|
| Status |
Public on Oct 16, 2019 |
| Title |
LN KO_2 |
| Sample type |
SRA |
| |
|
| Source name |
tumour-draining lymph nodes
|
| Organism |
Mus musculus |
| Characteristics |
tissue: tumour-draining lymph nodes
tumour: B16.F10 melanoma day 14
cell type: CD4+CD25+GITR+Foxp3+ T regulatory cells
strain/genotype: il33-/- in C57BL6 background
|
| Treatment protocol |
Mice were inoculateds.c. with 300000 B16.F10 cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
14 days upon tumour inoculation tumour-draining lymph nodes were isolated and Tregs were sorted (CD4+CD25+GITR+). Cells were lysed. Transposition reaction was performed with in-house Tn5 Transposase and DNA purification was effectuated by Qiagen MinElute kit and amplified using the NEBNext High-Fidelity PCR Master Mix
Transposition reaction was performed with in-house Tn5 Transposase and DNA purification was effectuated by Qiagen MinElute kit and amplified using the NEBNext High-Fidelity PCR Master Mix
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Reads were aligned to mm10 using bowtie2 (v2.3.1) with parameters --local --minins 50 --maxins 2000 --no-mixed --no-discordant
Duplicates were removed using picard (v 1.88) with LENIENT strigency option
Peaks were called using macs (v 2.1.1.20160309) with parameters: --nomodel --extsize=200 --shift -100 --bdg --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited files with peaks and their attributes per Sample as called by macs
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Oct 16, 2019 |
| Contact name |
Theodoros Sakellaropoulos |
| E-mail(s) |
Theodoros.Sakellaropoulos@nyulangone.org
|
| Organization name |
NYU Langone
|
| Street address |
550 1st Ave
|
| City |
New York |
| ZIP/Postal code |
10016 |
| Country |
USA |
| |
|
| Platform ID |
GPL18480 |
| Series (2) |
| GSE138871 |
Transposition of native chromatin (ATACseq) of tumour-exposed Tregs from IL33 genetical deficient mice |
| GSE138874 |
Tumour-exposed Tregs from IL33 genetical deficient mice |
|
| Relations |
| BioSample |
SAMN13031816 |
| SRA |
SRX6992734 |
