|
| Status |
Public on May 23, 2018 |
| Title |
BL2-2 |
| Sample type |
SRA |
| |
|
| Source name |
BL2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
treatment: unstimulated BL2 cell-line
|
| Treatment protocol |
For stimulation studies, cells were cultured in cell culture medium supplemented with 10 mM HEPES at 1 x 10^6 cells/ml and incubated with B-cell activating factor (BAFF) for up to 24 hrs.
|
| Growth protocol |
Cells were maintained in RPMI 160 supplemented with 10% fetal calf serum (FCS) and glutamine; peniciline; streptomycine at cell densities between 2x10^5 and 1x10^6 cells per ml.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA was isolated using Trizol reagent including a DNase I (Roche, Mannheim, Germany) digestion step.
Library preparation for RNA-Seq was performed using the TruSeq Stranded Sample Preparation Kit (Illumina, RS-122-2201) starting from 1000 ng of total RNA. Accurate quantitation of cDNA libraries was performed using the QuantiFluor TM dsDNA System (Promega). The size range of nal cDNA libraries was determined applying the SS-NGS-Fragment 1-6000 bp Kit on the Fragment Analyzer from Advanced Analytical (320 bp). cDNA libraries were amplied and sequenced by using the cBot and the HiSeq2000 from Illumina.
Non stranded mRNA-Seq
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Illumina Casava 1.8.2 software used for basecalling. Quality check was done via fastqc (v. 0.10.0, Babraham Bioinformatics)
Alignment was performed with STAR RNA-Seq aligner version 2.4.0h, by mapping the reads against transcriptome, and counting was performed using RSEM v1.2.19.
The transcriptome was generated with RSEM from Ensembl reference genome version GRCh38.76.
Data analysis was performed using R/Bioconductor (3.0.2/2.12) loading the edgeR package.
Genome_build: GRCh38
Supplementary_files_format_and_content: expected counts for each Sample
|
| |
|
| Submission date |
Jun 07, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Alexander Wolff |
| E-mail(s) |
alexander.wolff@med.uni-goettingen.de
|
| Organization name |
UMG
|
| Department |
Medical Statistics
|
| Lab |
Beissbarth Group
|
| Street address |
Humboldtallee 32
|
| City |
Goettingen |
| State/province |
Lower Saxony |
| ZIP/Postal code |
37073 |
| Country |
Germany |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE99768 |
B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line [RNA-Seq] |
| GSE100112 |
B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line |
|
| Relations |
| BioSample |
SAMN07203028 |
| SRA |
SRX2892764 |
