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| Status |
Public on Dec 21, 2024 |
| Title |
CACO2shADAR1-2.Input |
| Sample type |
SRA |
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| Source name |
colorectum
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| Organism |
Homo sapiens |
| Characteristics |
tissue: colorectum
cell line: CACO2 Cell
cell type: cancer cell
genotype: ADAR1 knockdown
treatment: none
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| Extracted molecule |
total RNA |
| Extraction protocol |
We extracted total RNA using Trizol reagent (Invitrogen, California, USA) following the manufacturer's instructions. Use the Ribo-Zero rRNA Removal Kit (Illumina, Inc., CA, USA) to reduce rRNA content. The quality of RNA is assessed using its OD260/OD280 ratio, which is a measure of nucleotide-to-protein ratio based on optical density measured using spectrophotometry. RNA purity with OD260/OD280 values in the range of 1.8-2.1 is considered acceptable, and RNA extracted from all samples meets this standard.
Total RNA was cleaved into 100 base pair fragments using the GenSeqTM O8G RNA IP Kit (GenSeq Inc, China), followed by O8G immunoprecipitation using the NEBNext® Ultra II Directed RNA Library Preparation Kit (New England Biolaboratories, USA), followed by RNA-seq library generation.The cDNA library was evaluated using the Bioanalyzer 2100 System (Agilent Technologies USA) and the library was sequenced using an Illumina Hiseq instrument with 150 bp pairing readings.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 1500 |
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| Description |
Library name: treat2
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| Data processing |
Pairing reads were quality controlled using a quality criterion of 1/1000 (Q30) error base call probability in the Illumina HiSeq 4000 sequencer: Q30>80% indicates good sequencing quality. After quality control, trim the 3/adapter using Cutadapt software (v1.9.3) and remove low-quality reads, and harvest high-quality clean reads. Align a clean read of the input library with a reference genome (GRCh38.Geocoding v32) using STAR software (Domin et al., 2013) and identify mRNA peaks using DCC software(Cheng et al., 2016) . Next, align clean reads of all libraries with reference genomes using Hisat2 software (v2.0.4)(Kim et al., 2015). Identify o8G peaks on mRNA using MACS software(Zhang et al., 2008). In addition, different methylation peaks were identified using DiffReps software (Shen et al., 2013): o8G peaks with a fold change of >2 or <0.5 (P<0.00001) in CRC were considered to be up-regulated methylation or down-regulated methylation.(Shen et al., 2013)Peaks that overlap exons of protein-coding genes identified using software and o8G sections were selected using internally developed scripts for further annotation.
Assembly: hg19
Supplementary files format and content: excel format
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| Submission date |
Dec 19, 2024 |
| Last update date |
Dec 21, 2024 |
| Contact name |
Yu Lin |
| E-mail(s) |
[email protected]
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| Phone |
020-62787911
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| Organization name |
Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital
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| Street address |
No. 1838, Guangzhou Dadao North, Baiyun District, Guangzhou
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| City |
Guangzhou |
| State/province |
China |
| ZIP/Postal code |
510515 |
| Country |
China |
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| Platform ID |
GPL18460 |
| Series (1) |
| GSE284992 |
Overview of distinct 8-Oxoguanine profiles of messenger RNA in normal and senescent cancer cells |
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| Relations |
| BioSample |
SAMN45912800 |
| SRA |
SRX27143968 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
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