|
| Status |
Public on Aug 22, 2019 |
| Title |
TIME37 |
| Sample type |
SRA |
| |
|
| Source name |
TIME
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: endothelial cell
cell line: TIME
treatment: AA supplemented/cytokine stimulated
|
| Treatment protocol |
The fatty acids docosahexaenoic acid (DHA, C22:6n3) or arachidonic acid (AA, C20:4n6) were included in the culture medium in concentrations of 15 µmol/L using ethanol as a vehicle (0.2 % v/v final ethanol concentration). Cells were cultured in the enriched media totaling either 72 h (RAW264.7) or 144 h (TIME). Stimulation of cells was performed in the last 24 h of fatty acid supplementation by addition of either LPS (1 µg/mL; from E. coli serotype 0111:B4) for cell line RAW264.7 or the cytokines IL-1β, TNF-α, and IFN-γ each in a concentration of 5 ng/ml for cell line TIME.
|
| Growth protocol |
Cells were cultured according to ATCC recommendations
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed based on TRIZOL according to the Manufacturer`s standard protocol.
Libraries were prepared according to Illumina's instructions accompanying the TruSeq Small RNA Prep kit v2. Size restriction (140-165bp), purification, and quantification of barcoded libraries were performed using the Library quantification kit - Illumina/Universal. For cluster generation up to 10 libraries per were factored using an Illumina cBot.
|
| |
|
| Library strategy |
miRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Description |
AA supplemented/cytokine stimulated
|
| Data processing |
Basecalls and Demultiplexing was performed using CASAVA version 1.4
Raw reads were adapter trimmed with cutadapt version 1.9.1. Only adapter trimmed reads between 15 and 27 bp lengthwere considered processed miRNAs and selected for alignment.
small RNA seq reads were aligned to the GRCm38/GRCh38 genome assembly using Bowtie2 version 2.2.7 allowing 1 mismatch and alignment to multiple targets
Reads were annotated by intersecting genome coordinates of known miRNAs from miRBase version 21 using Bedtools version 2.25.0
Reads were counted using the R/Bioconductor programming environment by application of the ShortRead library and the table function together with the miRNA name in the annotation
Count normalisation was done using the R/Bioconductor packages DESeq2 and EdgeR
Genome_build: GRCm38 (RAW264.7 samples) or GRCh38 (TIME samples)
Supplementary_files_format_and_content: Processed data files contain raw counts, DESeq and EdgeR normalised counts as labelled
|
| |
|
| Submission date |
Jun 07, 2019 |
| Last update date |
Aug 22, 2019 |
| Contact name |
Julia Schumann |
| E-mail(s) |
julia.schumann@uk-halle.de
|
| Organization name |
University Medicine Halle (Saale)
|
| Street address |
Franzosenweg 1a
|
| City |
Halle (Saale) |
| ZIP/Postal code |
06112 |
| Country |
Germany |
| |
|
| Platform ID |
GPL15456 |
| Series (1) |
| GSE132361 |
miRNA expression profiles of macrophages (cell line: RAW264.7) and endothelial cells (cell line: TIME) |
|
| Relations |
| BioSample |
SAMN11975341 |
| SRA |
SRX5985111 |
