|
| Status |
Public on Aug 29, 2021 |
| Title |
RL5_MET |
| Sample type |
SRA |
| |
|
| Source name |
human myeloid leukemia cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: U937
cell type: human myeloid leukemia cells
treatment: LPS 1 µg/mL + Methoxyamine 6mM
|
| Treatment protocol |
5 × 10^5 were treated with 1 µg/mL LPS (Cat. No: L2654; Sigma-Aldrich) for 24 h, other cell gruop were incubated with 1 µg/mL LPS for 24 h plus with 100 µM E3330 (≥98% pure; Sigma-Aldrich) or 6 mM methoxyamine (MX) for 4 h.
|
| Growth protocol |
U937 cells were cultured in Gibco RPMI-1640 medium (Thermo Fisher Scientific Inc.,Waltham, MA, USA), suplemented with 44 mM sodium bicarbonate (Sigma-Aldrich, St. Louis, MO, USA), Gibco 10% fetal bovine serum (Thermo Fisher Scientific Inc.), and 1% Penicillin-Streptomycin antibiotic solution (Sigma-Aldrich) in a humidified incubator at 37°C and a 5% CO2 atmosphere.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
IllustraTM RNAspin Mini RNA Isolation Kits (GE Healthcare Little Chalfont, UK)
RNA libraries were prepared for sequencing following the manufacturer's protocol 454 GS FLX Titanium (Roche Holdings AG.)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
454 GS FLX Titanium |
| |
|
| Description |
RL5
|
| Data processing |
The sequenced data were aligned against the Ref-Seq database of human expressed sequences provided by the University of California Santa Cruz (UCSC; http://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/refMrna. fa.gz), accessed on January 30, 2014. Sequences were aligned using BLAT
The results were filtered using the pslCDnaFilter tool (http://hgdownload.cse.ucsc.edu/admin/exe/), with a minimum identity of 98%, minimum coverage of 90%, and only one alignment per sequence.
All sequences that matched the ribosomal RNA (rRNA) were excluded.
Gene expression was normalized as counts per million (CPM), calculated by counting reads per gene (Xi) and the total number of reads per sample (N): CPM = (Xi/N)*10^7.
Genome_build: hg19
Supplementary_files_format_and_content: xlsx format files include gene type, gene name, normalized mensuraments
Supplementary_files_format_and_content: xlsx format files include gene name and counts
|
| |
|
| Submission date |
Aug 26, 2021 |
| Last update date |
Aug 31, 2021 |
| Contact name |
Thais Teixeira Oliveira |
| E-mail(s) |
thais.teixeira.085@ufrn.edu.br
|
| Organization name |
Federal University of Rio Grande do Norte, Brazil,
|
| Department |
Departamento de Biologia Celular e Genética
|
| Lab |
Laboratório de biologia molecular e Genômica
|
| Street address |
Rua das biociências
|
| City |
Natal |
| State/province |
Rio Grande do Norte |
| ZIP/Postal code |
59078-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL14603 |
| Series (1) |
| GSE182813 |
Chemical inhibition of APE1 redox and DNA repair functions affects the inflammatory response via different but overlapping mechanisms. |
|
| Relations |
| BioSample |
SAMN20985744 |
| SRA |
SRX11915991 |
