|
| Status |
Public on Sep 16, 2015 |
| Title |
20121015_STS4h |
| Sample type |
SRA |
| |
|
| Source name |
primary macrophages, STS 4h
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: primary macrophages
|
| Treatment protocol |
Human primary macrophages were treated with 1 µM staurosporine (STS). After 0, 4 and 6 hours, total RNA was extracted and submitted to small RNA sequencing.
|
| Growth protocol |
Human primary macrophages were prepared from peripheral blood monocytes obtained from healthy donors in agreement with the French legislation on human biomedical research
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Qiagen miRNeasy mini kit
NEBNext Small RNA Library Prep Set for SOLiD. Libraries were size selected on acrylamide gels (Library size: 110 to 150 nt).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB 5500xl Genetic Analyzer |
| |
|
| Description |
STS 4h
|
| Data processing |
Reads were first filtered to remove SOLiD adaptors, SOLiD barcodes and rRNAs reads.
Alignment was performed within Lifescope 2.5.1 software smallRNAs pipeline using default parameters.
Annotation process has been performed within home made pipeline. Alignment bam files with primary alignments (lowest MAPQV) were annotated with .GFF files with genomic coordinates of smallRNAs such as miRNAs (mirbase release 18), tRNAs (UCSC tracks), yRNAs, snoRNAs and piRNAs (fRNAdb) and ensembl ncRNAs tracks (release 69).
Processed data file submitted is a matrix file containning counts for each sample without normalization.
Genome_build: hg19
Supplementary_files_format_and_content: Tabular text-file with feature name, feature type, feature description, feature genomic coordinates and counts associated within each samples, ordered by expression decreasing
|
| |
|
| Submission date |
Jun 03, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Kevin Lebrigand |
| Organization name |
IPMC/CNRS
|
| Lab |
Functional Genomics Platform of Nice-Sophia-Antipolis, France.
|
| Street address |
660 route des lucioles
|
| City |
Valbonne - Sophia-Antipolis |
| ZIP/Postal code |
06560 |
| Country |
France |
| |
|
| Platform ID |
GPL16288 |
| Series (2) |
| GSE47608 |
small RNA Next Generation Sequencing of human primary macrophages treated with staurosporine |
| GSE47609 |
Atherogenic Stimuli Trigger Ago2-hnRNP A1-Dependent Processing of RNYs Regulating Apoptosis and Inflammatory Response in Macrophages |
|
| Relations |
| BioSample |
SAMN02189844 |
| SRA |
SRX290640 |
