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| Status |
Public on Feb 13, 2018 |
| Title |
H3K27Ac-mLats12tumor |
| Sample type |
SRA |
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| Source name |
mouse nerve tumor cells
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| Organism |
Mus musculus |
| Characteristics |
tissue: primary cultured nerve tumor cells
genotype: Lats1fl/fl;Lats2fl/+;CcGFPfl/+;Dhh-Cre
chip antibody: H3K27Ac (Rabbit, Abcam, 4729)
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Lats1/2-deficient (Lats1fl/fl;Lats2fl/+;CcGFPfl/+;Dhh-Cre) mouse paraspinal tumors were isolated, minced into 1 mm3 pieces and dissociated using collagenase type I (156 U/ml) and dispase protease II (1.25 U/ml) at 37oC. Tumor cells were propagated as an adherent layer on tissue culture dishes in proliferation medium composed of DMEM/10% FBS plus L-glutamine and penicillin/streptomycin.
Dissociated Lats1/2-deficient mouse tumor cells (∼20 million cells) were fixed for 15 min at room temperature with 1% formaldehyde-containing medium. Nuclei were isolated and sonicated in sonication buffer (10 mM Tris-HCl [pH 8.0], 1 mM EDTA, 0.5 mM EGTA, and protease inhibitor cocktail). Sonicated chromatin (∼300 μg) was used for immunoprecipitation by incubation with rabbit IgG or anti-Tead1, anti-H3K27ac, anti-H3K4me3, anti-H3K4me1 antibody (4 μg) overnight at 4°C.
The ChIP-seq libraries were prepared using NEBNext ChIP-seq Library Prep Master Mix Set for Illumina (NEB catalogue number E6240L) and then run on the Illumina sequencer HiSeq 2000.
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
Peak calling was performed using MACS1.4 with a default p value cut off.
genome build: mm10
processed data files format and content: wig files were generated by MACS1.4
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| Submission date |
May 17, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Richard Lu |
| Organization name |
Cincinnati Children's Hospital Medical Center
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| Department |
CBDI
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| Lab |
Lu Lab,T6.525
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| Street address |
3333 Burnet Ave
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| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
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| Platform ID |
GPL13112 |
| Series (1) |
| GSE99040 |
Reprogramming of Schwann Cells by LATS1/2-TAZ/YAP Signaling Drives Malignant Peripheral Nerve Sheath Tumorigenesis |
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| Relations |
| BioSample |
SAMN07138921 |
| SRA |
SRX2832618 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2631328_Lats-H3k27Ac.wig.gz |
395.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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