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Status |
Public on Dec 31, 2018 |
Title |
sh-TDP43_+_sh-SRSF3_rep2 |
Sample type |
SRA |
|
|
Source name |
total RNA from MDA-MB231 treated with sh-TDP43 &sh-SRSF3
|
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
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|
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 2000 |
|
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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 ...
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|
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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 |
SAMN06770081 |
SRA |
SRX2749168 |