|
| Status |
Public on Nov 30, 2022 |
| Title |
THP-1 SA LPS 4 |
| Sample type |
SRA |
| |
|
| Source name |
THP-1
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: THP-1
cell type: Myeloid leukemia
genotype: ACLY S455A
treatment: LPS 100 ng/ml 3h
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA of non-treated and LPS-treated THP-1 cells was isolated using RNeasy Mini Kit (Qiagen). 500 ng of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using QuantSeq 3’ mRNA-Seq Library Prep Kit FWD with UDI 12nt set B1 (Lexogen)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
Normalized counts SA_LPS
|
| Data processing |
Demultiplexed FASTQ files were generated with bcl2fastq2 software (Illumina).
Processed reads were subsequently mapped to the human genome (GRCh38) using Bluebee online platform (Lexogen).
Differential expression was evaluated using DESeq2 Pipeline (Bluebee)
Assembly: Homo sapiens (GRCh38)
Supplementary files format and content: Tab-delimited text files contain the normalized read counts for each condition
|
| |
|
| Submission date |
Oct 18, 2022 |
| Last update date |
Nov 30, 2022 |
| Contact name |
Dmitry Namgaladze |
| E-mail(s) |
namgalad@biochem.uni-frankfurt.de
|
| Organization name |
Goethe University Frankfurt
|
| Street address |
Theodor Stern Kai 7
|
| City |
Frankfurt |
| ZIP/Postal code |
60590 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE216003 |
Impact of ATP-citrate lyase catalytic activity and serine 455 phosphorylation on histone acetylation and inflammatory responses in human monocytic cells |
|
| Relations |
| BioSample |
SAMN31344040 |
| SRA |
SRX17933018 |
