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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Dec 31, 2024 |
| Title |
SKCRT 2 |
| Sample type |
SRA |
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| Source name |
Ovary
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| Organism |
Homo sapiens |
| Characteristics |
tissue: Ovary
cell line: SKOV3
cell type: Ovarian cancer
genotype: PKD inactivated
treatment: CRT0066101
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| Treatment protocol |
EOC cell lines were treated with 1 μM of PKD inhibitors CRT0066101 and kb-NB142-70 for 16 Hrs.
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| Growth protocol |
Epithelial ovarian cancer (EOC) cell lines OVCAR8 & SKOV3 were grown in DMEM and McCoy's media supplemented with 10% fetal bovine serum (FBS), 1× penicillin/streptomycin and maintained in humidified incubator containing 5% CO2 at 37 ◦C
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using Trizol reagent (Life technologies, USA) and 250 ng of total RNA was used for the construction of sequencing libraries
Library was prepared using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina (Catalog: E7775S, New England Biolabs).
mRNAs were primed with NEBNext Random Primers and chemically fragmented in a magnesium-based buffer in order to get an inserts of ~200 nucleotides. The fragmented mRNAs were reverse transcribed to form cDNA and the first strand cDNA reactions were converted to ds DNA. The double stranded cDNA fragments obtained were cleaned up by using 1.8X of AMPure XP beads (Catalog: A63881, Beckman Coulter). The library concentration was determined in a Qubit.3 Fluorometer (Catalog: Q33216, Life technologies using The Qubit dsDNA HS (High Sensitivity) Assay Kit (Catalog: Q32854, ThermoFisher Scientific). The library quality assessment was done using Agilent D5000 ScreenTape System (Catalog: 5067-5588, Agilent) and Agilent D1000 ScreenTape System (Catalog: 5067- 5582, Agilent) in a 4150 TapeStation System (Catalog: G2992AA, Agilent).
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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 |
All 150 bp paired end raw reads from Illumina NovaSeq 6000 sequencer were quality checked for low quality bases and adapter sequences, i.e AGATCGGAAGA (Processing of raw reads). Quality check was done using in-house perl scripts.
All the processed reads were aligned to Human hg38 genome (https://asia.ensembl.org/Homo_sapiens/Info/Index) using Hisat2-2.2.1.
StringTie-2-2.1 a fast and highly efficient assembler was used for alignments into potential transcripts.
The "R" package DESeq2 has been used for differential gene expression analysis based on the negative binomial distribution. DeSeq2 estimates variance-mean dependence in count data from high_x0002_throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.
Assembly: Human hg38 genome
Supplementary files format and content: gtf
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| Submission date |
Dec 01, 2023 |
| Last update date |
Dec 31, 2024 |
| Contact name |
Adhiraj Roy |
| E-mail(s) |
adhiraj.roy@gmail.com
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| Organization name |
Amity University
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| Department |
AIMMSCR
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| Lab |
Block J3, Room No 111
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| Street address |
Sector 125
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| City |
Noida |
| State/province |
Uttar Pradesh |
| ZIP/Postal code |
201313 |
| Country |
India |
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| Platform ID |
GPL24676 |
| Series (1) |
| GSE249168 |
Effect of protein kinase D inhibition on the transcriptome of epithelial ovarian cancer cells |
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| Relations |
| BioSample |
SAMN38575406 |
| SRA |
SRX22713228 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7927724_SCRT2_transcripts.gtf.gz |
17.2 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
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