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Sample GSM5287839 Query DataSets for GSM5287839
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

Supplementary file Size Download File type/resource
GSM5287839_1a_01.sortc.cnt.txt.gz 446.9 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record
Processed data provided as supplementary file

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