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| Status |
Public on Apr 03, 2012 |
| Title |
Patient16_smRNA-seq |
| Sample type |
SRA |
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| Source name |
tissue specimen
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| Organism |
Homo sapiens |
| Characteristics |
gender: M
age: 52
Stage: II
histologics: unknown
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| Extracted molecule |
total RNA |
| Extraction protocol |
The Miravana Kit (Ambion/Applied Biosystems, Foster City, CA, USA) was used to isolate total RNA according to the vendor’s protocol. The whole-transcriptome-sequencing (WT-seq) and small RNA-seq libraries were prepared using the small RNA expression kit (SREK, PN 4397682) of Applied Biosystems Inc. (ABI), based on SOLiD WT and small RNA standard protocols provided by ABI. The individual prepared “barcode” libraries were quantified and pooled equally together for multiplexing. The sequencing runs were performed on SOLiD v 3.0 for both WT-seq and small RNA-seq
WT-seq samples were sequenced in 1/4 slide per sample using 50-nucleotide (nt) single tags; and small RNA-seq samples were sequenced in 1/10 slide per sample using 35-nt single tags.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
size fractionation |
| Instrument model |
AB SOLiD System 3.0 |
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| Description |
smRNA-seq
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| Data processing |
WT-seq short reads were mapped to the human reference genome (hg19) and exon junctions (defined as RefSeq gene annotation) using the ABI BioscopeTM (version 1.21) WT-seq analysis pipeline with default parameters.
The reads mapped to the sequences that were not of biological interest, such as rRNAs, tRNAs, and repetitive elements, were first filtered. Then mapped reads with mapping SOLiD_native_quality ≥10 were defined as uniquely mapped reads and used in the downstream analysis.
The “reads per kilobase of exon per million mapped sequence reads” (RPKM) values of the human RefSeq genes were calculated using the RNA-seq flow in the Partek® Genomics Suite™ (version 6.5 beta, Partek Inc., St. Louis, MO, USA).
For the small RNA-seq dataset, the SOLiD System Small RNA Analysis Pipeline Tool (corona RNA2MAP version 0.50) was used: first, the reads mapped to the sequences of no biological interest were filtered, and then the remaining reads were mapped to annotated mature miRNAs (miRBase 13.0) and the human reference genome (key parameters: seed length = 18, seed error = 2, and maximum number of errors = 4).
MiRNA expression was quantified as reads per million (RPM) of reads mapped to known miRNAs.
Genome_build: hg19
Supplementary_files_format_and_content: GeneExpressionRPKM_30Sample_WT.xls; excel file; gene expression (in terms of RPKM) in 30 samples;
Supplementary_files_format_and_content: miRNAExpressionRPM_25Sample_smRNA.xls; excel file; miRNA expression (in terms of RPM) in 25 samples;
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| Submission date |
Mar 30, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Han Liang |
| E-mail(s) |
hliang1@mdanderson.org
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| Phone |
1-713-745-9815
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| Fax |
1-713-563-4242
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| Organization name |
University of Texas MD Anderson Cancer Center
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| Department |
Bioinformatics and Computational Biology
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| Lab |
Dr. Han Liang
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| Street address |
1400 Pressler Street
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platform ID |
GPL9442 |
| Series (1) |
| GSE36968 |
AMPKα Modulation in Cancer Progression: Multilayer Integrative Analysis of the Whole Transcriptome in Asian Gastric Cancer |
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| Relations |
| SRA |
SRX134902 |
| BioSample |
SAMN00848570 |
| Supplementary data files not provided |
SRA Run Selector |
| Processed data are available on Series record |
| Raw data are available in SRA |
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