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Status |
Public on Oct 03, 2017 |
Title |
CMC-_Rep3 |
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 with TRIzol. For dephosphorylation of 3' end, RNA fragments on C1 beads were first treated by FastAP enzyme and then by T4 PNK enzyme. 3' RNA linker ligation was performed with T4 RNA Ligase 1 high concentration. To remove excess adaptors, samples were washed five time, and then heated at 95 ℃ for 5 min to elute RNAs from beads followed by ethanol precipitation. Subsequently, the RNA was reverse transcribed with RT DNA primer, followed by ExoSAP treatment and cleanup with MyONE Silane beads. The cDNA product was subjected to 5' ligation with a second adaptor performed by T4 RNA Ligase 1 high concentration. cDNA ligated with 5' linker was purified by Silane beads and amplified by Index Primers, followed by cleanup and size-selection of PCR products using AMPure XP beads. Libraries were sequenced on Illumina HiSeq X Ten with double end reads.
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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 inline barcodes(10 random bases after the barcode added during the library construction at the 5' end of inserted sequences). Trimmed reads were mapped with Bowtie2 to the human rRNA reference. PCR duplications were removed according to the inline barcodes. 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 |
Aug 10, 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 |
SAMN07489198 |
SRA |
SRX3084938 |
Supplementary file |
Size |
Download |
File type/resource |
GSM2738554_Stat_CMC-_rep3.txt.gz |
173.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
Raw data are available in SRA |
Processed data provided as supplementary file |
Processed data are available on Series record |
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