|
| Status |
Public on Mar 01, 2023 |
| Title |
ATAC_cDC2_2 |
| Sample type |
SRA |
| |
|
| Source name |
Classical dendritic cell
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Classical dendritic cell
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Omni-ATAC-seq was performed according to with minor modifications. Prior to transposition dead cells were removed by centrifugation (800 rpm, 4 min, 4°C). The transposition reaction was with 7.5 μL Tagment DNA Enzyme 1 (TDE1) for 60 ‘min at 37°C. Pre-amplification was with NEBNext Ultra II Q5 Master Mix and Nextera PCR Primers (5 cycles). Quantitative PCR amplification was with NEBNext Ultra II Q5 Master Mix, Nextera PCR Primer and SYBR Gold to determine the number of additional cycles. PCR amplification of additional cycles was as for pre-amplification. PCR fragments were purified with Qiagen MinElute PCR Purification Kit and library concentration and quality were determined by Agilent High Sensitive DNA Kit and TapeStation, respectively. ATACseq libraries were sequenced on the Illumina NextSeq 500 Platform with 75 bps paired-end reads in duplicates.RNA-Seq libraries were prepared and subjected to strand-specific RNA-seq on the Illumina platform according to the manufacturer's protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adapter sequences using Trim Galore with -q 30 --trim1 --paired .
Reads mapped to mm9 whole genome by Bowtie2 with -X 2000 --no-mixed –no-discordant
Duplicates were remove. Reads were filtered for alignment quality of Q > 30 and were required to be properly paired
Reads mapping to chromosome Y, mitochondria and unassembled "random" contigs were removed from all downstream analysis
Peaks were called using MACS2 with -g mm --keep-dup all --call-summits –nomodel
Assembly: mm9
Supplementary files format and content: TDF
|
| |
|
| Submission date |
Mar 15, 2022 |
| Last update date |
Mar 03, 2023 |
| Contact name |
Zhijian Li |
| E-mail(s) |
zhijian.li@rwth-aachen.de
|
| Organization name |
RWTH Aachen University
|
| Lab |
Institute for Computational Genomics
|
| Street address |
Pauwelsstr. 19
|
| City |
Aachen |
| State/province |
North Rhine-Westphal |
| ZIP/Postal code |
52062 |
| Country |
Germany |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE198651 |
A lncRNA identifies Irf8 enhancer element in negative feedback control of dendritic cell differentiation |
|
| Relations |
| BioSample |
SAMN26669885 |
| SRA |
SRX14466990 |
