|
| Status |
Public on Apr 07, 2024 |
| Title |
Control-3 |
| Sample type |
SRA |
| |
|
| Source name |
Human breast cancer cell line
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB-231
treatment: Control
|
| Treatment protocol |
Ellagic acid or control was added into MDA-MB-231 cells (n=3 per group) for 24 hours.
|
| Growth protocol |
MDA-MB-231 cells were maintained in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum (FBS), 100 units/ml penicillin, and 100 mg/ml streptomycin.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from the MDA-MB-231 cells using Trizol reagent (Invitrogen). RNA quality was checked by Agilent 2100 Bioanalyzer (Agilent Technologies, USA).
RNA libraries were prepared for sequencing using standard CapitalBio Technology protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
SOAPnuke (version: v1.5.2) was used for filter reads, parameters: -1 15 -q 0.5 -n 0.1.
Bowtie2 (version: v2.2.5) was used to map clean reads to reference gene, parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -p 16 -k 200.
HISAT (version: v2.0.4) was used to align clean reads to the mouse genome, parameters: -p 8 --phred64 --sensitive -I 1 -X 10000.
RSEM (version: v1.2.12) was used for abundance measurement, parameters: default.
FPKM method was used in calculated expression level.
Genome_build: hg 38
Supplementary_files_format_and_content: tab-delimited text files ChIPseeker
|
| |
|
| Submission date |
Apr 07, 2021 |
| Last update date |
Apr 07, 2024 |
| Contact name |
yan wang |
| E-mail(s) |
yanwang@tmu.edu.cn
|
| Organization name |
National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences
|
| Street address |
17 panjiayuan nanli, chaoyang district, Beijing, China
|
| City |
beijing |
| ZIP/Postal code |
100021 |
| Country |
Zimbabwe |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE171618 |
RNA-seq analysis CARM1 inhibitor Ellagic acid effect on MDA-MB-231 cells |
|
| Relations |
| BioSample |
SAMN18646837 |
| SRA |
SRX10531580 |
