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Sample GSM2356910 Query DataSets for GSM2356910
Status Public on Oct 20, 2016
Title PBS, TN, Replicate 3
Sample type SRA
 
Source name Dendritic cells (DC)
Organism Mus musculus
Characteristics strain: C57BL/6
Sex: female
tissue: Auricular lymph nodes
cell type: Dendritic cells (DC)
number of mice/sample: 15
ercc mix: Mix1
cell population: CD11c int, MHCII hi, CD103 neg, CD326 neg, CD11b lo (TN)
treatment: PBS
Treatment protocol N/A
Growth protocol N/A
Extracted molecule total RNA
Extraction protocol Total RNA was prepared from frozen purified cell pellets using QIAzol Lysis Reagent and RNeasy Micro Kit.
Ribosomal RNA was removed using RiboZero before RNA libraries were prepared for sequencing using the Illumina TruSeq kits.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Exp_TN.PBS.3_1257.6
PBS-treated Triple Negative cells
Data processing Paired-end raw read FASTq files ere pre-processed using Trimmomatic (v0.32) and quality checked using qrqc R package (v1.20.0)
Reads were mapped to mouse and ERCC reference transcripts using TopHat2 (v2.0.10)
Read hits to annotated genes were counted using HtSeq-count (HT-Seq, v0.6.0)
Technical replicates (across multiple flow cell lanes) were combined,see processed data file ('JEMsampleFiltered_collapsed_counts_JEM_2016-May-05.csv')
Data were split into the two experiments (Nb, DBP+FITC), then analysed separately with DESeq2 (v1.6.3) with sex as an additional model covariate for the Nb experiment
A variance-stabilised transformation was generated from the count data using DESeq2 (v1.6.3), and normalised based on the sum of gene exon lengths
Genome_build: C57BL/6 mouse reference genome (GRCm38.p3)
Supplementary_files_format_and_content: JEMsampleFiltered_collapsed_counts_JEM_2016-May-05.csv -- Gene Count Data as determined by HTSeq-count
 
Submission date Oct 20, 2016
Last update date May 15, 2019
Contact name Franca Ronchese
E-mail(s) fronchese@malaghan.org.nz
Phone +64 4 499 6914
Organization name Malaghan Instititute of Medical Research
Department Immune Cell Biology
Street address Kelburn Parade
City Wellington
ZIP/Postal code 6012
Country New Zealand
 
Platform ID GPL13112
Series (1)
GSE88998 Th2 responses are primed by skin dendritic cells with distinct transcriptional profiles
Relations
BioSample SAMN05930801
SRA SRX2255224

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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