|
| Status |
Public on Jan 01, 2018 |
| Title |
CD40 null 1 |
| Sample type |
SRA |
| |
|
| Source name |
Dendritic cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
tissue: popliteal lymph node
cell type: Dendritic cells
genotype: Cd40-/-
population: Cd11c-int, Mhc-II-high, Cd11b+
|
| Treatment protocol |
Cd40G5/G5 DCs were pulsed with OVA323-339 and transferred subcutaneously (5 x 10^5/footpad) into Cd40G5/G5 recipients. Eighteen hours later, 3 x 10^5 CD40lgSrtA/Y CD4-Cre OT-II CD4+ T cells were transferred intravenously. Biotin-LPETG was administered subcutaneously (300 nmol/footpad) 46 hours post T cell transfer. 48 hours post T cell transfer popliteal lymph nodes were processed and stained for surface markers as above and endogenous biotin+ and biotin- MHC-IIhi CD11c+ CD11b+ XCR1– DCs were sorted. As controls, MHC-IIhi CD11c+ CD11b+ XCR1– DCs were also sorted from Cd40-/- mice treated as above, except that they received WT (instead of Cd40G5/G5) DCs and WT OT-II (instead of CD40lgSrtA/Y CD4-Cre OT-II) CD4+ T cells
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Fresh cells were sorted (150 cells/sample) directly into plates containing TCL buffer (Qiagen) supplemented with 1% β-mercaptoethanol using a FACS Aria II (BD Biosciences). RNA from sorted populations was isolated using Agencourt RNAClean XP beads (Beckman Coulter).
Full-length cDNA and sequencing libraries were prepared using the Smart-seq2 protocol as described in Picelli et al., 2014. Libraries were sequenced on a Nextseq500 (Illumina) to generate 38 base pair, paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
dendritic cells from Cd40-/- mice
CD40N_1
[processed data files:]
counts-rsem.txt
counts-norm-filtered.txt
|
| Data processing |
Short sequencing reads were aligned to the UCSC mm10 transcriptome using Bowtie2 (version 2.1.0; Langmead et al., 2012).
Bowtie2 alignments were used as input in RSEM (version 1.2.8; Li et al., 2011) to quantify gene expression levels.
Data were normalized using R Package DESeq2 (version 1.16.0; Love et al., 2014).
Genes with low read counts, defined as the ones without at least 100 normalized counts in 3 samples, were filtered out.
Genome_build: mm10
Supplementary_files_format_and_content: raw and normalized count text files
|
| |
|
| Submission date |
Dec 04, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Ang Cui |
| E-mail(s) |
angcui@broadinstitute.org
|
| Organization name |
Broad Institute
|
| Street address |
415 Main St.
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02139 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE107643 |
RNA sequencing of dendritic cells undergoing interaction with T cells in vivo |
|
| Relations |
| BioSample |
SAMN08127194 |
| SRA |
SRX3440431 |
