|
| Status |
Public on Dec 31, 2021 |
| Title |
RubKO-30min_apopJC-rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Differentiated bone marrow cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: FLT3L-derived bone marrow dendritic cells
genotype: Rubcn KO
treatment: Apoptotic Jurkat cells (30 mins)
|
| Treatment protocol |
On day 6-7, the BMDCs were incubated with Jurkat cells. Appropriate controls were used for different timepoints and treatment conditions.
|
| Growth protocol |
BMDCs were differentiated for 6-7 days in complete media supplemented with 200 ng/ml FLT3L.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were harvested and washed with PBS. The RNA was extracting using Trizol and RNAeasy step kit with DNAse digestion as per manufacturer's instructions.
Libraries were prepared according to Illumina's instructions using TruSeq RNA Library Prep Kit v2;
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw reads were filtered to retain only those with mean base quality score >20.
Filtered reads were aligned to the mm10 reference genome via STAR v2.5 with parameters "--outMultimapperOrder Random --outSAMattrIHstart 0 --outFilterType BySJout --alignSJoverhangMin 8 --limitBAMsortRAM 55000000000".
Subread featureCounts v1.5.0-p1 was used to collect read per gene for all gene models in RefSeq as downloaded from UCSC as of November 7, 2017.
Depth tracks were generated by STAR v2.5 with parameters "--outWigType bedGraph --outWigStrand Unstranded --outWigNorm None", followed by normalization by size factors as reported by DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: normalized depth as bigWig; counts per gene as tab-delimited text
|
| |
|
| Submission date |
Jul 08, 2019 |
| Last update date |
Dec 31, 2021 |
| Contact name |
Jennifer Martinez |
| E-mail(s) |
jennifer.martinez3@nih.gov
|
| Phone |
9842874089
|
| Organization name |
NIEHS
|
| Lab |
Jennifer Martinez
|
| Street address |
111 TW Alexander Dr.
|
| City |
Research Triangle Park |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE133945 |
Cross-presentation by dendritic cells is limited by non-canonical autophagy. |
|
| Relations |
| BioSample |
SAMN12230840 |
| SRA |
SRX6413799 |
