|
| Status |
Public on Nov 21, 2016 |
| Title |
ATAC seq WT iNKT BR1 |
| Sample type |
SRA |
| |
|
| Source name |
wild type iNKT cells biological replicate (BR) 1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Thymus
cell type: Invariant NKT (iNKT) cells
genotype: Wild Type
|
| Treatment protocol |
N/A
|
| Growth protocol |
iNKT cells were isolated from thymi of the desired genotypes after staining and FACS sorting of B220-, aGalCer tetramer+, TCRb+ cells.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
50.000 iNKT cells were sorted, washed once with PBS and lysed in 100 ul of ice cold lysis buffer (10 mM Tris-HCl, pH 7.4, 10 mM NaCl, 3mM MgCl2 and 0.1% IGEPAL CA-630). Then, nuclei were spun at 500g for 10 min and the pellet was resuspended in 50 ul transposase reaction mix [2.5 ul transposase (Illumina), 25 ul 2x TD buffer (Illumina) and 22.5 nuclease free water). The reaction was incubated for 30 minutes at 37. Samples were purified using MinElute kit (Qiagen).
The purified DNA was amplified using Kapa Real time library amplification kit (Kapa Biosystems). Libraries were amplified for 10-11 cycles.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Library strategy: ATAC-Seq
Raw fastq ATAC files were mapped to genome mm9 using bowtie and setting (-p 8 -m 1 --best --strata -X 2000)
Unmapped reads were processed with trim_galore and remapped using the same settings. Both results were merged together
Duplicates were removed using picards and reads mapping to the mitochondrial genome were filtered out.
Peaks were called using MACS2 with nomodel and the best peaks per condition within replicates were obtained using the Irreproducibility discovery rate from ENCODE
Reproducible peaks were filtered using ENCODE's blacklist for mm9 genome as well as regions in chrY
DEseq was used to determine differentially accessible sites between wild type and TET2/3 double knockout
Genome_build: mm9
Supplementary_files_format_and_content: BED files containing the accessible regions for each condition.
|
| |
|
| Submission date |
Aug 17, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Sini Rautio |
| Organization name |
Aalto University
|
| Street address |
Konemiehentie 2
|
| City |
Espoo |
| ZIP/Postal code |
02100 |
| Country |
Finland |
| |
|
| Platform ID |
GPL17021 |
| Series (2) |
| GSE66834 |
TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells |
| GSE85743 |
TET proteins regulate lineage specification and TCR-mediated expansion of iNKT cells (ATAC-Seq) |
|
| Relations |
| BioSample |
SAMN05583748 |
| SRA |
SRX2033491 |
