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Sample GSM2935198 Query DataSets for GSM2935198
Status Public on Dec 07, 2020
Title T18A [RNA-seq]
Sample type SRA
 
Source name Colorectal tumor tissues_poorly-differentiated
Organism Homo sapiens
Characteristics tissue type: Colorectal tumor tissues
differentiation stage: poorly-differentiated
tnm: T3N2M0
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from tissues using Trizol (Invitrogen, Carlsbad, CA, USA) according to the manufacturer’s instructions. After DNase I treatment, Ribo-Zero Magnetic Kit is used to remove rRNA before constructing the RNA-seq libraries.By using the fragmentation buffer, the mRNAs and non-coding RNAs are fragmented into short fragments(about 200~500nt), then the first-strand cDNA is synthesized by random hexamer-primer using the fragments as templates, and dTTP is substituted by dUTP during the synthesis of the second strand. Short fragments are purified and resolved with EB buffer for end reparation and single nucleotide A (adenine) addition. After that, the short fragments are connected with adapters, then the second strand is degraded using UNG(Uracil-N-Glycosylase) finally. After agarose gel electrophoresis, the suitable fragments are selected for the PCR amplification as templates. During the QC steps, Agilent 2100 Bioanaylzer and ABI StepOnePlus Real-Time PCR System are used in quantification and qualification of the sample library.
RNA libraries were prepared for sequencing using standard Illumina protocols
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 2000
 
Description Sample 15
Data processing RNA-seq raw data were filtered using the following steps. We removed reads with sequence adaptors and reads with more than 10% ‘N’ bases, and further removed reads with more than 50% bases with QA ≤ 10.
RNA-seq clean data were mapped to hg19 using HISAT2(v.0.1.5)
Gene expression files were obtained using StringTie (1.2.2)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample
 
Submission date Jan 15, 2018
Last update date Dec 07, 2020
Contact name Zhu Hao
E-mail(s) zhuhao@smu.edu.cn
Phone 8613533979750
Organization name Southern Medical University
Street address Shatai Road
City GuangZhou
ZIP/Postal code 510515
Country China
 
Platform ID GPL11154
Series (2)
GSE109203 The Epigenetic dysregulation of lncRNA on gene expression in Colorectal tumor [RNA-seq]
GSE109204 The Epigenetic dysregulation of lncRNA on gene expression in Colorectal tumor
Relations
BioSample SAMN08366072
SRA SRX3584959

Supplementary file Size Download File type/resource
GSM2935198_T18A_stringte_final.gtf.gz 23.2 Mb (ftp)(http) GTF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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