|
| Status |
Public on Oct 14, 2019 |
| Title |
ATAC-seq_Brx07_lung_mets_30_2 |
| Sample type |
SRA |
| |
|
| Source name |
lung
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Brx07
parental or metastasis?: metastatic sample
metastatic site: lung
grown_in_culture: yes
dissociation_protocol: lungdisso
generation: 2
|
| Growth protocol |
CTC lines were cultured in ultra-low attachment plates with RPMI 1640 medium, supplemented with EGF (20ng/ml), bFGF (20ng/ml), 1X B27 and 1X antibiotic/antimycotic, in 4% O2 and 5% CO2. Metastatic tumors were established by inoculation of 100,000 GFP-LUC labeled CTCs in 100 µl of PBS into the left cardiac ventricles of 6-8 weeks old female NSG mice supplemented with subcutaneous slow release estrogen pills. Metastatic lesions were further dissociated into single-cell suspension by automated dissociation. CTC-derived metastatic cells (GFP+ cells) were sorted for ATAC sequencing.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Nuclei preparation was generated by resuspension of 25,000 or 50,000 sorted cells in nonionic lysis buffer (10 mM Tris pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% (v/v) Igepal CA630).
Transposition reaction was performed by using the Tn5 transposase (Nextera kit) at 37ºC for 30 minutes. Transposed DNA was further amplified by PCR, and the generated libraries were purified using Agencourt AMPure XP (Beckman Coulter). Library quality was controlled by using a Bioanalyzer high-sensitivity DNA analysis kit (Agilent)
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
metastatic sample
X07lung.30.2
|
| Data processing |
Sequencing reads were trimmed for Nextera adapter sequences with trimgalore and mapped to hg19 reference using Bowtie2 v2.2.8 with parameters -X 2000 –fr –no-discordant –no-mixed –minins 38. Only non-mitochondrial reads with a minimum mapping quality score (>= 30) were kept for the downstream analysis.
Duplicate reads were removed using Picard. All mapped reads were offset by +4 bp for the positive strand and -5 bp for the negative strand.
Accessible sites were identified for each sample using MACS2 with parameters -q 0.01 –shift -100 –extsize 200 –nomodel –nolambda. Peaks intersecting with the ENCODE blacklisted regions were removed.
Peaks across conditions were merged using BEDtools to obtain a union set, and reads aligning to this set were counted using featurecounts
Genome_build: hg19
Supplementary_files_format_and_content: bed files of MACS2 peaks, bigwig files,raw counts table
|
| |
|
| Submission date |
Apr 09, 2018 |
| Last update date |
Oct 16, 2019 |
| Contact name |
Min Yu |
| Organization name |
University of Southern California
|
| Department |
USC Norris Comprehensive Cancer Center, Keck School of Medicine
|
| Street address |
1450 Biggy Street, NRT 3507
|
| City |
Los Angeles |
| State/province |
CA |
| ZIP/Postal code |
90033 |
| Country |
USA |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE112852 |
Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [ATAC-seq] |
| GSE112856 |
Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants |
|
| Relations |
| BioSample |
SAMN08896843 |
| SRA |
SRX3907939 |
