|
Status |
Public on Jan 01, 2022 |
Title |
1a_01 |
Sample type |
SRA |
|
|
Source name |
THP-1
|
Organism |
Homo sapiens |
Characteristics |
cell type: acute monocytic leukemia agent: 1 microM 1a time point: 16 hours
|
Treatment protocol |
THP-1 cells were left untreated or treated with 1 µM of 1a for 16 hours
|
Growth protocol |
THP-1 cells were cultured in RPMI 1640 medium containing 10% FBS and 5% L-Glu
|
Extracted molecule |
total RNA |
Extraction protocol |
Total RNA fractions were obtained usind TRIzol reagent NEBNext Ultra Directional RNA II Library Prep kit was used for the construction of sequencing libraries, which were then sequenced with the Illumina NextSeq 500 System and NextSeq v2 sequencing reagent kit in a single read-mode with a read-length of 75 bp.
|
|
|
Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NextSeq 500 |
|
|
Data processing |
The sequences were demultiplexed (bcl2fastq2) to fastq data and quality controlled. Trimmomatic (v. 038) was used for adapter trimming and read filtering. (Parameter: SE -phred33, ILLUMINACLIP:adapters/NEB-SE.fa:2:30:10, LEADING:3 TRAILING:3 MINLEN:15) The resulted reads were aligned to the hg38 using Hisat2 (v.2.1.0; Parameter: default) and sorted using SAM tools (v. 1.9) The sorted and aligned reads were counted into genes using HTSeq (v.0.11.1; Parameter: --minaqual 0, --stranded reverse) Testing for differential expression was performed using DESeq2 r-package (v. 1.22.2) Genome_build: GRCh38 Supplementary_files_format_and_content: tab-delimited text files
|
|
|
Submission date |
May 10, 2021 |
Last update date |
Jan 01, 2022 |
Contact name |
Luca Abdel Ghani |
Organization name |
Westfälische Wilhelms-Universität
|
Street address |
Corrensstrasse 36
|
City |
Münster |
ZIP/Postal code |
48149 |
Country |
Germany |
|
|
Platform ID |
GPL18573 |
Series (1) |
GSE174138 |
Expression profiling of THP-1 cells treated with 1a by high thorughput sequencing |
|
Relations |
BioSample |
SAMN19092072 |
SRA |
SRX10827297 |