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| Status |
Public on Feb 02, 2024 |
| Title |
XD_ATAC_6 |
| Sample type |
SRA |
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| Source name |
-
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| Organism |
Homo sapiens |
| Characteristics |
tissue: -
cell line: XD
cell type: primary tumor-derived cell line
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| Treatment protocol |
No treatment
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| Growth protocol |
Four biological replicates for each cell population were considered. 50000 cells for each replicate were harvested and washed once with PBS; nuclei were isolated together with homogenized tissues collected from primary lung tumours (PT) (Poli et al., 2018).
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
Samples were resuspended in 50uL Tn5 transposase mixture: 1x Tagment DNA Buffer, 0.5uL Tagment DNA Enzyme (Nextera DNA Library Preparation Kit, Illumina). Transposition reaction was incubated at 37°C for 45 minutes, followed by DNA isolation using a Qiagen MinElute PCR purification kit (QIAGEN, Hilden, Germany).
Libraries were amplified for 5 cycles using the NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs, MA, USA) with primers (0.5uM each) from (Buenrostro et al., 2015) and the following the following cycling program: 5 minutes at 72°C, 30 s at 98°C, followed by 5 cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s] and a final extension at 72°C for 5 minutes. To avoid overamplification of libraries, 2uL of the eluted DNA were subjected to a side-qPCR for defining the optimal number of PCR cycles for each sample.The remaining libraries were subjected to a second round of PCR in a volume of 50uL with NEBNext High-fidelity 2x PCR master mix, respective primers (1.25uM each) and the following thermal cycles: 30 s hot-start at 98°C, followed by 7-13 cycles [98°C for 10 s, 63°C for 30 s and 72°C for 60 s] and a final extension at 72°C for 5 minutes. The final libraries were purified using Agencourt AMPure XP beads, eluted in 30uL Tris HCl 10mM pH 8 and quantified using the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. #Q33226)
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| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Quality of the reads was checked using FastQC and trimmed using Trimmomatic v0.39
Reads were aligned to the human genome hg19 using BowTie2
SAM files were processed using samtools v1.10
Tag directories for the merged files were created and peaks were called with callPeaks hg19 –peak size 500 –distance 1000 –L 0 –C 3 using HOMER
Differential accessibility analysis was undertaken using the edgeR v3.20.9 and limma v3.34.9 software packages (McCarthy et al., 2012; Ritchie, M.E., Phipson, B., Wu, D., Hu, Y., Law, C.W., Shi, W., and Smyth, 2015). Normalization factors were calculated with calcNormFactors using the TMM. Differential accessibility between all cell types was assessed using the quasi-likelihood (QL) framework of the edgeR package. P-values were adjusted for multiple testing using the Benjamini-Hochberg method. Peaks with a FDR below 0.1% and absolute fold change > 0.5 were defined as differentially accessible regions. Peaks were annotated using the assignChromosomeRegion function in the ChiPpeakAnno (Zhu et al., 2010) (v 3.18.2') package in R.
Assembly: hg19
Supplementary files format and content: bigwig files of replicates
Supplementary files format and content: peak list with cpm-normalized counts and differential accessibiity analysis
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| Submission date |
Aug 19, 2022 |
| Last update date |
Feb 02, 2024 |
| Contact name |
CIBIO Zippo |
| E-mail(s) |
alessio.zippo@unitn.it
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| Organization name |
University of Trento
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| Department |
Cellular, Computation and Integrative Biology (CIBIO)
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| Lab |
Chromatin Biology & Epigenetics
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| Street address |
via sommarive 9
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| City |
Trento |
| State/province |
Not Applicable |
| ZIP/Postal code |
38123 |
| Country |
Italy |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE211605 |
Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting a transcriptional memory [ATAC-seq] |
| GSE211610 |
Oncogenic enhancers prime quiescent metastatic cells to escape NK immune surveillance by eliciting a transcriptional memory |
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| Relations |
| BioSample |
SAMN30409854 |
| SRA |
SRX17147612 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6481363_XD6.bw |
101.8 Mb |
(ftp)(http) |
BW |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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