|
| Status |
Public on Sep 26, 2018 |
| Title |
S7721_E2 |
| Sample type |
SRA |
| |
|
| Source name |
Hepatocellular carcinoma
|
| Organism |
Homo sapiens |
| Characteristics |
cell strain: SMMC-7721
treatment: EPZ-6438
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the Ambion PureLinkTM RNA Mini Kit (Invitrogen) according to the manufacturer’s instructions
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
S7721_EvsS7721_c_DEG.xls
|
| Data processing |
Illumina Casava1.7 software was used for basecalling.
Data filtering were performed as follows:1 ) Remove reads with adaptor sequences; 2). Remove reads in which the percentage of unknown bases (N) is greater than 10%; 3). Remove low quality reads. If the percentage of the low quality base (base with quality value ≤ 5) is greater than 50% in a read, this read is defined as low quality. No more than 2 mismatches were allowed in the alignment.
Fragments per kilobase of exon per million fragments mapped (FPKM) method is used in calculated expression level (Mortazavi et al., 2008)
Genome_build: hg19
Supplementary_files_format_and_content: FPKM
|
| |
|
| Submission date |
Aug 27, 2018 |
| Last update date |
Sep 26, 2018 |
| Contact name |
Juan Yan |
| E-mail(s) |
yanjuan1357@163.com
|
| Phone |
15002135233
|
| Organization name |
Shanghai Institute of Materia Medica
|
| Department |
Antitumor Pharmacology
|
| Lab |
Meiyu Geng
|
| Street address |
555 Zuchongzhi Road
|
| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE119088 |
Transcriptomes change differerntly in differernt cancer cells upon EPZ-6438 treatment |
|
| Relations |
| BioSample |
SAMN09917831 |
| SRA |
SRX4614435 |
