|
| Status |
Public on Jan 01, 2017 |
| Title |
siControlN2 |
| Sample type |
SRA |
| |
|
| Source name |
MCF-7 breast cancer cells, siControl
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MCF-7
cell type: breast cancer cell line
sirna: scramble
|
| Treatment protocol |
Cells were treated with 50nM siSHARPIN or siControl for 48hrs.
|
| Growth protocol |
MCF-7 cells were cultured in DMEM with 10% FBS.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
The total RNA was extracted from cells by the Qiagen RNA extraction kit.
Libraries were prepared according to Illumina's instructions accompanying the RNA Sample Kit (Part# 0801-0303).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Illumina HiSeq 4000 used for basecalling.
Sequence reads were trimmed for adaptor sequence and 3'-end was trimmed by quality, reads were filtered by quality and mapped to GRCh37 using the HISAT2 software.
Mapping QC by SAMtools and Picard software.
Quantification was done by using Cufflinks to produce gene-level expression values (FPKMs).
Genome_build: GRCh37
Supplementary_files_format_and_content: *.fpkm_tracking: Tab-delimited text files include FPKM values for each Sample.
|
| |
|
| Submission date |
Jan 26, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Qiangzu Zhang |
| E-mail(s) |
qiangzuzhang@gmail.com
|
| Organization name |
Lemondata BioTechnology Limited
|
| Street address |
Nan Hai Da Dao Chuang Shi Ji Bin Hai Hua Yuan Building9 9A , Nanshan District, Shenzhen City, Guangdong Province
|
| City |
Shenzhen |
| ZIP/Postal code |
518054 |
| Country |
China |
| |
|
| Platform ID |
GPL20301 |
| Series (1) |
| GSE77261 |
Genome-wide expression change by SHARPIN knockdown in MCF-7 cells |
|
| Relations |
| BioSample |
SAMN04441297 |
| SRA |
SRX1548277 |
