|
| Status |
Public on Oct 18, 2017 |
| Title |
GCTB09 |
| Sample type |
SRA |
| |
|
| Source name |
stromal cell
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: female
h3f3a status: WT
disease: GCTB
|
| Treatment protocol |
-
|
| Growth protocol |
GCTB stromal cells in DMEM medium supplemented with 10% fetal bovine serum (FBS) and 5ug/ml of Gentamycin at 37C in a 5% CO2 pressure.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We collected the cultured GCTB cell with 0.25 % EDTA-trypsin and extract the RNA used QIAGEN Rneasy mini kit followed the standard protocol. QIAshredder spin columns and Dnase I digestion step was included
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 whole genome using bowtie2 v2.2.3 with default parameters
Transcript is assembled by Cufflinks v2.2.1 with aligned reads that contain paired-end information.
Expression profiles (FPKM) of assembled transcripts for each sample are calculated by Cufflinks. Expression profiles are represented as normalization value which is based on transcript length and depth of coverage as FPKM values (Fragments Per Kilobase of transcript per Million Mapped reads).
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
|
| |
|
| Submission date |
Sep 06, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jinyeong Lim |
| E-mail(s) |
aster1217@ncc.re.kr
|
| Organization name |
National Cancer Center
|
| Street address |
Ilsan
|
| City |
Ilsan |
| ZIP/Postal code |
10142 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE103559 |
The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing [RNA-seq] |
|
| Relations |
| BioSample |
SAMN07610265 |
| SRA |
SRX3164056 |
