|
| Status |
Public on Dec 31, 2018 |
| Title |
input-flag-TDP43 |
| Sample type |
SRA |
| |
|
| Source name |
input RNA of MDA-MB231 overexpressed flag-TDP43
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: MDA-MB231
cell type: breast cancer cell line
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Cells were collected, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RIP-Seq |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
RIP-Seq reads were aligned to the h19 genome assembly using hisat2 version 2.0.5 with the following configurations: --no-unal --dta --dta-cufflinks --score-min L,0,-0.2 --no-mixed --no-discordant --no-unal --known-splicesite-infile
expression value were calculated using stringtie version 1.3.0 with the following configurations: -a 6
RIP enrichment were called using ASPeak.pl version 2.0.0 with default setting
RNA-seq: Reads were aligned to the h19 genome assembly using STAR_2.5.2a_modified; expression value were calculated using Version 1.4.6-p5 with the following configurations: -T 5 -a $gtf2 -t exon
Genome_build: GRCh37
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample ...
|
| |
|
| Submission date |
Apr 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Baowei Jiao |
| E-mail(s) |
jiaobaowei@mail.kiz.ac.cn
|
| Phone |
+8613678709351
|
| Organization name |
Chinese Academy of Sciences
|
| Department |
Kunming Institute of Zoology
|
| Lab |
State Key Laboratory of Genetic Resources and Evolution
|
| Street address |
32 Jiaochang Donglu Kunming
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650223 |
| Country |
China |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE98016 |
Transcriptome analysis on TDP43 and SRSF3 downstream genes and binding RNAs in MDA-MB231 cells by Next Generation Sequencing |
|
| Relations |
| BioSample |
SAMN06770080 |
| SRA |
SRX2749169 |
