|
| Status |
Public on Jun 26, 2024 |
| Title |
NEJF10-3D-Nor-01 |
| Sample type |
SRA |
| |
|
| Source name |
NEJF10
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NEJF10
cell type: HB
treatment: 3D Culture with 21% O2
|
| Treatment protocol |
NEJF10 cells were cultured in 21% and 1% oxygen in monolayer, or 21% oxygen in 3D spheroid.
|
| Growth protocol |
NEJF10 cells were cultured in DMEM supplemented with 10% Fetal Bovine Serum, 1% L-Glutamine, and 1% Penicillin/Streptomycin at 37 °C in an atmosphere of 5% CO2 with 21% oxygen or 1% oxygen.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Fresh cultured NEJF10 cells (100,000 per sample) under different culture conditions were harvested and washed with 150µl cold Dulbecco's Phosphate-Buffered Saline (DPBS) containing protease inhibitor (PI). Nuclei were collected by centrifuging at 500 g for 10 minutes at 4°C after cell pellets were resuspended in lysis buffer (10 mM Tris-Cl pH 7.4, 10 mM NaCl, and 3 mM MgCl2 containing 0.1% NP-40 and PI. Nuclei were incubated with Tn5 transposon enzyme in transposase reaction mix buffer (Illumina) for 30 min at 37°C. DNAs were purified from transposition sample by using Min-Elute PCR purification kit (Qiagen, Valencia, CA) and measured by Qubit.
Polymerase chain reaction (PCR) was performed to amplify with High-Fidelity 2X PCR Master Mix [72°C/5mins+ 98 °C /30 s +12 × (98 °C /10 s + 63 °C /30 s + 72 °C /60 s) + 72 °C /5 min]. The libraries were purified using Min-Elute PCR purification kit (Qiagen, Valencia, CA). ATAC-seq libraries followed by pair-end sequencing on HiSeq4000 (Illumina) in the Hartwell Center at St Jude Children's Research Hospital.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq X Plus |
| |
|
| Data processing |
The ATAC-seq raw reads were aligned to the mouse reference genome (mm10) using BWA (version 0.7.12-r1039) to and then removed duplicated reads with Picard (version 1.65), with only properly paired uniquely mapped reads were extracted by samtools (version 1.3.1 parameters used were -q 1 -f 2 -F 1804) . Reads mapping to mitochondrial DNA were excluded from the analysis. All mapped reads were offset by +4 bp for the + strand and -5 bp for the – strand.
Nucleosome free reads was used to generate bigwig files and call eanriched regions. MACS2 (version 2.2.7.1) parameters are “-q 0.01 –nomodel –extsize 200 –shift 100 -f BEDPE --keep-dup all”.
Assembly: GRCm38(mm10)
Supplementary files format and content: narrowPeak
|
| |
|
| Submission date |
Mar 20, 2024 |
| Last update date |
Jun 26, 2024 |
| Contact name |
Hongjian Jin |
| E-mail(s) |
hongjian.jin@STJUDE.ORG
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Center for Applied Bioinformatics
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38015 |
| Country |
USA |
| |
|
| Platform ID |
GPL34290 |
| Series (1) |
| GSE262074 |
Cellular fitness of MYC-driven cancer cells to genetic and pharmacologic perturbations in normoxia, hypoxia and 3D |
|
| Relations |
| BioSample |
SAMN40558967 |
| SRA |
SRX24005775 |
