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Sample GSM2856705 Query DataSets for GSM2856705
Status Public on Sep 25, 2018
Title mLN_SPF_Tx_resDC_2
Sample type SRA
 
Source name mLN_SPF_Tx
Organism Mus musculus
Characteristics ln: gut-draining
transplanted: yes
strain: BALB/c
Treatment protocol For RNA‑seq analysis, CD45+ cells enriched with autoMACS were stained using fluorescence‑coupled antibodies and sorted for resident 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 resident 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 DESeq2_genes_diffexp_by_fc_Res_mLN_SPF_Tx_vs_Res_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 Nov 14, 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)
GSE106882 Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [resDCs]
GSE116633 Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells
Relations
BioSample SAMN08025307
SRA SRX3390873

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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