|
| Status |
Public on Mar 13, 2018 |
| Title |
B16F0 exosome-treated CTLL2 cells 4 hr rep 3 |
| 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 |
Set2_4hr_5
Batch 2
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 |
SAMN07549799 |
| SRA |
SRX3121825 |
