|
| Status |
Public on Jul 15, 2014 |
| Title |
control_CD19_FasGl7_R1 |
| Sample type |
SRA |
| |
|
| Source name |
GC (CD19+Fas+GL7+) B cells from littermate controls
|
| Organism |
Mus musculus |
| Characteristics |
cell type: GC (CD19+Fas+GL7+) B cells
genotype/variation: littermate controls
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with Trizol (Invitrogen). RNA samples were first processed through the "Ovation RNA-seq system" (NuGEN) and then retrotranscribed, and cDNA was amplified by the SPIA isothermal linear amplification procedure. The resulting ds-cDNA was fragmented to a range of 150-200bp in a Covaris S2 shearing instrument
cDNA (200ng of per sample) was processed through succeeding enzymatic treatments of end-repair, dA-tailing, and ligation to indexed adapters, according to "TruSeq DNA Sample Preparation Guide" (Illumina). Ligation products were purified with AMPure XP Beads. Adapter-ligated libraries were amplified by PCR with Illumina PE primers for 10 cycles. The resulting purified DNA libraries were applied to an Illumina flow cell for cluster generation, and sequenced on the Illumina Genome Analyzer IIx with SBS TruSeq v5 reagents. Image analysis and per-cycle basecalling were performed with Illumina Real Time Analysis software (RTA1.9)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Description |
Replicate 1
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence and filtered the ones with a quality less than 20% over the 80% of nt and more than 5 Ns
Mapped to mm9 whole genome using tophat v2.0.7
Number of reads falling in the genes calculated using htseq-count version 0.5.3p9 over the mm9 gtf file from UCSC.
Genome_build: mm9
Supplementary_files_format_and_content: tab-delimited text files include number of reads per gene for each Sample
|
| |
|
| Submission date |
Jun 12, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Almudena Ramiro |
| E-mail(s) |
aramiro@cnic.es
|
| Organization name |
Centro Nacional de Investigaciones Cardiovasculares
|
| Department |
Vascular Biology and Inflammation
|
| Lab |
B Cell Biology Lab
|
| Street address |
Melchor Fernandez Almagro 3
|
| City |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL11002 |
| Series (1) |
| GSE47877 |
Transcriptome analysis of Germinal Center and naïve B cells from miR-217TG and control mice by RNAseq |
|
| Relations |
| BioSample |
SAMN02202284 |
| SRA |
SRX304966 |
