|
| Status |
Public on Mar 03, 2023 |
| Title |
Lipo863B-ATAC-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Cell Line; Lipo863B; Liposarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Liposarcoma
cell line: Lipo863B
|
| Growth protocol |
Liposarcoma cell lines were cultured in Dulbecco's Modified Eagle's Medium supplemented with 15% FBS and additional 1 mM GlutaMax supplement (ThermoFisher, 35050061).
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50,000 cells were washed with PBS, counted and kept on ice as a pellet. Pelleted cells were reconstituted in a freshly made lysis buffer to remove unwashed mitochondria DNA, spun down, and the buffer was discarded. Then, the pelleted nuclei were tagmented with Tn5 transposase (Illumina ref: 15027866 & 15027865) in 50 μl volume for 30 min at 37 °C and the DNA was subsequently purified using Qiagen MinElute kit (Qiagen).
The transposal DNA was purified with the Qiagen MinElute PCR Purification Kit (Qiagen, 28006) and then amplified with appropriate number of cycles.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Cell Line
|
| Data processing |
RNA-seq reads were aligned to hg38 genome assembly using STAR; The TPM value of gene expression was caculated using RSEM.
ChIP-seq and ATAC-seq reads were aligned to hg38 genome assembly using Bowtie2;H3K27ac ChIP-Seq peaks were called using MACS2.
Hi-C raw FASTQ files and then mapped the trimmed files against hg38 human reference genome using runHiC pipeline. Hi-C matrix was generated using cooler.
WGS raw FASTQ files were first trimmed for adapter and then mapped against hg38 human reference genome using BWA-MEM algorithm (0.7.17-r1188). Duplicate reads were removed using Picard Tools.
Nanopore raw FASTQ files were mapped against the hg38 reference genome using the minimap2. The structure variations were identified using Sniffles.
Assembly: hg38 (GRCh38)
Supplementary files format and content: tab-delimited text files include TPM values for each Sample; the bigwig files included sequencing reads enrichment signal for each Sample; The .cool file were the multi-resolution matrix of Hi-C for each Sample; the .vcf files included the structure variation information.
|
| |
|
| Submission date |
Apr 19, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Feng Yue |
| E-mail(s) |
yue@northwestern.edu
|
| Organization name |
Northwestern University Feinberg School of Medicine
|
| Street address |
303 E. Superior Simpson Querrey
|
| City |
CHICACO |
| State/province |
ILLINOIS |
| ZIP/Postal code |
60611 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE201056 |
Integrated epigenomic analysis identifies structural alterations associated with oncogenic gene expression in liposarcoma |
|
| Relations |
| BioSample |
SAMN27646099 |
| SRA |
SRX14923643 |
