MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq
Abstract
:1. Summary
2. Data Description
2.1. Quality Assessment of miRNA-Seq Data
2.2. Identification of Potential miRNA Biomarkers for Lung Adenocarcinoma
3. Methods
3.1. miRNA Extraction
3.2. miRNA Sequencing (miRNA-Seq)
3.3. miRNA-Seq Data Analysis
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Variables | Data |
---|---|
Age, years, median (range) | 71 (57–80) |
≤65 | 4 |
>65 | 6 |
Sex | |
Male | 3 |
Female | 7 |
Smoking status | |
Current | 1 |
Former | 0 |
Never | 9 |
Pathological TNM stage | |
I | 5 |
II | 3 |
≥III | 2 |
Histology | |
ADC | 10 |
WHO differentiation | |
Well | 2 |
Moderate | 6 |
Poor | 2 |
Vascular invasion | |
Yes/no | 1/9 |
Lymphatic invasion | |
Yes/no | 3/7 |
Perineural invasion | |
Yes/no | 1/9 |
Oncogenic alteration | |
EGFR mutation | 2 |
ALK fusion | 0 |
ROS1 fusion | 1 |
NA | 7 |
PD-L1 (22C3 pharmDx) | |
≥50% | 3 |
1–40% | 3 |
<1% | 4 |
Sample ID | Total Read Bases (bp) | Total Reads | GC (%) | AT (%) | * Q20 (%) | * Q30 (%) |
---|---|---|---|---|---|---|
B170406001GTV_N | 4,147,448,010 | 81,322,510 | 52.16 | 47.84 | 97.79 | 95.31 |
B170406001GTV_T | 3,550,079,400 | 69,609,400 | 52.42 | 47.58 | 97.7 | 95.14 |
B170906001GTV_N | 3,770,231,610 | 73,926,110 | 51.98 | 48.02 | 97.69 | 95.13 |
B170906001GTV_T | 3,875,673,141 | 75,993,591 | 51.81 | 48.19 | 97.6 | 94.91 |
LC1_N | 4,856,731,173 | 95,230,023 | 51.21 | 48.79 | 96.63 | 93.38 |
LC1_T | 5,010,892,647 | 98,252,797 | 51.82 | 48.18 | 96.15 | 92.29 |
LC16_N | 3,399,036,576 | 66,647,776 | 53.28 | 46.72 | 97.85 | 95.48 |
LC16_T | 3,308,668,656 | 64,875,856 | 51.34 | 48.66 | 97.6 | 95.16 |
LC17_N | 5,021,178,276 | 98,454,476 | 51.11 | 48.89 | 96.46 | 93.13 |
LC17_T | 4,987,210,185 | 97,788,435 | 50.44 | 49.56 | 96.55 | 93.23 |
LC25_N | 3,348,770,772 | 65,662,172 | 51.73 | 48.27 | 97.46 | 94.84 |
LC25_T | 3,505,634,124 | 68,737,924 | 51.74 | 48.26 | 97.55 | 95.1 |
LC27_N | 3,796,142,772 | 74,434,172 | 53.17 | 46.83 | 97.59 | 95.1 |
LC27_T | 3,871,575,444 | 75,913,244 | 51.13 | 48.87 | 97.69 | 95.39 |
LC28_N | 4,147,733,049 | 81,328,099 | 51.58 | 48.42 | 97.22 | 94.29 |
LC28_T | 3,516,179,751 | 68,944,701 | 52.21 | 47.79 | 97.56 | 95.13 |
LC36_N | 4,993,322,025 | 97,908,275 | 50.43 | 49.57 | 96.32 | 92.74 |
LC36_T | 3,435,999,540 | 67,372,540 | 51.43 | 48.57 | 97.77 | 95.3 |
LC37_N | 5,015,314,500 | 98,339,500 | 51.45 | 48.55 | 96.4 | 92.87 |
LC37_T | 3,364,431,291 | 65,969,241 | 52.99 | 47.01 | 97.56 | 94.77 |
This Study | GSE110907 | |||||||
---|---|---|---|---|---|---|---|---|
miRNA | Wx Score | Wx Ranking | log2FC | p-Value | Adjusted p-Value | log2FC | p-Value | Adjusted p-Value |
hsa-miR-21-5p | 1959.04 | 1 | 2.04 | 6.0166 × 10−8 | 3.9384 × 10−6 | 1.97 | 1.20584 × 10−75 | 4.68589 × 10−73 |
hsa-miR-182-5p | 10.63 | 24 | 2.00 | 3.4852 × 10−7 | 1.7683 × 10−5 | 2.59 | 1.54338 × 10−72 | 4.99798 × 10−70 |
hsa-miR-21-3p | 8.32 | 25 | 3.43 | 1.9516 × 10−12 | 1.4471 × 10−9 | 2.23 | 1.21784 × 10−59 | 2.62918 × 10−57 |
hsa-miR-375-3p | 1.23 | 41 | 1.62 | 2.7079 × 10−5 | 0.00068064 | 1.92 | 8.14185 × 10−28 | 3.22849 × 10−26 |
hsa-miR-1260b | 0.01 | 81 | 1.30 | 2.8204 × 10−5 | 0.00068568 | 1.19 | 5.25835 × 10−11 | 3.74248 × 10−10 |
hsa-miR-30a-5p | 506.47783 | 4 | −2.20 | 2.344 × 10−7 | 1.24148 × 10−5 | −2.20 | 3.47735 × 10−42 | 3.2174 × 10−40 |
hsa-miR-486-5p | 282.77259 | 8 | −1.91 | 1.3091 × 10−5 | 0.000413072 | −2.35 | 2.5355 × 10−24 | 7.6976 × 10−23 |
hsa-miR-126-5p | 23.869159 | 16 | −1.34 | 0.00080494 | 0.00856405 | −2.10 | 1.45179 × 10−56 | 2.5644 × 10−54 |
hsa-miR-126-3p | 11.193731 | 22 | −1.51 | 0.00237473 | 0.019350109 | −2.08 | 1.43505 × 10−47 | 1.9917 × 10−45 |
hsa-miR-195-5p | 0.1943744 | 55 | −1.23 | 0.00524937 | 0.035547075 | −1.02 | 1.65558 × 10−17 | 2.6153 × 10−16 |
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Park, J.; Na, S.J.; Yoon, J.S.; Kim, S.; Chun, S.H.; Kim, J.J.; Kim, Y.-D.; Ahn, Y.-H.; Kang, K.; Ko, Y.H. MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq. Data 2023, 8, 94. https://doi.org/10.3390/data8060094
Park J, Na SJ, Yoon JS, Kim S, Chun SH, Kim JJ, Kim Y-D, Ahn Y-H, Kang K, Ko YH. MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq. Data. 2023; 8(6):94. https://doi.org/10.3390/data8060094
Chicago/Turabian StylePark, Jihye, Sae Jung Na, Jung Sook Yoon, Seoree Kim, Sang Hoon Chun, Jae Jun Kim, Young-Du Kim, Young-Ho Ahn, Keunsoo Kang, and Yoon Ho Ko. 2023. "MicroRNA Profiling of Fresh Lung Adenocarcinoma and Adjacent Normal Tissues from Ten Korean Patients Using miRNA-Seq" Data 8, no. 6: 94. https://doi.org/10.3390/data8060094