|
| Status |
Public on Dec 31, 2019 |
| Title |
ATAC_Mono_LP_Toxo_rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Lamina Propria
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lamina Propria
cell type: Monocyte
infection: Toxoplasma gondii infection
strain: C57BL/6
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
20000 sorted monocytes were washed with cold PBS and resuspended in cold lysis buffer (10 mM Tris·Cl, pH 7.4, 10 mM NaCl,3 mM MgCl2, 0.1% (v/v) Igepal CA-630).
Nuclei were subject to transposition reaction in 1x TD Buffer containing 2.5 μl transposase Nextera enzyme and DNA was purified. Purified DNA was amplified by PCR with 10-12 cycles. Amplified libraries were purified and quality controlled.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
ATAC-seq in monocytes from the Small intestine lamina propria from T. gondii infected mice, replicate 2
|
| Data processing |
Reads were aligned to mm10 by Bowtie2
Reads with quality lesser than 1 (=mapping to multiple locations and/or insufficient mapping quality) were filtered out with samtools view
Reads in ENCODE blacklist were removed with bedtools intersect
Reads mapping in chrM were removed with a custom script and samtools view
Duplicate reads were filtered out using MarkDuplicate tool from Picard suite
Peak calling was performed with MACS2 callpeak, using standard parameters for paired-end reads and q-value threshold=0.05
Genome_build: mm10
Supplementary_files_format_and_content: Bed: peaks ; bigwig: signal
|
| |
|
| Submission date |
Oct 15, 2019 |
| Last update date |
Dec 31, 2019 |
| Contact name |
Stanislas Goriely |
| E-mail(s) |
stgoriel@ulb.ac.be
|
| Phone |
+3226509586
|
| Organization name |
Université Libre de Bruxelles
|
| Lab |
IMI
|
| Street address |
Rue Adrienne Bolland 8
|
| City |
Gosselies |
| ZIP/Postal code |
B-6041 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE129724 |
Multi-step Epigenetic Programming of Monocytes during Infection |
|
| Relations |
| BioSample |
SAMN13030295 |
| SRA |
SRX6991011 |
