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Sample GSM2738552 Query DataSets for GSM2738552
Status Public on Oct 03, 2017
Title CMC-_Rep1
Sample type SRA
 
Source name HEK293T cells
Organism Homo sapiens
Characteristics genotype: wild type
Growth protocol HEK293T cells were maintained in DMEM medium supplemented with 10% FBS and 1% penicillin/streptomycin and grown at 37 ℃ with 5% CO2.
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.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model HiSeq X Ten
 
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
 
Submission date Aug 10, 2017
Last update date May 15, 2019
Contact name Chengqi Yi
E-mail(s) chengqi.yi@pku.edu.cn
Organization name Peking University
Street address 5 Yiheyuan Road, Haidian District
City Beijing
ZIP/Postal code 100871
Country China
 
Platform ID GPL20795
Series (1)
GSE102476 A radiolabeling-free, qPCR-based method for locus-specific pseudouridine detection
Relations
BioSample SAMN07489200
SRA SRX3084936

Supplementary file Size Download File type/resource
GSM2738552_Stat_CMC-_rep1.txt.gz 171.8 Kb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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