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Sample GSM2874045 Query DataSets for GSM2874045
Status Public on Jan 01, 2018
Title Biotin positive 5
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.
 
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_5
[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 SAMN08127191
SRA SRX3440423

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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