|
| Status |
Public on Jan 01, 2019 |
| Title |
Activated B cells – Mzb1 wt – Replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
CD138- Blimp1-GFP- cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: Spleen
genotype: Mzb1+/+ Prdm1+/gfp
cell type: Activated B cells
|
| Treatment protocol |
The cells were treated with 25ug/ml LPS (L5668-Sigma) and after 4 days cells were sorted with a FACSAria (Becton Dickinson) as Act B (CD138-Blimp1-GFP-), Pre-PB (CD138-Blimp-GFP+) and PB (CD138+Blimp-GFP+) cells, using CD138 antibody (BD).
|
| Growth protocol |
Splenic B cells were purified using anti-B220 magnetic beads and cultured in the presence of LPS for 4 days in IMDM Medium (12440-053-Gibco) in 10% FCS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from sorted in vitro differentiated Act B, Pre-PB and PB cells using RNeasy Mini Kit (Qiagen) according to the manufacturer's instructions. The total mRNA was enriched by using Oligo dT magnetic beads.
The libraries were prepared by using TruSeq® Stranded mRNA library preparation protocol according to the manufacturer's instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
| |
|
| Description |
Activated B cells – Mzb1 wt – Replicate 1
|
| Data processing |
The base calling was performed by using BCL2Fastq pipeline (version: 0.3.1) and bcl2fastq (version 2.17.1.14).
The paired-end RNA-Seq datasets were mapped to the mouse reference genome (mm9) using Tophat (v2.0.14)
The mapped reads were further assembled by using Cufflinks (v2.2.1) and the expression level of the annotated genes (UCSC, mm9) was calculated by Cuffquant
The differential gene expression between the conditions was calculated by using Cuffdiff.
Genome_build: mm9
Supplementary_files_format_and_content: The normalized gene expression values (FPKM) calculated by Cuffnorm (v2.2.1) is provided in TXT format
|
| |
|
| Submission date |
Aug 03, 2018 |
| Last update date |
Jan 01, 2019 |
| Contact name |
Senthilkumar Ramamoorthy |
| E-mail(s) |
senthilkumar@ie-freiburg.mpg.de
|
| Phone |
00497615108731
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Cellular & Molecular Immunology
|
| Lab |
Laboratory Rudolf Grosschedl
|
| Street address |
Stübeweg 51
|
| City |
Freiburg |
| ZIP/Postal code |
D-79108 |
| Country |
Germany |
| |
|
| Platform ID |
GPL21493 |
| Series (1) |
| GSE118124 |
Co-chaperone Mzb1 is a key effector of Blimp1 in plasma cell differentiation and b1 integrin function |
|
| Relations |
| BioSample |
SAMN09765672 |
| SRA |
SRX4507424 |
