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Status |
Public on Mar 22, 2023 |
Title |
Lung cancer celll-H1299-normoxia 2 |
Sample type |
SRA |
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Source name |
H1299 cells
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Organism |
Homo sapiens |
Characteristics |
cell line: H1299 tissue/cell type: Lung adenocarcinoma (LUAD) treatment: 21% O2 / 5% CO2 / 74% N2
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Treatment protocol |
Smartor118-three gas incubator (China Innovation Instrument, Ningbo, China) was used to mimic protocols of supplemental oxygen delivery in vitro. H1299 cells were treated with hyperoxia (60% O2 / 5%CO2 / 35%N2) for 24.
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Extracted molecule |
total RNA |
Extraction protocol |
H1299 cells were flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit was used with 1 ug of total RNA for the construction of sequencing libraries. RNA libraries were prepared for sequencing using standard Illumina protocols
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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Data processing |
The ribosomal RNA (rRNA) was removed from the total RNA using the NEBNext® rRNA Depletion Kit (New England Biolabs, Inc., Ipswich, MA, USA) following the manufacturer's instructions. RNA libraries were constructed by using NEBNext® Ultra™ II Directional RNA Library Prep Kit (New England Biolabs, Inc., Massachusetts, USA) according to the manufacturer’s instructions. Then, HTSeq software (v0.9.1) was used to obtain the transcript level (lncRNA) raw count as the expression profiling, and edgeR (v3.16.5) was used to perform normalization, and differentially expressed mRNAs were identified by p-value and fold change. Genome_build: mm9 Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample: Column A: gene_id, the Ensembl gene identifier. Column B: gene, the gene name. Column C: gene description. Column D: Length, the length of the locus. It equals to end-start of the locus. Column E~I:Statistical results, statistical results by edgeR. Column J ~ U: raw counts, raw counts of all samples of the gene by HTSeq. Column V, W: Trans Per Million. Column X ~ AG: annotation information, including dbXrefs (other database ID), chromosome, map_location, description, pathway and GO annotations.
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Submission date |
Dec 31, 2021 |
Last update date |
Mar 22, 2023 |
Contact name |
Xiucheng Liu |
E-mail(s) |
2010692@tongji.edu.cn
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Organization name |
Shanghai pulmonary hospital
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Street address |
zhengmin road 557
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City |
shanghai |
ZIP/Postal code |
200433 |
Country |
China |
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Platform ID |
GPL20301 |
Series (1) |
GSE192839 |
RNA Sequencing Analysis of H1299 cells with Hyperoxia Treatment and Control Cells |
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Relations |
BioSample |
SAMN24538076 |
SRA |
SRX13569505 |
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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