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| Status |
Public on Dec 07, 2020 |
| Title |
N40A [RNA-seq] |
| Sample type |
SRA |
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| Source name |
Colorectal tissues_Normal tissue
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| Organism |
Homo sapiens |
| Characteristics |
tissue type: Colorectal tissues
differentiation stage: Normal tissue
tnm: Normal
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
Sample 2
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| 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
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| Submission date |
Jan 15, 2018 |
| Last update date |
Dec 07, 2020 |
| Contact name |
Zhu Hao |
| E-mail(s) |
zhuhao@smu.edu.cn
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| Phone |
8613533979750
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| Organization name |
Southern Medical University
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| Street address |
Shatai Road
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| City |
GuangZhou |
| ZIP/Postal code |
510515 |
| Country |
China |
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| 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 |
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| Relations |
| BioSample |
SAMN08366085 |
| SRA |
SRX3584946 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2935185_N40A_stringte_final.gtf.gz |
23.0 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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