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Series GSE148036 Query DataSets for GSE148036
Status Public on Oct 07, 2020
Title Lung transcriptional profiling of pulmonary tuberculosis, adenocarcinoma and sarcoidosis patients using RNA-Seq
Organism Homo sapiens
Experiment type Expression profiling by high throughput sequencing
Summary Purpose: Pulmonary tuberculosis (TB), caused by Mycobacterium tuberculosis (Mtb), has long been associated with the development of lung adenocarcinoma (LUAD) and sarcoidosis. These chronic lung diseases share histopathological similarities that challenge differential diagnosis.
Methods: Human lung tissues were used for total RNA extraction with RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol. RNA purity was assessed using a Nanodrop ND-2000 (Thermo Scientific), and each RNA sample had an A260:A280 ratio above 1.8 and an A260:A230 ratio above 2.0. RNA integrity was evaluated using the Agilent 2200 TapeStation (Agilent Technologies), and each sample had the RNA Integrity Number (RIN) above 7.0. The ribosomal RNAs (rRNAs) were removed using Ribo-Zero rRNA Removal Kits (Illumina). RNA libraries were then constructed by NEBNext Ultra RNA Library Prep Kit for Illumina (New England Biolabs) and evaluated using the Agilent 2200 TapeStation and Qubit® 2.0 (Life Technologies). Sequencing was performed by RiboBio Co., Ltd. on an Illumina HiSeq 3000 machine with paired-end 150-bp reads. The adaptors and low quality bases assessed using FASTQC 0.11.3 were trimmed by Trimmomatic 0.39 using the following options: TRAILING:20, MINLEN:235 and CROP:235. Trimmed reads were then aligned to the ensembl 79 (GRCh38.p2) reference genome using STAR 2.4.2a. FeatureCounts 1.6.2 was subsequently employed to convert aligned short reads into read counts for each sample. Genes with less than ten counts in two or more samples were removed. The data were then analyzed using R 3.4.4 and DEseq2 1.18.1. Differentially expressed genes of each disease group were identified using Wald statistics test, with fold-change > 2 and Benjamini–Hochberg (BH)-adjusted P < 0.1 as compared to NC group.
Results: These findings provide novel pathogenic links and molecular markers for better understanding and differential diagnosis of pulmonary TB, LUAD and sarcoidosis.
Overall design Lung Tissue mRNA profiles of NM, TB, LUAD and sarcoidosis diseases were generated by RNAseq, in five replicates, using Illumina Hiseq 3000.
Contributor(s) Chai Q, Lu Z, Liu Z, Zhong Y, Zhang F, Qiu C, Li B, Wang J, Zhang L, Pang Y, Liu C
Citation(s) 33097805
BioProject PRJNA609278
Submission date Apr 03, 2020
Last update date Nov 02, 2020
Contact name lu z
Organization name institution of microbology
Lab liuch
Street address beijing
City beijing
State/province - 选择 -
ZIP/Postal code 10010
Country China
Platforms (1)
GPL21290 Illumina HiSeq 3000 (Homo sapiens)
Samples (20)
GSM4452862 Normal Lung Tissue Rep1
GSM4452863 Normal Lung Tissue Rep2
GSM4452864 Normal Lung Tissue Rep3
SRA SRP251945

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE148036_PRJNA609278count_matrix.txt.gz 1.1 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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