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| Status |
Public on Feb 17, 2017 |
| Title |
C2C12_ND_TEAD1 |
| Sample type |
SRA |
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| Source name |
C2C12 cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: myoblasts
strain: C3H
chip antibody: TEAD1 BD Biosciences
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| Treatment protocol |
C2C12 cells were harvested either in non-differentiated or differentiated state and resuspended in sonication buffer for 10 mins and then sonicated using covarys sonicator. Muscle from hind limbs of three wil-type B6 were minced and homogenised, fixed in 1% formaldehyde and incubated for 10 min at room temperature. Cross-linking was stopped by the addition of glycine to final concentration 0.125 M. Tissue fragments were washed with cold PBS supplemented with protease inhibitors. The tissues were then homogenized in hypotonic buffer inorder to obtain nuclei, the nuclear pellet was resuspended in sonication buffer and were sonicated to obtain DNA fragments <500 bp and centrifuged. The soluble chromatin fraction was pretreated with blocked protein G sepharose beads. Subsequently, samples were incubated overnight at 4°C with antibodies to AcH3K27 (Abcam, ab4729) or 7C2 RNAPII antibody. Blocked beads were then added and the mixture was incubated for 2 h at 4°C. Prot G beads were washed, protein-DNA complexes were eluted from the beads and decrosslinked, and DNA recovered by phenol chloroform extraction and ethanol precipitation after treatment with ribonuclease A (Abcam) and proteinase K.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
ChIP-seq libraries were prepared using NEXTflex ChIP-Seq Kit (#5143-02, Bioo Scientific) following the manufacturer's protocol (V12.10) with some modifications. Briefly, 10 ng of ChIP enriched DNA or INPUT DNA were end repaired using T4 DNA polymerase, Klenow DNA polymerase and T4 PNK, then size selected and cleaned-up using Agencourt AMPure XP beads (#A63881, Beckman). A single ‘A’ nucleotide was added to the 3’ ends of the blunt DNA fragments with a Klenow fragment (3' to 5'exo minus). The ends of the DNA fragments were ligated to double stranded barcoded DNA adapters (NEXTflex ChIP-Seq Barcodes - 6, #514120, Bioo Scientific) using T4 DNA Ligase. The ligated products were enriched by PCR (2 min at 98°C; [30 sec at 98°C, 30 sec at 65°C, 60 sec at 72°C] x 14 cycles; 4 min at 72°C) and cleaned-up using Agencourt AMPure XP beads.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Image analysis and base calling were performed using RTA 1.17.21.3 and CASAVA 1.8.2.
Sequence reads were mapped to reference genome mm9/NCBI37 using Bowtie -m 1 --strata --best -y -S -l 40 -p 2.
Genome_build: mm9
Supplementary_files_format_and_content: Wig files were generated using with an in-house script (Variable step, span=25, reads were elongated to 200b)
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| Submission date |
Jun 02, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Shilpy Joshi |
| E-mail(s) |
shilpy.joshi@gmail.com
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| Organization name |
IGBMC
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| Street address |
1 Rue laurent Fries
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| City |
Illkirch |
| ZIP/Postal code |
67404 |
| Country |
France |
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| Platform ID |
GPL17021 |
| Series (2) |
| GSE82190 |
Specific and redundant roles of TEAD transcription factors in C2C12 cell and primary myoblast differentiation (ChIP-Seq) |
| GSE82193 |
Specific and redundant roles of TEAD transcription factors in C2C12 cell and primary myoblast differentiation |
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| Relations |
| BioSample |
SAMN05199429 |
| SRA |
SRX1817466 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2186205_wigs_for_TEAD1_mb.wig.gz |
209.5 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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