|
| Status |
Public on Jun 09, 2021 |
| Title |
C1qbp-KO-ATAC rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: spleen
genotype: C1qpb KO
Sex: female
treatment: day 5 post-infection
age: 12 weeks
|
| Treatment protocol |
On day 5 post-infection with LCMV Armstrong, transferred P14 cells were sorted from the spleen of donor mice.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were lysed using RIPA buffer. The unfixed nuclei of these cells were tagged using Tn5 transposase (TruePrep DNA Library Prep Kit V2 for Illumina).
Library fragments were generated by 10–12 PCR cycles, and finally sequenced on an Illumina Nova-PE150 following the manufacturer's protocols.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Illumina Casava1.8 software used for basecalling.
Adapter trimming was performed using trimmomatic version 0.39
reads were aligned to the mm10 genome using Bowtie2 version 2.3.4.3
peaks were called using MACS2 version 2.2.7.1 with the following setting: -f BAMPE -q 0.05 -B --SPMR
Genome_build: mm10
Supplementary_files_format_and_content: bigwig files were generated using deeptools version 3.2.1
Supplementary_files_format_and_content: peak text files
|
| |
|
| Submission date |
Jun 08, 2021 |
| Last update date |
Jun 09, 2021 |
| Contact name |
liu kai |
| E-mail(s) |
21620170155362@stu.xmu.edu.cn
|
| Phone |
15959281581
|
| Organization name |
Xiamen University
|
| Street address |
Xiang'an Campus, Xiamen University, Xiang'an District
|
| City |
Xiamen |
| State/province |
Fujian |
| ZIP/Postal code |
361102 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE176369 |
ATAC-seq analysis of C1qbp sufficient and deficient CD8+ T cells sorted from mice post infection with LCMV Armstrong |
|
| Relations |
| BioSample |
SAMN19606211 |
| SRA |
SRX11093740 |
