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Status |
Public on May 01, 2024 |
Title |
U2OS, pLVX-NAB2-STAT6, 2 days doxycycline, ATAC, biol rep2 |
Sample type |
SRA |
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Source name |
U2OS
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Organism |
Homo sapiens |
Characteristics |
cell line: U2OS cell type: osteosarcoma genotype: pLVX-NAB2-STAT6 treatment: 2 days 1ug/mL doxycycline chip antibody: None
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Treatment protocol |
Lentiviruses were produced in HEK293T cells by co-transfection 8 ug of pLVX-Tet-On Advanced (ClonTech) and pLVX-NAB2-STAT6-FLAG-Tight-Puro. U2OS were passaged into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of virus medium per well (cell medium with 4 ul of lentiviral particles per ml and 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G)) was added to replace old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with 200 ug/ml of Neomycin (Corning, cat#MT30234CR) in fresh medium. Cells were selected in Neomycin for two weeks with fresh media being added 3-4 weeks and cells split 1:3 when reaching 80-90% confluency. Then cells were plated into a 6-well plate at 30-40 % confluence. When the cells reached 60-70% confluence, 2 ml of medium fresh lentivirus media generated using pLVX-NAB2-STAT6-FLAG-Tight-Puro with 8 ug/ml polybrene (Thermo Fisher, cat#TR1003G) per well was added to replace the old medium. 24 hours after induction, the virus medium was removed and replaced with fresh cell culture medium for another 48 hours. After that, cells were selected with 0.5 ug/ml of puromycin in fresh medium (InvivoGen, cat#ant-pr-1). 48 hours after selection with puromycin, cells were disassociated with Trypsin and plated at a low density in a 15 cm dish. Single cells were cultured with 0.5 ug/ml of puromycin for the next 2-3 weeks until colonies appeared. Individual microcolonies were moved to a 96-well plate for clonal expansion. Clones were screened after addition of 1ug/mL Doxycline by verified by Western Blot. ATAC-seq was done without doxycycline treatment and after 2 days of 1ug/mL doxycycline treatment.
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Growth protocol |
U2OS cells were cultured and maintained in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with 10% super calf serum and Glutmax.
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Extracted molecule |
genomic DNA |
Extraction protocol |
Omni ATAC-seq was performed on both control and 2 days 1ug/mL doxycycline treated U2OS pLVX-NAB2-STAT6 cells according to Corces et al 2017. Briefly, 50,000 cells were washed in ATAC-resuspension buffer (RSB) with 0.1% Tween-20 and then lysed by incubated on ice for 3 minutes in RSB with 0.1% NP-40 and 0.1% Tween-20. Lysis was washed out in RSB 0.1% Tween-20 and nuclei was pelleted by centrifugation at 600g/4°C/5 minutes. Nuclei were then incubated in transposition mixture for 30 minutes at 37°C while shaking at 1000rpm. DNA was then purified using Zymo DNA clean and concentrator-5 Kit (cat# D4014). DNA was then amplified for 5 cycles with ATAC index primers and NEBNext Ultra II Q5 Master Mix (NEB #M0544). Additional amplification cycles were then determined by qPCR using 5uL of original amplification with PerfeCTa SYBR Green FastMix Reaction Mixes (Quantabio 95072-012). After additional amplification cycles with remaining 15uL DNA was then purified using Zymo DNA clean and concentrator-5 Kit (cat# D4014) and quantified by QUBIT. Omni-ATAC-seq (Corces et al. 2017)
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Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
NextSeq 2000 |
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Description |
ATAC in U2OS pLVX-NAB2-STAT6 cells after 2 days 1ug/mL doxycycline treatment
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Data processing |
Image analysis: Firecrest (Illumina pipeline 1.9, default parameters) Base calling: Bustard (Illumina pipeline 1.9, default parameters) Quality control: FastQC Adapter trimming: Trim Galore! Alignment: BWA-MEM Tag density files: deepTools bamCoverage Genome_build: GRCh37/hg19 Assembly: hg19 Supplementary files format and content: Supplementary_files_format_and_content: strand-specific bigWig, compatible with UCSC Genome Browser, generated using the deepTools package (bamCoverage function, with RPGC [reads per genome coverage] normalization)
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Submission date |
Dec 08, 2023 |
Last update date |
May 01, 2024 |
Contact name |
Alessandro Gardini |
E-mail(s) |
agardini@wistar.org
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Phone |
2158983755
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Organization name |
The Wistar Institute
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Lab |
Gardini Lab
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Street address |
3601 Spruce St, Room 230
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City |
Philadelphia |
State/province |
PA |
ZIP/Postal code |
19104 |
Country |
USA |
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Platform ID |
GPL30173 |
Series (2) |
GSE249700 |
NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors (ATAC-Seq) |
GSE249703 |
NAB2-STAT6 drives an EGR1-dependent neuroendocrine program in Solitary Fibrous Tumors |
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Relations |
BioSample |
SAMN38739408 |
SRA |
SRX22839652 |
Supplementary file |
Size |
Download |
File type/resource |
GSM7958838_U2OS-pLVX-NAB2-STAT6-2days-Dox-rep2-ATAC_mem_srt_noMT_q10_rmdup_S_offset_offset_srt_normalized.bw |
161.4 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
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