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| Status |
Public on Feb 13, 2018 |
| Title |
ATAC-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
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Dissociated Lats1/2-deficient mouse tumor cells (∼50,000 cells) were spun down at 500 x g for 5 min at 4C, lysed in cold Lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% IGEPAL CA-630). Afterspinning down at 500 x g for 10 min at 4C, nuclei were resuspended in transposition mix containing 25 μl TD (2x reaction buffer) 2.5 μl TDE1 (Nextera Tn5 Transposase), 22.5 μl Nuclease Free H2O, at 37°C for 30 min. Immediately following transposition, DNA were purified using a Qiagen MinElute PCR Purification Kit. Transposed DNA fragments were subsequently amplified and the amplified library was purified using Qiagen MinElute PCR Purification Kit.
Libraries were generated using the Ad1_noMX and Ad2.1–2.4 barcoded primers and were amplified for 7–9 total cycles. Libraries were purified with AMPure beads (Agencourt) to remove contaminating primer dimers. All libraries were sequenced on the Illumina HiSeq 2000.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
Illumina Casava software used for basecalling.
Sequenced reads were trimmed for adaptor sequence.
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 |
SAMN07138919 |
| SRA |
SRX2832620 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2631330_Lats-ATAC.wig.gz |
60.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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