|
| Status |
Public on May 04, 2021 |
| Title |
U20S_siDDX41_RNA-seq_3 |
| Sample type |
SRA |
| |
|
| Source name |
U20S_DDX41 knockdown
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U20S
treatment: DDX41 knockdown
replicate: 3
|
| Treatment protocol |
Knockdowns were induced for 48 hourse using pool siRNAs.
|
| Growth protocol |
U2OS cells were cultured in DMEM containing 10% FBS, Pen-Strep,1% Glutamine
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
RNA extraction was performed using Qiagen Rneasy Plus mini kit.
NGS library prep was performed with Illumina's TruSeq stranded mRNA LT Sample Prep Kit following TruSeq Stranded mRNA Reference Guide (Oct.2017) (Document # 1000000040498v00). Libraries were prepared with a starting amount of 1000 ng and amplified in 10 PCR cycles. Libraries were profiled in a High Sensitivity DNA on a 2100 Bioanalyzer (Agilent Technologies) and quantified using the Qubit dsDNA HS Assay Kit, in a Qubit 2.0 Fluorometer (Life Technologies).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
imb_beli_2020_05_08_siDDX41_3_S8
|
| Data processing |
Basecalling was done using RTA v 2.4.11. Demultiplexing was done using bcl2fastq v. 2.19.
Samples were mapped using STAR (v2.7) against hg38 with the Gencode annotation (v25) as gene reference.
Reads per gene were counted using Subread/featureCounts ( v.1.6).
Sequencing depth normalised tracks were created using Deeptools (v3.4.1).
Genome_build: hg38
Supplementary_files_format_and_content: sequencing depth normalised bigwig files; read counts per gene (tab separated value file)
|
| |
|
| Submission date |
Mar 03, 2021 |
| Last update date |
May 04, 2021 |
| Contact name |
Petra Beli |
| E-mail(s) |
p.beli@imb-mainz.de
|
| Organization name |
Institute of Molecular Biology (IMB)
|
| Street address |
Ackermannweg 4
|
| City |
Mainz |
| ZIP/Postal code |
55128 |
| Country |
Germany |
| |
|
| Platform ID |
GPL18573 |
| Series (2) |
| GSE168171 |
RNA-seq after DDX41 knockdown in U2OS cells |
| GSE168173 |
MapR in U2OS and HCT116 cells and RNA-seq in U2OS |
|
| Relations |
| BioSample |
SAMN18128718 |
| SRA |
SRX10229660 |
