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| Status |
Public on May 28, 2024 |
| Title |
H3_Hypoxia |
| Sample type |
SRA |
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| Source name |
cell line
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| Organism |
Homo sapiens |
| Characteristics |
tissue: cell line
cell line: Hep3B
cell type: liver cancer cell
treatment: Hypoxia
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| Treatment protocol |
THLE-3 and Hep3B cell lines were treated for 48h under normoxia or hypoxia and extracted total mRNA for furthur nanopore sequencing.
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| Growth protocol |
Hep3B, and THLE-3 cell lines were cultured in DMEM supplemented with 10% FBS and 1% penicillin/streptomycin. Cells were kept at 37℃ in humidified 5% CO2 in air. Hypoxia condition was achieved by placing cells in a hypoxic working station which contains 1% O2, 5% CO2, and 94% N2.
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
According to the manufacturer’s instructions, total RNA was extracted from cells or tissues using TRIzol (Life Technologies)
Using the standard adapter-ligation method for library construction, optional DNA fragmentation, end-repair, A-tailing, followed by ligation of sequencing adapters, motor protein, and Tether protein to prepare the cDNA library
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
PromethION |
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| Data processing |
The original sequences were basecalled using the official Oxford Nanopore software Guppy, followed by filtering based on sequence length and quality (length_100, quality_7) to obtain clean data.
Identification of full-length transcripts was performed using Pinfish software. Subsequently, alignment was conducted using Minimap 2 software, followed by clustering based on the alignment results to obtain Consensus sequences
Gffcompare software was used to annotate the Consensus sequences and organize the results, obtaining information on known transcripts and novel transcripts.
The structural analysis includes new gene prediction and database annotation, alternative splicing analysis, novel transcript identification, transcription factor analysis, and LncRNA analysis.
Database functional annotation is performed on the identified novel transcripts.
Differential enrichment analysis includes gene/transcript expression level analysis, differential gene/transcript analysis, as well as GO, KEGG enrichment analysis, and clustering analysis of differential genes.
Assembly: hg38
Supplementary files format and content: tab-delimited txt files include raw counts for each sample
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| Submission date |
Apr 03, 2024 |
| Last update date |
May 28, 2024 |
| Contact name |
shengqi shen |
| E-mail(s) |
[email protected]
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| Phone |
+8618355103391
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| Organization name |
GDPH
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| Street address |
zhongshan road #104
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| City |
guangzhou |
| ZIP/Postal code |
510080 |
| Country |
China |
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| Platform ID |
GPL26167 |
| Series (1) |
| GSE263126 |
Identification of hypoxia-induced isoforms and novel genes with nanopore long reads sequencing |
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| Relations |
| BioSample |
SAMN40739935 |
| SRA |
SRX24143238 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8186203_H3_H_anno.tsv.gz |
49.2 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
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