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Sample GSM5766469

Query DataSets for GSM5766469

Status

Public on Mar 22, 2023

Title

Lung cancer celll-H1299-normoxia 2

Sample type

SRA

Source name

H1299 cells

Organism

Homo sapiens

Characteristics

cell line: H1299
tissue/cell type: Lung adenocarcinoma (LUAD)
treatment: 21% O2 / 5% CO2 / 74% N2

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.

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

Library strategy

RNA-Seq

Library source

transcriptomic

Library selection

cDNA

Instrument model

Illumina HiSeq 4000

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.

Submission date

Dec 31, 2021

Last update date

Mar 22, 2023

Contact name

Xiucheng Liu

E-mail(s)

2010692@tongji.edu.cn

Organization name

Shanghai pulmonary hospital

Street address

zhengmin road 557