|
| Status |
Public on Dec 13, 2023 |
| Title |
FDCs, Ngfr KO, 2 |
| Sample type |
SRA |
| |
|
| Source name |
Lymph node
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Lymph node
cell type: Follicualr dendritic cells
genotype: Ngfr KO
|
| Treatment protocol |
Non-immunized male mice from 8 to 12 weeks of age were used to sample popliteal lymph nodes
FACS isolated cells were collected into lysis buffer (TakaraBio) containing recombinant RNase Inhibitor (TakaraBio)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
cDNA was amplified from the collected cells using the SMART-Seq v4 Ultra Low Input RNA Kit (TakaraBio).
1ng of amplified cDNA was used to generate barcoded libraries with the Nextera XT DNA library preparation kit (Illumina). The size of the libraries was checked using the Agilent 2100 Bioanalyzer High Sensitivity DNA chip and their [EMG1] concentration was determined using the Qubit® fluorometer (ThermoFisher Scientific).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
RTA v1.18.66.3
FastQ files for each sample were obtained using bcl2fastq v2.20.0.422 software (Illumina).
Sequencing reads were aligned to the mouse reference transcriptome (mm10 v90) and quantified with RSem v1.3.1
Raw counts were normalized with TPM (Transcripts per million) and TMM (Trimmed mean of M-values) methods, transformed into log2 expression (log2(rawCount+1)) and compared to calculate fold-change and corrected p-value (FDR) using a Benjamini and Hochberg procedure.
Only those genes expressed with at least 1 count in a number of samples equal to the number of replicate samples of the condition with less replicates were taken into account.
Assembly: mm10 v90
Supplementary files format and content: Tab-delimited text file include TMM values for each sample
|
| |
|
| Submission date |
Jul 05, 2023 |
| Last update date |
Dec 13, 2023 |
| Contact name |
Alberto Hernández-Barracno |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
Spanish National Cancer Research Center
|
| Department |
Molecular Oncology
|
| Lab |
Microenvironment and Metastasis
|
| Street address |
Melchor Fernandez Almagro 3
|
| City |
Madrid |
| State/province |
Madrid |
| ZIP/Postal code |
28029 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE236511 |
NGFR regulates germinal center B-cell activation and negative selection |
|
| Relations |
| BioSample |
SAMN36303210 |
| SRA |
SRX20897604 |
