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Status |
Public on Mar 02, 2020 |
Title |
CN3 |
Sample type |
SRA |
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Source name |
colorectal cancer adjacent tissue
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Organism |
Homo sapiens |
Characteristics |
tissue: adjacent tissue
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Extracted molecule |
total RNA |
Extraction protocol |
Total RNA enriched in small RNA population was extracted using miRNeasy kit (Qiagen) as per the manual’s protocol. RNA libraries were constructed for sequencing using standard Illumina protocols
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Library strategy |
miRNA-Seq |
Library source |
transcriptomic |
Library selection |
size fractionation |
Instrument model |
Illumina HiSeq 2500 |
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Data processing |
The raw sequencing reads were subjected to the Illumina pipeline filter (Solexa 0.3), and the dataset was then further processed using an in-house program, ACGT101-miR (LC Sciences, Houston, TX, United States) to remove adapter dimers, low complexity reads, common RNA families (rRNA, tRNA, snRNA, snoRNA), repeats in the NCBI GenBank1, Repbase2, and Rfam3) databases. the remaining non-annotated sequences were mapped to specific species precursors in miRbase 21.04 by BLAST searches to identify known miRNAs. On the basis of sequence similarity to human genome, these miRNA sequences were classified into subgroups 1a, 1b, 2a, 2b, and 3 with high-to-mid confidence in order All non-annotated reads with lengths of 18–25 nt were mapped to the reference genome sequences using the Bowtie package; only perfectly matched sRNAs were used in further analyses. Novel miRNAs were identified using the MIREAP software based on their precursors, and the hairpin RNA structures containing sequences were predicated from the flanking 120 nt sequences using RNAfold software. Genome_build: mm8 Supplementary_files_format_and_content: tab-delimited text files including RPKM values for each sample
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Submission date |
Jan 31, 2019 |
Last update date |
Mar 02, 2020 |
Contact name |
Fangbin Zhou |
E-mail(s) |
[email protected]
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Phone |
+8618801768978
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Organization name |
Tongji University School of Medicine
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Street address |
Siping Road 1239
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City |
Shanghai |
State/province |
State... |
ZIP/Postal code |
200092 |
Country |
China |
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Platform ID |
GPL16791 |
Series (1) |
GSE125961 |
Identification of miRNAs and Their targets in Colorectal Cancer (miRNA) |
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Relations |
BioSample |
SAMN10853053 |
SRA |
SRX5316203 |
Supplementary data files not provided |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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