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| Status |
Public on Aug 03, 2022 |
| Title |
N4_a549_siCTRL_rep4 |
| Sample type |
SRA |
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| Source name |
A549 treated with siCTRL condition
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| Organism |
Homo sapiens |
| Characteristics |
cell line: A549
treatment: siCTRL
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was obtained from A549 cell line. The size profiles of the individual libraries were analyzed with LabChip GX II using a DNA High Sensitivity kit (both PerkinElmer, USA). Libraries were quantified on a Qubit with the DNA High Sensitivity kit (Life Technologies).
Library preparation was performed using SMARTer smRNA-Seq kit (Clontech/Takara, USA) protocol with minor changes to increase the chance of identifying also pri-miR in addition to miRNAs.
RNA-Seq on a Illumina HiSeq 2500 instrument, in rapid run mode, using a 100-bp, dual-indexed, single-end sequencing configuration
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Basecalls performed using CASAVA (Illumina Inc.)
Transcript quantification was conducted with STAR (v2.5.3a) (assigned to a gene using using the STAR function “quantMode GeneCounts”) mapped to the human genome version GRCh38 and with reference annotation.
Read counts generated by STAR were analysed by using DESeq2 package (Love, 2014) for detecting genes that were differentially expressed. An adjusted p-value cut off of 0.05 was decided as threshold for detection of DEGs.
Genome_build: human genome version GRCh38 and with reference annotation.
Supplementary_files_format_and_content: tab-delimited text files include COUNTS values for each Sample
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| Submission date |
Feb 12, 2021 |
| Last update date |
Aug 03, 2022 |
| Contact name |
Silvano Piazza |
| E-mail(s) |
silvano.piazza@icgeb.org
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| Organization name |
ICGEB
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| Lab |
Computational Biology
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| Street address |
localita' Padriciano 99
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| City |
Trieste |
| ZIP/Postal code |
34149 |
| Country |
Italy |
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| Platform ID |
GPL16791 |
| Series (2) |
| GSE166664 |
APE1 controls DICER expression through functional regulation of miRNA33a: a novel hypothesis for NSCLC cancer progression [RNA-Seq] |
| GSE166750 |
APE1 controls DICER expression through functional regulation of miRNA33a: a novel hypothesis for NSCLC cancer progression |
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| Relations |
| BioSample |
SAMN17885743 |
| SRA |
SRX10085728 |
| 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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