|
| Status |
Public on Oct 15, 2015 |
| Title |
Control |
| Sample type |
SRA |
| |
|
| Source name |
Control
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: macrophage
treatment: Control
time: Control
concentration sample (ng/ul): 626.7
ratio 260/280: 2.08
ratio 260/230: 2.25
rin number: 10.0
|
| Treatment protocol |
1 mM Staurosporine (STS) treatment samples for 4h and 6h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction with Trizol
1.5 µg of total RNA were ligated, reverse transcribed and amplified (11 cycles) with the reagents from the NEBNext Small RNA Library Prep Set for SOLiD. Amplified libraries were size-selected from 110 nt to 150 nt on a 8% acrylamide gel. Libraries were then quantified with the Bioanalyzer High Sensitivity DNA Kit (Agilent).
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB 5500 Genetic Analyzer |
| |
|
| Description |
Sample name: 20121015_21
Control
SOLiD5500, Life Technology. Sequencing of 35b. with 10b. barcoding sequences.
Small-RNA seq
Processed data file: norm1Msignal_human.txt
|
| Data processing |
Lifescope v2.5 smallRNA pipeline. Mapping with mapreads, default parameters.
Bam files were then merged per samples with keeping read group per lane.
Bam files were then processed with a java home made class, based on picard java classes to perform identification and produce raw data count of microRNAs (mirbase release 18), tRNAs from UCSC web server (UCSC tables), yRNAs and ncRNAs from ensembl ncRNAs release 69 and piRNAs from fRNAdb.
Genome_build: hg19
Supplementary_files_format_and_content: [norm1Msignal_human.txt] Tabulated text file of raw data counts normalized to 1000000 count in each sample.
|
| |
|
| Submission date |
Dec 03, 2014 |
| 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 |
GPL16558 |
| Series (2) |
| GSE63799 |
High-throughput small RNA sequencing of human primary macrophages stimulated with staurosporine |
| GSE63802 |
Small RNA-sequencing in apoptotic macrophages |
|
| Relations |
| BioSample |
SAMN03249356 |
| SRA |
SRX794041 |
