 |
 |
GEO help: Mouse over screen elements for information. |
|
Status |
Public on Dec 31, 2019 |
Title |
ATAC_Mono_LP_Toxo |
Sample type |
SRA |
|
|
Source name |
Lamina Propria
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: Lamina Propria cell type: Monocyte infection: Toxoplasma gondii infection
|
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 NextSeq 500 |
|
|
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 |
Apr 12, 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 |
GPL19057 |
Series (1) |
GSE129724 |
Multi-step Epigenetic Programming of Monocytes during Infection |
|
Relations |
BioSample |
SAMN11405724 |
SRA |
SRX5674982 |
Supplementary file |
Size |
Download |
File type/resource |
GSM3720849_ATAC_Mono_LP_Toxo.bigwig |
46.0 Mb |
(ftp)(http) |
BIGWIG |
GSM3720849_ATAC_Mono_LP_Toxo.narrowPeak.gz |
973.5 Kb |
(ftp)(http) |
NARROWPEAK |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
|
|
|
|
 |