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Sample GSM3195918 Query DataSets for GSM3195918
Status Public on Sep 25, 2018
Title mLN_SPF_Tx_migDC_4
Sample type SRA
 
Source name mLN_SPF_Tx
Organism Mus musculus
Characteristics strain background: BALB/c
ln: gut-draining
transplanted: yes
cell type: FACS-sorted migratory DCs
Treatment protocol For RNA‑seq analysis, CD45+ cells enriched with autoMACS were stained using fluorescence‑coupled antibodies and sorted for migratory DCs by FACS (Aria II, 100 μm nozzle).
Growth protocol ex vivo
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from FACS‑sorted migratory DCs using the RNeasy Plus Micro Kit (Qiagen).
cDNA was synthesized and amplified using template switching technology of the SMART‑Seq v4 Ultra Low Input RNA Kit (Clontech Laboratories), followed by purification using the Agencourt AMPure XP Kit (Beckman Coulter). Library preparation was performed with Nextera XT DNA Library Prep Kit (Illumina). The Agilent Technologies 2100 Bioanalyzer was used to control quality and integrity of nucleic acids after each step.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2500
 
Description processed data file:
DESeq2_genes_diffexp_by_fc_Migr_mLN_SPF_Tx_vs_Migr_pLN_SPF_Tx.csv
Data processing Libraries were aligned versus the mouse reference genome (assembly: GRCm38) using the splice junction mapper Tophat2 v1.2.0 with default parameterization.
Reads aligned to annotated genes were quantified with the htseq-count program [Anders, Pyl, Huber, 2015, Bioinformatics 31, 166-169].
Determined read counts served as input to DESeq2 [Love, Huber, Anders, 2014, Genome Biology 15, 550] for pairwise detection and quantification of differential gene expression.
RPKM (reads per kilobase maximal transcript length per million mapped reads) values were computed for each library from the raw gene counts.
Genome_build: GRCm38
Supplementary_files_format_and_content: .csv files include RPKM values, q-value and log2(FC) for each pair-wise comparison
 
Submission date Jun 18, 2018
Last update date Sep 26, 2018
Contact name Joern Pezoldt
E-mail(s) jorn.pezoldt@epfl.ch
Phone 0041766040171
Organization name EPFL
Department SV
Lab Laboratory Systems Biology and Genetics
Street address Station 19, SV 3818.A
City Lausanne
ZIP/Postal code 1015
Country Switzerland
 
Platform ID GPL17021
Series (2)
GSE115950 Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [migDC]
GSE116633 Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells
Relations
BioSample SAMN09442868
SRA SRX4231037

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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