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| Status |
Public on Oct 03, 2017 |
| Title |
18S rRNA 1045+1056_CMC+ |
| Sample type |
SRA |
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| Source name |
HEK293T cells
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| Organism |
Homo sapiens |
| Characteristics |
genotype: wild type
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| Growth protocol |
HEK293T cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin and grown at 37 ℃ with 5% CO2.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted, fragmented and then CMC-reacted or mock-treated, followed by developed reverse transcription using our method. The RT-PCR products of specific qPCR amplicons were subjected to high-throughput sequencing.
Libraries were prepared using NEBNext® Ultra II DNA Library Prep Kit. Briefly, DNA was end-repaired by an enzyme mix to yield a protruding 3'- 'A' base for ligation with our in-house synthesized adaptors which have a single 'T' base overhang at the 3’ end. After adaptor ligation, DNA was PCR amplified with Illumina primers for 15 cycles, followed by size-selection and purification using AMPure XP beads (New England Biolabs). Libraries were sequenced on Illumina HiSeq X Ten with double end reads (150 bp).
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
HiSeq X Ten |
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| Data processing |
Sequenced reads were trimmed for low-quality reads, adaptor sequences, and paired reads without any adaptor sequence(as our insert is only 65-85 bp).
Duplicative reads were removed according to their unique molecular identifier (6 random bases adjacent to each side of insert added during adaptor ligation: 5'-CGCGNNNNNNACT-3').
The remaining reads were mapped with Bowtie2 to the human mRNA or lncRNA reference (downloaded from NCBI).
Misincorporation information were analyzed based on translated Pileup files.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include numbers of miscorporation events of different types at each site on the reference
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| Submission date |
Sep 22, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Chengqi Yi |
| E-mail(s) |
chengqi.yi@pku.edu.cn
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| Organization name |
Peking University
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| Street address |
5 Yiheyuan Road, Haidian District
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| City |
Beijing |
| ZIP/Postal code |
100871 |
| Country |
China |
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| Platform ID |
GPL20795 |
| Series (1) |
| GSE102476 |
A radiolabeling-free, qPCR-based method for locus-specific pseudouridine detection |
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| Relations |
| BioSample |
SAMN07689085 |
| SRA |
SRX3206866 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2790961_Stat_18S_rRNA_1045+1056_CMC+.txt.gz |
2.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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