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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jun 05, 2024 |
| Title |
B36 cells, ATAC, DMSO, BR1 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
cell line: B36
cell type: glioblastoma stem cell
treatment: DMSO
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
We followed the omniATAC protocol (Corces et al., Nature Methods, 2017)
We followed the omniATAC protocol (Corces et al., Nature Methods, 2017)
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| Library strategy |
ATAC-seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
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| Data processing |
Sequencing reads were trimmed with using Cutadapt (v1.10) with "-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -A CTGTCTCTTATACACATCTGACGCTGCCGACGA --quality-cutoff=15,10 --minimum-length=36"
Trimmed reads were aligned to hg38 reference genome using bowtie2 (v2.3.4.1) with " --very-sensitive -X 2000".
Reads aligned to chrM were eliminated.
Duplicated reads were discarded using Picard (v2.8.1, http://broadinstitute.github.io/picard/).
Only properly paired reads with at least 10 mapping quality were retained
hg38
bigwig
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| Submission date |
Mar 09, 2023 |
| Last update date |
Jun 05, 2024 |
| Contact name |
Daofeng Li |
| E-mail(s) |
lidaof@gmail.com
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| Phone |
(314) 286-0866
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| Organization name |
Washington University in St. Louis
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| Department |
Genetics
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| Lab |
Ting Wang Lab
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| Street address |
4515 McKinley Avenue
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| City |
SAINT LOUIS |
| State/province |
MO |
| ZIP/Postal code |
63110 |
| Country |
USA |
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| Platform ID |
GPL18573 |
| Series (1) |
| GSE227059 |
Epigenetic therapy activates TE-chimeric transcripts to provide additional source of antigens in glioblastoma stem cells |
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| Relations |
| BioSample |
SAMN33706462 |
| SRA |
SRX19627033 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7090835_ATAC_B36_DMSO_BR1.RPGC_10M.bw |
278.9 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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