|
| Status |
Public on Apr 28, 2024 |
| Title |
ATAC_U2OS_FOXA2dCTD_day4_biol rep1 |
| Sample type |
SRA |
| |
|
| Source name |
cell line
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: U2OS
cell type: Human Osteosarcoma
genotype: Tet-on FOXA2dCTD
treatment: 500ng/ml doxycycline for 4 days
|
| Treatment protocol |
500ng/ml Doxycycline for 4 days
|
| Growth protocol |
U2OS cells were cultured with 10% FBS with DMEM media
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
U2OS cells were seeded in 6 cm plates and treated with Doxycycline (500 ng/ml) for 4 days. 50,000 viable cells were collected by centrifugation at 500g for 10 min at 4 °C. Cell pellets were lysed in 50 ul RSB Buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween-20 and 0.01% Digitonin) on ice for 3 mins. Then cells were washed with 1 ml wash buffer (0.1% Tween-20, 10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2). Nuclei were collected by centrifugation at 500g for 10 min at 4°C. The pellet was resuspended in a 50 μl transposes mix (Vazyme TD501) incubated at 37 °C for 30 min in a PCR machine, and further cleaned by a Zymo DNA purification kit.
ATAC-seq libraries were prepared using the library preparing kit (Vazyme, TD501). Transposed DNA was amplified for 10 cycles, and the library DNA was further size selected with VAHTSTM DNA Clean Beads (Vazyme, N411) to the range of 150bp - 700bp./
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Nova-seq output paired ATAC-seq raw reads quality control performed with FastQC (version 0.10.1) ATAC-seq raw reads were trimmed by trim_galore function with --paired mode and default parameters. ATAC-seq reads were aligned to hg38 genome with bowtie2 v2.4.4 in the following options: bowtie2 -t -q -p 10 -N 1 -L 25 -X 700. Resulted sam files were converted to bam with samtools (v.0.1.18) ATAC-seq bam files of the two replicates were called peaks individually using MACS2 with default parameters. For each group, peak files of the two replicates were used to call peaks by the IDR method with parameter: idr --input-file-type narrowPeak --rank p.value -soft-idr-threshold 0.1 The bigwig files of ATAC-seq data were generated using deeptools (v2.4.1) kit with the following configurations: bamCoverage -of bigwig --binSize 50 --normalizeUsing RPKM --ignoreDuplicates. Assembly: hg38 Supplementary files format and content: Bigwig -- visualization of track information Supplementary files format and content: NarrowPeak -- Binding Sites for ChIP-seq/ Opening Site for ATAC-seq
|
| |
|
| Submission date |
Dec 28, 2023 |
| Last update date |
Apr 29, 2024 |
| Contact name |
Wulan Deng |
| E-mail(s) |
denglabpku@outlook.com
|
| Organization name |
Peking University
|
| Department |
BIOPIC
|
| Street address |
Beijing Haidian District Yiheyuan Road #5
|
| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE203649 |
Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells [ATAC-seq] |
| GSE203650 |
Mesoscale chromatin confinement facilitates target search of pioneer transcription factors in live cells |
|
| Relations |
| BioSample |
SAMN39181610 |
| SRA |
SRX23051362 |
