|
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 |