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Sample GSM2752336 Query DataSets for GSM2752336
Status Public on Mar 13, 2018
Title B16F0 exosome-treated CTLL2 cells 2 hr rep 2
Sample type SRA
 
Source name CTLL2 cytotoxic T cells
Organism Mus musculus
Characteristics strain: C57BL/6
treatment: B16F0 exosome-treated
Treatment protocol Following the addition of fresh complete media, CTLL2 cells were either unstimulated or treated with fresh B16F0 exosomes resuspended in PBS, to a final exosome concentration of 0.2 mg/ml. The transcriptome was assayed at the indicated time points.
Growth protocol CTLL2 cells were grown in complete media for 24 hrs prior to the start of the experiment.
Extracted molecule total RNA
Extraction protocol Total RNA was isolated from CTLL2 cells by TRIzol reagent extraction (Thermo Fisher Scientific). Prior to RNA-Seq library preparation, RNA quality and integrity was determined using the Agillent Bioanalyzer 2100. Only RNA with RIN values >8.0 were used for the experiment.
RNA-Seq libraries were built with Illumina's TruSeq RNA Kit V2 (RS-122-2001) as per manufacturers protocol. All libraries were indexed in such a way as to ensure only one index/lane on the HiSeq. Finished libraries were quality checked with a High Sensitivity DNA chip on the Bioanalyzer to determine average size and quantified on a Qubit with high sensitivity DNA reagents. The libraries were then sent to the Marshall Genomics Core Facility where they were pooled in equimolar ratios and run on three lanes of an Illumina HiSeq1500 in a 2 x 50 base paired end design yielding a minimum of 49.1 million reads per sample.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 1500
 
Description Set1_2hr_9
Batch 1
RNAseq_All_normalized_counts.csv
Data processing Demultiplexing of samples and conversion from Illumina's bcl format to standard fastq format was performed using CASAVA 1.8.4 (Illumina).
Sequenced reads were trimmed for adaptor sequence, and then mapped to Mus musculus assembly GRCm38.p2 whole genome using STAR aligner v2.4.2
The number of reads associated with a transcript was determined using featureCounts v.1.5.0 with the parameters specified to ignore duplicates, use base pair ends to avoid counting each end twice, only count fragments that had both ends present.
Transcript abundance was determined using the DESeq2 package in R v3.3.2 and reported as variance stabilized normalized counts.
Genome_build: GRCm38.p2
Supplementary_files_format_and_content: comma separated values file include normalized count values determined using DEseq2 for each Sample ...
 
Submission date Aug 23, 2017
Last update date May 15, 2019
Contact name David John Klinke
E-mail(s) David.Klinke@mail.wvu.edu
Phone 304-293-9346
Organization name West Virginia University
Department Chemical Engineering
Street address P.O. Box 6102
City Morgantown
State/province WV
ZIP/Postal code 26506-6102
Country USA
 
Platform ID GPL18480
Series (2)
GSE102951 Expression data from parental B16F0 cells and B16F0 exosomes
GSE103000 Impact of B16F0 exosomes on the transcriptome of CTLL2 cytotoxic T cells
Relations
BioSample SAMN07549817
SRA SRX3121818

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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