|
| Status |
Public on Mar 16, 2017 |
| Title |
LMP1/2a_mouse5_Bcell |
| Sample type |
SRA |
| |
|
| Source name |
Spleen
|
| Organism |
Mus musculus |
| Characteristics |
cell type: B220+ B splenocytes
strain: C57BL/6
|
| Growth protocol |
Mature B cells or B220+ B cells from splenocytes were purified using the magnetic cell sorting-based B-cell isolation kit or B220 MicroBeads, according to the manufacturer’s protocol (Miltenyi Biotec). The cells were cultured in RPMI 1640 medium containing 10% (vol/vol) FBS, streptomycin/penicillin, 2-mercaptoethanol, and minimal essential medium (MEM) Nonessential Amino Acid Solution (all obtained from GIBCO).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were isolated using PureLink RNA Mini Kit (Thermo Fisher Scientific) following the manufacturer’s manual. An in-column DNA digestion step was included to remove any residual genomic DNA contamination.
To construct RNA-seq libraries, 500 ng total RNA was used for ribosomal RNA depletion, followed by library construction using SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (#634874, Clontech Laboratories, Inc., CA).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Ribosomal RNA depleted RNA
Raw_counts.txt
Normalized_counts.txt
LMP1,2a_vs_GFP.txt
|
| Data processing |
Adaptor-trimmed Illumina reads for each individual library were mapped back to the mouse GRCm38.86 transcriptome assembly using STAR v2.5.2b
featureCounts v1.5.1 was used to estimate the number of reads mapped to each contig. Only transcripts with at least 10 cumulative mapping counts were used in this analysis.
DESeq2 v1.14.1 was used to evaluate gene differential expression (DE)
Each DE analysis was composed of a pairwise comparison between LMP1/2a group and the GFP group. Differentially expressed genes were identified after a correction for false discovery rate (FDR 0.05).
Genome_build: GRCm38.86
Supplementary_files_format_and_content: tab-delimited text files include Log2FoldChange value (experimental v.s. control), p value and FDR corrected p value (padj). Separate tab-delimited text files are also provided for raw counts and normalized counts of genes, respectively
|
| |
|
| Submission date |
Jan 19, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Benjamin Gewurz |
| E-mail(s) |
[email protected]
|
| Organization name |
Brigham and Women's Hospital
|
| Department |
Medicine
|
| Street address |
181 Longwood Ave
|
| City |
Boston |
| State/province |
Massachusetts |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE93827 |
A Mouse Model of Epstein-Barr virus LMP1 and LMP2A Driven Germinal Center B-cell Lymphoproliferative Disease |
|
| Relations |
| BioSample |
SAMN06241862 |
| SRA |
SRX2504292 |
