 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Nov 26, 2024 |
| Title |
Tumor_plus_NK, Cell_line_B, timepoint_1, EXP_9.5, rep_2 |
| Sample type |
SRA |
| |
|
| Source name |
B
|
| Organism |
Mus musculus |
| Characteristics |
cell line: B
time: Day 4
timepoint: timepoint_1
treatment: Tumor_plus_NK
|
| 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.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| 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
|
| |
|
| Submission date |
Sep 25, 2024 |
| Last update date |
Nov 26, 2024 |
| Contact name |
Aleksandr Bykov |
| E-mail(s) |
[email protected]
|
| Organization name |
CCRI
|
| Department |
BiCU
|
| Street address |
Zimmermannpl. 10
|
| City |
Vienna |
| ZIP/Postal code |
1090 |
| Country |
Austria |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE278010 |
NK cell cytotoxicity shapes the clonal evolution of B cell leukemia [ATAC-seq] |
|
| Relations |
| BioSample |
SAMN43929705 |
| SRA |
SRX26202079 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8537429_EXP9_5_13H_Tumor_plus_NK_Day4_REP2.mLb.clN_peaks.broadPeak.gz |
1.2 Mb |
(ftp)(http) |
BROADPEAK |
SRA Run Selector |
| Raw data are available in SRA |
|
|
|
|
 |
