|
| Status |
Public on Oct 15, 2015 |
| Title |
BMDM_MCSF_W_B |
| Sample type |
SRA |
| |
|
| Source name |
M-CSF withdrawal_Small
|
| Organism |
Mus musculus |
| Characteristics |
strain/background: C57BL/6J
cell type: Bone Marrow Derived Macrophage
treatment: M-CSF withdrawal
rna extract: small RNA
concentration sample (ng/ul): 333.6
ratio 260/280: 1.97
ratio 260/230: 2.38
rin number: 8.4
|
| Treatment protocol |
BMDM upon 36 hr with or without M-CSF withdrawal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA extraction with Trizol
50 ng of RNA were treated with the trilink library kit (TriLink Biotechnologies). 17 cycles of PCR were performed. Libraries were size-selected for the 130 to 155 nt fraction on a caliper 300 XT chip. Libraries were sequenced on the Ion proton, 10 libraries were loaded on one P1 Chip.
|
| |
|
| Library strategy |
ncRNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
Ion Torrent Proton |
| |
|
| Description |
Sample name: BMDM_MCSF_B.004
M-CSF withdrawal replicate 2
Instrument model: Ion Proton (P1 chip)
Small-RNA seq
Processed data file: mm10_tableCount.txt
|
| Data processing |
Adaptor trimming with cutadapt-1.2.1, then bowtie2 v2.2.4 mapping versus mm10 build with " --local --very-sensitive-local -k 10" parameters.
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 21), tRNAs from UCSC web server (UCSC tables) and ncRNAs from ensembl ncRNAs release 73.
Genome_build: mm10
Supplementary_files_format_and_content: [mm10_tableCount.txt] Tabulated text file containing raw data of small RNAs, including miRNA from miRBase v21, tRNAs for tRFs identification from UCSC table browser and Ensembl non-coding RNAs r73, no normalisation.
|
| |
|
| Submission date |
Jun 01, 2015 |
| 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 |
GPL18635 |
| Series (2) |
| GSE63801 |
High-throughput small RNA sequencing of mouse primary macrophages treated with M-CSF withdrawal |
| GSE63802 |
Small RNA-sequencing in apoptotic macrophages |
|
| Relations |
| BioSample |
SAMN03754584 |
| SRA |
SRX1045308 |
