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Sample GSM2040466 Query DataSets for GSM2040466
Status Public on Jan 01, 2017
Title Tick15
Sample type SRA
Source name cell culture
Organism Ixodes ricinus
Characteristics cell line: IRE/CTVM20
time: Day7
infection status: Anaplasma phagocytophilum infected
Treatment protocol Tick cells were infected with Anaplasma phagocytophilum (NY18 human strain), and cells/supernatant sampled at 7 post-infection. Mock infected (uninfected) cells/supernatant were sampled at day 0.
Growth protocol IRE/CTVM20 cells were maintained in a 1:1 mixture of L-15 (Leibovitz) medium and L-15B medium, and ISE6 cells were maintained in L-15B300 medium.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using TRIzol (Invitrogen), according to the manufacturer's protocol, and further purified using the Rneasy Mini kit (Qiagen). Ribosomal RNA was depleted using Terminator Exonuclease (Epicentre).
Double stranded cDNA synthesis using Roche cDNA Synthesis System. Illumina library construction using NexteraXT kit
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina Genome Analyzer IIx
Data processing Basecalling with CASAVA v1.8
Alignment using BowTie2
Identification of splice junctions using TopHat2
Estimation of gene abundance and differential gene expression using Cufflinks.
Normalization of biological replicates using Cuffmerge
Estimation of abundance across normalized samples using Cuffquant.
Identification of differentially expressed genes using Cuffdiff.
Genome_build: Ixodes scapularis 1.3
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
Submission date Jan 15, 2016
Last update date May 15, 2019
Contact name Richard Ellis
Organization name Animal and Plant Health Agency
Street address APHA Weybridge
City Addlestone
ZIP/Postal code KT15 3NB
Country United Kingdom
Platform ID GPL21340
Series (1)
GSE76906 Tissue-specific signatures in the transcriptional response to Anaplasma phagocytophilum infection of Ixodes scapularis and Ixodes ricinus tick cell lines
BioSample SAMN04417542
SRA SRX1531987

Supplementary file Size Download File type/resource
GSM2040466_Tick15_genes.fpkm_tracking.gz 535.6 Kb (ftp)(http) FPKM_TRACKING
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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