 08, 2020 |
| Last update date |
May 03, 2021 |
| Contact name |
Joana Esteves de Lima |
| E-mail(s) |
joanaesteveslima@gmail.com
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| Organization name |
INSERM
|
| Department |
IMRB INSERM U955
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| Lab |
Team RELAIX
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| Street address |
8 rue du general sarrail
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| City |
Creteil |
| ZIP/Postal code |
94000 |
| Country |
France |
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| Platform ID |
GPL21103 |
| Series (2) |
| GSE161054 |
Genome-wide chromatin state in myoblasts lacking Hira [ChIP-seq] |
| GSE161056 |
ATAC-seq, ChIP-seq and RNA-seq studies in myoblasts lacking Hira |
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| Relations |
| BioSample |
SAMN16706606 |
| SRA |
SRX9460296 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM4889018_C2C12_H3K27me3.bigwig |
342.3 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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