|
| Status |
Public on Sep 09, 2021 |
| Title |
Vehicle_Ribosome-free_replicate-3 |
| Sample type |
SRA |
| |
|
| Source name |
NIH/3T3 cells treated with 100 nM PBS at 37ºC for 24 hrs.
|
| Organism |
Mus musculus |
| Characteristics |
cell line: NIH/3T3
tissue: mouse fibroblasts
|
| Treatment protocol |
NIH/3T3 cells were grown to ~60-70% confluency and treated with 100 nM halofuginone or the same volume of vehicle (PBS) at 37ºC for 24 hrs.
|
| Growth protocol |
NIH/3T3 cells were cultured in DMEM supplemented with 10% bovine calf serum (VWR) and 1% penicillin/streptomycin (ThermoFisher) at 37ºC.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The RNA extraction was performed using TRIzol reagent (ThermoFisher) following instructions in the manual. For the cell samples, total RNA was extracted using regular TRIzol reagent (1 ml for a plate of cells) and placed at room temperatur for 5 mins to lyse the cells. For the polysome profiling fraction samples, RNA extraction was performed using TRIzol LS reagent at a volume ratio of 1:3 following the manual.
Illumina TruSeq Stranded mRNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
DATA FORMATTING (Illumina -> FastQ) & DEMULTIPLEXING - bcltofastq-2.19.0
CLEANING - Trimmomatic-0.36 "TRAILING:13 LEADING:13 ILLUMINACLIP:adapters.fasta:2:30:10 SLIDINGWINDOW:4:20 MINLEN:15"
MAPPING - STAR_2.5.2b "--twopassMode Basic --runMode alignReads --genomeDir ${GENOME} --readFilesIn ${SAMPLE} --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outFilterIntronMotifs RemoveNoncanonical"
READ COUNTING - subread-1.5.0p3, featurecounts, "-s 2 -t exon -g gene_name"
Genome_build: GRCm38.p5 + Gencode-M12
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample
|
| |
|
| Submission date |
Sep 04, 2019 |
| Last update date |
Sep 09, 2021 |
| Contact name |
Peng Yao |
| E-mail(s) |
[email protected]
|
| Phone |
2166507876
|
| Organization name |
Aab Cardiovascular Research Institute
|
| Department |
Medicine
|
| Lab |
Peng Yao lab
|
| Street address |
601 Elmwood Avenue
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14534 |
| Country |
USA |
| |
|
| Platform ID |
GPL17021 |
| Series (1) |
| GSE136838 |
Genome-wide transcriptomic and translatomic profiling in halofuginone and vehicle treated mouse fibroblasts |
|
| Relations |
| BioSample |
SAMN12690294 |
| SRA |
SRX6799419 |
