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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 24, 2020 |
| Title |
ATAC-seq_shTopors-2 |
| Sample type |
SRA |
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| Source name |
shTopors
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| Organism |
Mus musculus |
| Characteristics |
cell line: AML12 cells
genotype/variation: shTopors
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| Growth protocol |
AML12 cells were cultured in DMEM/F12 supplemented with 10% fetal bovine serum, ITS Liquid Media Supplement, and 0.1μM dexamethasone at 37 °C and 5% CO2.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
The ATAC-seq was performed as described (Buenrostro et al., 2015) with minor modifications: starting with 30,000 AML12 cells and transposition reaction at 37°C for 45 min.
Illumina sequencing library were prepared according to the standard Illumina protocol.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Paired-end reads were aligned to the mouse genome (mm9) using Bowtie2 (Langmead and Salzberg, 2012) with parameters “-X 2000”.
Mitochondrial and PCR duplicate reads were removed after alignment.
Peaks were identified using MACS2 (Zhang et al., 2008) with a q value threshold of 0.01.
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files contain ATAC-seq signal for each replicate.
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| Submission date |
Jul 22, 2019 |
| Last update date |
Jun 26, 2020 |
| Contact name |
Bo Wen |
| E-mail(s) |
bowen75@fudan.edu.cn
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| Organization name |
Fudan University
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| Street address |
130 Dongan Rd.
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| City |
ShangHai |
| ZIP/Postal code |
200032 |
| Country |
China |
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| Platform ID |
GPL21273 |
| Series (2) |
| GSE134619 |
TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes [ATAC-seq] |
| GSE134624 |
TOPORS, a tumor suppressor protein, maintains higher-order chromatin organization in mouse hepatocytes |
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| Relations |
| BioSample |
SAMN12333897 |
| SRA |
SRX6484415 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3959422_shTopors-2.bigwig |
124.5 Mb |
(ftp)(http) |
BIGWIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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