|
| Status |
Public on Dec 03, 2016 |
| Title |
NIH3T3_GDF15 |
| Sample type |
SRA |
| |
|
| Source name |
NIH3T3 fibroblast
|
| Organism |
Mus musculus |
| Characteristics |
stimulation: 100 ng/mL of GDF15 protein
|
| Treatment protocol |
NIH3T3 fibroblasts were incubated in serum-free IMDM supplemented with 100 ng/mL of GDF15 or 4 ng/mL of TGF-β for 24 h.
|
| Growth protocol |
NIH3T3 fibroblasts were grown in IMDM with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted by using the MagNA pure compact RNA isolation kit (Roche).
RNA-seq libraries were prepared for sequencing using TruSeqStranded mRNA LT Sample Prep Kit according to standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
| |
|
| Data processing |
Illumina Casava1.7 software used for basecalling.
Read were aligned with TopHat v1.3.2 and Bowtie version 0.12.9. Command,line options for Tophat were '-r 100.'
Fragments per kilobase of exon model per million mapped fragments (FPKM) were calculated using Cufflinks v2.0.2. Command line options for cufflinks were '--max-bundle-flags 4000000.'
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Dec 17, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Masaki Fukuyo |
| E-mail(s) |
fukuyo@chiba-u.jp
|
| Organization name |
Chiba University
|
| Department |
Department of Molecular Oncology
|
| Street address |
1-8-1 Inohana, Chuo-ku
|
| City |
Chiba |
| ZIP/Postal code |
260-8670 |
| Country |
Japan |
| |
|
| Platform ID |
GPL18480 |
| Series (1) |
| GSE64296 |
RNA-seq of GDF15 or TGF-β stimulated NIH3T3 fibroblasts. |
|
| Relations |
| BioSample |
SAMN03268016 |
| SRA |
SRX815829 |
