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| Status |
Public on May 01, 2024 |
| Title |
HEY_shPQBP1_1 |
| Sample type |
SRA |
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| Source name |
HEY
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| Organism |
Homo sapiens |
| Characteristics |
cell line: HEY
cell type: ovarian cancer cells
genotype: PQBP1 knockdown
treatment: Dox inducement (1 microg/ml)
time: Day 3
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| Extracted molecule |
total RNA |
| Extraction protocol |
1 µg total RNA was employed for cDNA library construction according to Oxford Nanopore Technology (ONT) protocol.
Full length mRNAs were reverse transcripted by SuperScript IV First-Strand Synthesis System (Invitrogen) and amplified for 14 circles with LongAmp Tag (NEB). Then PCR products were under FFPE DNA repair and end-repair (NEB) steps and adaptor ligation using T4 DNA ligase (NEB). DNA purification was performed by Agencourt XP beads according to ONT protocol.
Long-read nanopore sequencing
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| Data processing |
Thresholds for raw reads filtration were minimum average read quality score=7 and minimum read length=500bp, and ribosomal RNA (rRNA) were discarded.
Full-length, non-chemiric (FLNC) transcripts were obtained after mapping to the hg38 genome with minimap2 (version 2.18) and removing redundant transcripts with cDNA_Cupcake package.
Full length reads were mapped to the reference transcriptome sequence. Reads with match quality above 5 were further used to quantify. Expression levels were estimated by reads per gene/transcript per 10,000 reads mapped.
Differential transcript expression was obtained by DESeq R package (1.18.0). Significant different expression was filtered out by |Fold change| > 2 and p <0.05].
Assembly: hg38
Supplementary files format and content: tab-delimited text files include Count values of trancripts for each Sample
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| Submission date |
Jan 17, 2023 |
| Last update date |
May 01, 2024 |
| Contact name |
Xihan Liu |
| E-mail(s) |
[email protected]
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| Phone |
15106917320
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| Organization name |
Shandong University
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| Street address |
Wenhuaxi Road #44
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| City |
Jinan |
| State/province |
Shandong |
| ZIP/Postal code |
250012 |
| Country |
China |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE223088 |
Long-read nanopore sequencing (Nanopore-seq) of PQBP1 knockdown in ovarian cancer cells |
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| Relations |
| BioSample |
SAMN32771102 |
| SRA |
SRX19053420 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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