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Sample GSM2844140 Query DataSets for GSM2844140
Status Public on Sep 25, 2018
Title pLN_SPF_FSC_1
Sample type SRA
 
Source name pLN_SPF
Organism Mus musculus
Characteristics ln: skin-draining
transplanted: no
strain: BALB/c
Treatment protocol For RNA‑seq analysis, CD45 cells depleted with autoMACS were stained using fluorescence‑coupled antibodies and sorted FSCs by FACS (Aria II, 100 μm nozzle; purity).
Growth protocol ex vivo
Extracted molecule polyA RNA
Extraction protocol Total RNA was extracted from FACS‑sorted FSC 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 DESeq2_genes_diffexp_by_fc_mLN_SPF_vs_pLN_SPF.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 Nov 07, 2017
Last update date May 15, 2019
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)
GSE106636 Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [Tx FSC]
GSE116633 Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells
Relations
BioSample SAMN07988902
SRA SRX3372265

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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