|
| Status |
Public on Nov 23, 2016 |
| Title |
01-02s-Normal |
| Sample type |
SRA |
| |
|
| Source name |
Colon tissue biopsy during colonoscopy
|
| Organism |
Homo sapiens |
| Characteristics |
patient #: #01
biopsy #: #02
tissue: biopsied normal colon
mutation: --
cell type: laser capture microdissected stromal cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
OCT-embedded colon biopisies were sectioned at 9-um thickness onto PEN membrance slides and subjected to LCM of stromal and epithelial cells onto separate caps. RNA was extracted from caps using Picopure RNA isolation kit following manufacturer's protocols. Half of extracted RNA was used for each library preparation panel
RNA libraries were prepared for sequencing using standard IonTorrent RNA Ampliseq protocols for two separate panels (Apoptosis and custom Senesence). Libraries were barcoded with IonXpress Adapters.
Targetted RNA-seq, Barcoded (provided in the barcode.txt) to run 4 samples per 318 chip
each raw data file is named as 'Patient#-Biopsy#-Epithelia/Stroma-Apoptosis/Senescence Panel-ACF/Normal' and the original file names (associated with each sample)/their checksums are included in the barcode.txt.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Ion Torrent PGM |
| |
|
| Description |
Each biopsy specimen requires four separate library preps: epithelia, stroma and two RNA Ampliseq Panels
|
| Data processing |
IonTorrent Suite (v4.4) for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, mapped to targetted regions using coverageAnalysis plugin and aligned to hg19_RNA_CanTran_v1
Total reads were normalized to one million per panel, and all samples were combined into one large processed datamatrix (possible pseudogenes were removed)
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text file with RPKM values for each sample panel
|
| |
|
| Submission date |
Jan 27, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Allen Mo |
| Organization name |
UConn Health
|
| Department |
Center for Molecular Medicine
|
| Lab |
Rosenberg
|
| Street address |
263 Farmington Avenue
|
| City |
Farmington |
| State/province |
CT |
| ZIP/Postal code |
06030-3101 |
| Country |
USA |
| |
|
| Platform ID |
GPL17301 |
| Series (1) |
| GSE77312 |
Profiling of epithelial and stromal cells in early proximal colon preneoplasia with matched normals. |
|
| Relations |
| BioSample |
SAMN04444956 |
| SRA |
SRX1549937 |
