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Status |
Public on Sep 01, 2022 |
Title |
A549 cells, Treated_1, 72h |
Sample type |
SRA |
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Source name |
Lung
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Organism |
Homo sapiens |
Characteristics |
tissue: Lung cell line: A549 cell type: Human non-small cell lung cancer cell genotype: WT treatment: treated with 2μM B35 for 72h
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Treatment protocol |
A549 cells was treated by B35 (2μM) or untreated for 72h
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Growth protocol |
A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C
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Extracted molecule |
total RNA |
Extraction protocol |
RNA was harvested using TRIzol (Invitrogen, USA). 1 ug of total RNA was used for the construction of sequencing libraries. RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina NovaSeq 6000 |
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Data processing |
Quality control:Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing N base and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality. Reads mapping to the reference genome: Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5. We selected Hisat2 as the mapping tool for that Hisat2 can generate a database of splice junctions based on the gene model annotation file and thus a better mapping result than other non-splice mapping tools Quantification of gene expression level:featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene. FPKM, expected number of Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced, considers the effect of sequencing depth and gene length for the reads count at the same time, and is currently the most commonly used method for estimating gene expression levels. Assembly: hg38 Supplementary files format and content: tab-delimited text files include FPKM values and raw gene counts for each Sample
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Submission date |
May 08, 2022 |
Last update date |
Sep 02, 2022 |
Contact name |
海蓝 黄 |
E-mail(s) |
havehappylong@outlook.com
|
Phone |
13318030705
|
Organization name |
Shenyang Pharmaceutical University
|
Street address |
No.103,Wenhua Street, Shenhe District
|
City |
Shengyang |
State/province |
Liaoning |
ZIP/Postal code |
110000 |
Country |
China |
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|
Platform ID |
GPL24676 |
Series (1) |
GSE202477 |
Effect of LSD1 inhibitor B35 on gene expression of A549 cells |
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Relations |
BioSample |
SAMN28156551 |
SRA |
SRX15206694 |