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| Status |
Public on Nov 26, 2024 |
| Title |
Tumor_only, Cell_line_B, timepoint_1, EXP_9.7, rep_3 |
| Sample type |
SRA |
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| Source name |
B
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| Organism |
Mus musculus |
| Characteristics |
cell line: B
time: Day 6
timepoint: timepoint_1
treatment: Tumor_only
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were processed with the Illumina Tagmentation kit
Library preparation was conducted as in Buenrostro et al, 2015. PCR products were purified with Agencourt AMPure XP beads.
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Raw data was processed with nf-core/atacseq pipeline
Mapping reads to the reference genome with STAR alligner (v2.7.10a)
Duplicates identification with Picard (v2.27.4)
Peak calling with MACS2 (v2.2.7.1)
Assembly: GRCm38
Supplementary files format and content: broadPeak files, containting coordinates of called peaks and counts assigned to them
Supplementary files format and content: Consensus peaks with coordinates and counts assigned to them
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| Submission date |
Sep 25, 2024 |
| Last update date |
Nov 26, 2024 |
| Contact name |
Aleksandr Bykov |
| E-mail(s) |
[email protected]
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| Organization name |
CCRI
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| Department |
BiCU
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| Street address |
Zimmermannpl. 10
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| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE278010 |
NK cell cytotoxicity shapes the clonal evolution of B cell leukemia [ATAC-seq] |
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| Relations |
| BioSample |
SAMN43929627 |
| SRA |
SRX26202133 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8537507_EXP9_7_13H_Tumor_only_REP3.mLb.clN_peaks.broadPeak.gz |
906.1 Kb |
(ftp)(http) |
BROADPEAK |
SRA Run Selector |
| Raw data are available in SRA |
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