|
| Status |
Public on Apr 06, 2018 |
| Title |
Nuclear_RNA_seq_Random_GOF |
| Sample type |
SRA |
| |
|
| Source name |
MLE-12
|
| Organism |
Mus musculus |
| Characteristics |
cell line: MLE-12
genotype/variation: control
sample type: control
|
| Treatment protocol |
MLE-12 cells were transfected with 25nM of Biotinylated microRNA (Random or Mirlet7d) and harsvested after 48 h
|
| Growth protocol |
MLE-12 cells were kept at 37°c in DMEM medium containing 10 % Fetal Calf Serum, and 1% P/S/G (penicillin/Streptomycin/L-glutamine)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TRIzol(R) (Invitrogen)
[Nuclear_RNA_seq] Libraries were prepared according to SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (including rRNA depletion RiboGone)
[Pull_Down_Input_Mirlet7d] Libraries were treated the Kit for rRNA depletion by RiboGone™ - Mammalian and Pre-amplification step was performed with pre-amplification using SMARTer® Universal Low Input RNA Kit for Sequencing
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent Proton |
| |
|
| Data processing |
Raw reads was done using FastQC, trimmed of the raw reads using Trimmomatic (Bolger et al. 2014) with the following parameters( ILLUMINACLIP:adapters/TruSeq3-PE.fa:2:30:10 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:17 CROP:60 HEADCROP:6)
RNA_seq reads were aligned to the mm9 genome.
After mapping, the sam files were converted to bam format by using samtools view (-Sb) followed by samtools sort. Mapping was performed using bowtie2 following the Parameters (bowtie2 -D 15 -R 3 -N 0 -L 20 -i S,1,0.56 -p8). For the
MakeTaqlibrary -format sam; was used to create the taq library
to quantify the libraries ;
analyzeRepeats.pl mm9 -count genes -strand both was used for the Protein-coding whereas for the ncRNAs (analyzeRepeats.pl NONCODE_v4.gtf mm9 -count genes -strand both and -rpkm) was used.
homer makeUCSC (normalized to 10 millions) was used to obtain bedgraph files to Visualize in UCSC genome browser
Genome_build: Mouse mm9
Supplementary_files_format_and_content: Bedgraph_UCSC files to load in the UCSC genome Browser
|
| |
|
| Submission date |
Dec 22, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Guillermo Barreto |
| E-mail(s) |
guillermo.barreto@univ-lorraine.fr
|
| Organization name |
CNRS Director of Research
|
| Department |
Campus Biologie-Santé. Faculté de Médecine
|
| Lab |
Laboratoire IMoPA. UMR 7365 CNRS
|
| Street address |
9, Avenue de la Forêt de Haye ‐ BP 20199
|
| City |
Nancy Cedex |
| ZIP/Postal code |
54505 |
| Country |
France |
| |
|
| Platform ID |
GPL18635 |
| Series (1) |
| GSE76248 |
MiCEE: a ncRNA-protein complex mediates epigenetic silencing and nucleolus organization |
|
| Relations |
| BioSample |
SAMN04361748 |
| SRA |
SRX1496392 |
