|
Status |
Public on Jan 01, 2018 |
Title |
Biotin positive 4 |
Sample type |
SRA |
|
|
Source name |
Dendritic cells
|
Organism |
Mus musculus |
Characteristics |
strain: C57BL/6 tissue: popliteal lymph node cell type: Dendritic cells genotype: G5-Cd40+/+ population: Cd11c-int, Mhc-II-high, Cd11b+, Biotin+
|
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.
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|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Description |
dendritic cells likely have interacted with T cells via Cd40 ligation BiotinP_4 [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 |
SAMN08127192 |
SRA |
SRX3440422 |