GEO Accession viewer

NCBI > GEO > Accession Display

Not logged in | Login

GEO help: Mouse over screen elements for information.

Sample GSM4433472

Query DataSets for GSM4433472

Status

Public on May 27, 2020

Title

HeLa cells, TDCPP, 20uM-1day

Sample type

SRA

Source name

HeLa cell line treated with 20 µM tris(1,3-dichloro-2-propyl)phosphate for 24 hr

Organism

Homo sapiens

Characteristics

cell line: HeLa
treatment: 20 µM tris(1,3-dichloro-2-propyl)phosphate for 24 hr

Treatment protocol

Tris(1,3-dichloro-2-propyl)phosphate (2, 20 and 100 µM) ware treated in the HeLa cells for different time points (2 and 24 hr). Final DMSO concentration was 0.1%.

Growth protocol

HeLa cells were grown in DMEM supplemented with 10% FBS, 100 units/mL penicillin, and 100 μg/mL streptomycin in humidified atmosphere containing 5% CO2 at 37 0C.

Extracted molecule

total RNA

Extraction protocol

After the incubation time, the cells were PBS washed, trypsinized and centrifuged for 5 min at 1,200 rpm. The supernatant was discarded, and the remained cell pellet was resuspended in Trizol. Trizol extraction of total RNA was performed according to the manufacturer's instructions.
TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

Data processing

FastQC v0.11.7 was used to see the average base quality per cycle. Phred quality score of 20 (99%) or higher was considered as acceptable.
Before entering the analysis, the adapter sequence is removed through the Trimmomatic 0.38 program. Bases less than base quality 3 from the ends of the reads are removed and bases are removed if the window size equals to 4 and mean quality equals to 15 are not satisfied by the sliding window trim technique. After that, trimmed data was generated by removing reads shorter than min length (36 bp).
Pre-processed trimmed reads are mapped to known reference genomes. HISAT2 program (version 2.1.0) was used to process spliced read mapping through Bowtie2 2.3.4.1 aligner. A genomic DNA reference (UCSC hg19) was used to map the cDNA fragments obtained through RNA-seq experiments.
After Read mapping, transcript assembly was performed through the StringTie program, version 1.3.4d. As a result, the expression profile value for each sample was obtained for the known transcript, and the read count and Fragment per Kilobase of transcript per Million mapped reads (FPKM) values were summarized based on the transcript/gene. For the sample’s raw signal, normalized counts calculated as transformed logarithm and normalization using the quantile method.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: xlsx file with indicated normalized counts, FPKM and read counts for each of 7 samples.

Submission date

Mar 26, 2020

Last update date

May 27, 2020

Contact name

Jun-Seok Lee

E-mail(s)

junseoklee@kist.re.kr

Phone

+82-2-958-5092

Organization name

Korea Institute of Science and Technology (KIST)