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Status |
Public on Jun 26, 2024 |
Title |
NEJF10-3D-Nor-02 |
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.
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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.
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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
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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 |
SAMN40558966 |
SRA |
SRX24005776 |