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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 01, 2023 |
| Title |
mouse CCS, pol2-1 |
| Sample type |
SRA |
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| Source name |
Tumor
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| Organism |
Mus musculus |
| Characteristics |
tissue: Tumor
antibody: pol2-1
genotype: EWSR1::ATF1
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Tumor samples from mouse models were processed by cryogenic grinding, fixed with formaldehyde, and quenched with glycine. Nuclei were extracted via lysis and douncing, followed by lysis of nuclear pellets. The chromatin was fragmented by sonication, then incubated with primary antibodies (anti-V5, anti-RNAPOL2, or anti-H3K27ac) and DynaBeads, subsequently eluted and purified for DNA analysis using a commercial kit.(Zymo )
Libraries were constructed with the NEBNext ChIP-seq Library Prep kit with Unique Dual Index Primers (New England Biolabs).
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| Library strategy |
ChIP-Seq |
| Library source |
genomic |
| Library selection |
ChIP |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
18064X2
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| Data processing |
Sequencing was performed on an Illumina NovaSeq instrument using the 2 x 50 bp protocol to a depth of approximately 30 million reads per sample. ChIP-seq reads were aligned to the mm10 using BWA-MEM (version 0.7.10-r789) for paired-end reads
Assembly: mm10
Supplementary files format and content: Bigwig files are generated with MACS2 and bdg2bigwig and Peaks were called from each aligned bam file against input reads using MACS2 version 2.2.6
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| Submission date |
Nov 27, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Li Li |
| E-mail(s) |
li.li@hci.utah.edu
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| Phone |
3467174255
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| Organization name |
University of Utah
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| Street address |
201 PRESIDENTS CIRCLE
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| City |
Salt Lake City |
| State/province |
Utah |
| ZIP/Postal code |
84112 |
| Country |
USA |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE248749 |
EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and A Mouse Genetic Model [ChIP-Seq 1] |
| GSE248753 |
EWSR1::ATF1 Orchestrates the Clear Cell Sarcoma Transcriptome in Human Tumors and A Mouse Genetic Model |
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| Relations |
| BioSample |
SAMN38453938 |
| SRA |
SRX22655574 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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