|
| Status |
Public on Aug 23, 2018 |
| Title |
T47D_siHNRNPC |
| Sample type |
SRA |
| |
|
| Source name |
T47D_siHNRNPC
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: T47D
genotype/variation: HNRNPC knock-down
molecule subtype: cytoplasmic RNA
|
| Treatment protocol |
Reverse transfections of the siRNAs (10nM) were performed using Lipofectamine RNAiMAX Reagent (Invitrogen) following the manufacturer’s instructions. siRNAs and RNAiMAX were separately diluted in optimem medium and mixed together for 20 minutes incubation. For 96-well plates, 100ul medium containing 10^5 cells were added to the transfection mixture. 6 hours after transfection, replace the cell supernatant with fresh cell medium.
|
| Growth protocol |
T47D was grown in RIPM 1640 (Corning) with 10% FBS and 0.2U/ml insulin.
Culture medium for different cell lines are discribed in the SAMPLES section. All cells were maintained in a humidified atmosphere with 5% CO2 at 37°C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected 48 hours after siRNA transfection. The nuclear and cytoplasmic fractions were separated with Nuclear/Cytosol Fractionation Kit (Biovision, K266-25). Total RNA were then extracted from the cytoplasmic lysates, with Trizol reagent (Invitrogen). The residual genome DNA was removed by Turbo DNase (Ambion), and ribosomal RNA was removed with the ribozero kit for human (Epicentre).
About 100ng ribosomal RNA-depleted cytoplasmic RNA was used for cDNA library preparation with Truseq RNA sample Preparation Kit (Illumina).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
| |
|
| Data processing |
Basecalls performed using CASAVA version 1.8
Truseq library were first pre-processed using Cutadapt (version 1.11) to remove adaptors and trim low-quality bases from 5’ and/or 3’ ends. Reads shorter than 20bp were discarded.
Trimmed and filtered reads were aligned to GENCODE v23 reference transcriptome using RSEM (v.1.2.15) invoking Bowtie2 (v2.1.0) with default parameters. Expected read counts of each gene were also estimated with RSEM.
Genome_build: hg38
Supplementary_files_format_and_content: Tab-delimited text files include rounded count values for each Sample
|
| |
|
| Submission date |
Jun 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Xuerui Yang |
| E-mail(s) |
yangxuerui@tsinghua.edu.cn
|
| Organization name |
Tsinghua University
|
| Department |
School of Life Sciences
|
| Street address |
Haidian District
|
| City |
Beijing |
| ZIP/Postal code |
100084 |
| Country |
China |
| |
|
| Platform ID |
GPL20795 |
| Series (1) |
| GSE100451 |
Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response |
|
| Relations |
| BioSample |
SAMN07276654 |
| SRA |
SRX2955414 |
