|
| Status |
Public on Jan 01, 2017 |
| Title |
si_LARP4B_3 |
| Sample type |
SRA |
| |
|
| Source name |
HEK293
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HEK293
si-rna: si-LARP4B
replicate: 3
|
| Treatment protocol |
HEK293 cells were transfected with siRNA targeting LARP4B and firefly luciferase (Thermo Fisher Scientific).
|
| Growth protocol |
HEK293 cells were grown in DMEM (Gibco) supplemented with 10% FBS (Gibco) and 1% penicillin/streptomycin (Gibco).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy Mini Kit (Qiagen) including on-column DNase digestion 48 h after transfection. Poly-A RNA was isolated from total RNA using the NEBNext Poly(A)mRNA Magnetic Isolation Module (E7490).
Libraries for the RNA-seq samples were constructed using the NEBNext Library Prep Kit (6100) following the instruction manual. Briefly, poly-A RNA was fragmented to generate 200 nucleotides long fragments. First and second strand cDNA synthesis was performed and the resulting cDNA was end-repaired, ligated to NEBNext adaptors. The cDNA was size selected using agarose gels and amplified by PCR. For the resulting RNA-seq libraries, amplicon sizes and quantities were determined using the Biorad Experion system. Libraries were sequenced on an Illumina Genome Analyzer IIx following the manufacture’s instructions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Basecalling was performed with the real time analysis (RTA) package within the Genome Analyzer Sequencing Control Software (SCS2.10).
Demultiplexing and generation of Fastq files was done with the CASAVA software only considering high quality sequences (PF-cluster).
Reads were aligned to the human genome (hg19) with BOWTIE v0.12.8.
Differential expression and statistical inference was done using EdgeR.
Genome_build: hg19
Supplementary_files_format_and_content: The txt-file contains a table showing the differential expression (as log FoldChange) of ensemble annotated genes (ensemble gene ids, in rows) between samples (=experimental conditions) and the calculated p-value and adjusted p-value for each FoldChange.
|
| |
|
| Submission date |
Feb 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Martin Eilers |
| Organization name |
University of Wuerzburg
|
| Department |
Chair for Biochemistry and Molecular Biology
|
| Lab |
Martin Eilers
|
| Street address |
Am Hubland
|
| City |
Wuerzburg |
| ZIP/Postal code |
97074 |
| Country |
Germany |
| |
|
| Platform ID |
GPL10999 |
| Series (1) |
| GSE66155 |
LARP4B is an mRNA stability factor that acts via AU-rich sequence elements |
|
| Relations |
| BioSample |
SAMN03360373 |
| SRA |
SRX884660 |
