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Sample GSM3930493 Query DataSets for GSM3930493
Status Public on Dec 31, 2021
Title RubWT-30min_apopJC-rep2
Sample type SRA
 
Source name Differentiated bone marrow cells
Organism Mus musculus
Characteristics cell type: FLT3L-derived bone marrow dendritic cells
genotype: Rubcn WT
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 SAMN12230850
SRA SRX6413815

Supplementary file Size Download File type/resource
GSM3930493_RubWT-30min_apopJC-rep2.depthNorm.bigWig 147.7 Mb (ftp)(http) BIGWIG
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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