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Status |
Public on May 13, 2024 |
Title |
162_50_2 |
Sample type |
SRA |
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Source name |
TMPyP4 50umol replicates2
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Organism |
Drosophila melanogaster |
Characteristics |
cell line: S2 drug concentration: 50 micromol/L treatment: TMPyP4 library type: fr-firststrand (dUTP)
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Treatment protocol |
S2 cells were treated with different concentration of TMPyP4 (25μmol/L, 50μmol/L, 100μmol/L, respecticely), and DMSO was severed as control. After 48 hours, the S2 cells were sampled for sequencing.
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Growth protocol |
Drosophila line 2 cells (S2) were maintained at 28°C in Hyclone TNM-FH insect medium containing 10% Gibico serum and antibiotics (0.5 U/ml penicillin and 0.5 μg/ml streptomycin).
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Extracted molecule |
polyA RNA |
Extraction protocol |
We extracted the total RNA using the Trizol method. We added 1 ml of Trizol (invitrogen) to the sample (4-7 million cells) stored at -80 ° C, and carefully piped the sample with a pipette, which was the homogenate of the tissue cells. Then, 200 μl of chloroform was added to the homogenate, and the sample was shaken for 15 seconds using a vortex shaker until the phase separation disappeared. After standing at room temperature for 2-3 minutes, the sample was centrifuged at 12,000 g for 15 minutes at 4 °C. The colorless supernatant was transferred to another new centrifuge tube, mixed well with an equal volume of isopropanol, held at -20 ° C for 10 minutes, and then centrifuged at 12,000 g for 10 minutes at 4 ° C to precipitate RNA. The supernatant was carefully removed, the precipitate was gently washed 2-3 times with 1 ml of fresh 75% ethanol, dried at room temperature for 2 to 3 minutes and dissolved in 50 μl of RNase-free water. Stranded PolyA+ RNA libraries were prepared at Majorbio (Shanghai, China) with in-house kits. A total of 12 qualified cDNA libraries were constructed and were sequenced on the Illumina HiSeq XTen System (Illumina Inc., San Diego, CA).
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
HiSeq X Ten |
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Description |
mixed species RNA preparation prepared with zebrafish RNA
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Data processing |
RNA-Seq: High-throughput sequencing raw image data files were converted to reads using fqtools_plus analysis. RNA-Seq: We used FastqC (0.11.8) to evaluate the raw reads quality. Sequencing report tool was MultiQC (0.9). RNA-Seq: Reads were mapped to the corresponding reference genomes (flybase dm6) by Hisat2 (2.0.5) with parameters “-x --rna-strandness RF” and “--known-splicesite-infile” followed by gene annotation in GTF format RNA-Seq: The output of Hisat2 were converted to BAM format, sorted and reads with MAPQ <30 were discarded by Samtools (1.7) RNAseq: HTSeq (0.9.1) was used for counting reads with parameters “-t exon -i gene_id -r name -s reverse”. Genome_build: Dm6 Supplementary_files_format_and_content: Tab-delimited text files include raw or normalized read counts of all the genes for each RNAseq sample.
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Submission date |
May 23, 2019 |
Last update date |
May 13, 2024 |
Contact name |
Zhen-Xia Chen |
E-mail(s) |
zhen-xia.chen@mail.hzau.edu.cn
|
Organization name |
Huazhong Agricultural University
|
Department |
College of Life Science and Technology
|
Street address |
No.1 Shizishan Street
|
City |
Wuhan |
State/province |
Hubei |
ZIP/Postal code |
430070 |
Country |
China |
|
|
Platform ID |
GPL23702 |
Series (1) |
GSE131691 |
The effect of G-quadruplex on gene expression by treating S2 cell with different concentration of TMPyP4 |
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Relations |
BioSample |
SAMN11840273 |
SRA |
SRX5887769 |