|
| Status |
Public on Apr 10, 2014 |
| Title |
NE CT1 |
| Sample type |
SRA |
| |
|
| Source name |
Illeum
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Illeum
tumor type: Small intestinal neuroendocrine tumor
donor age: 66
gender: Female
synaptofysin staining: +
chromogranin staining: +
serotonin staining: NA.
cd117 staining: NA.
ppp staining: NA.
vip staining: NA.
ghrelin staining: NA.
cka staining: +
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Immediately after tumor resection, tumor tissue samples from the surgical specimens were placed in RNAlater® for overnight incubation. Samples were subsequently stored at 80°C until RNA was extracted using TRIzol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Helicos HeliScope |
| |
|
| Description |
Tumor sample obtained from a patient undergoing surgery at the Department of Surgical Gastroenterology, Rigshospitalet.
|
| Data processing |
Ts at the begining of reads were trimmed from sequenced reads
Trimmed reads were mapped to the genome (hg19) with HeliSphere software using a seed length of 18nt and allowing only one mismatch in the seed region.
Only uniquely mapped reads with a minimum length of 21nt and a minimum score of 4 where further analyzed.
Reads arising from internal priming events were further discarded.
To identify polyA sites, read starts that were than 24nt apart were iteratively clustered. Cleavage sites were defined as the median position of the cleavage sites in the cluster.
Genome_build: hg19
Supplementary_files_format_and_content: Bed files of mapped reads
Supplementary_files_format_and_content: Bed files of polyA site clusters. The score represents the number of reads in each cluster.
|
| |
|
| Submission date |
Apr 09, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Mireya Plass |
| E-mail(s) |
mireya.plassportulas@mdc-berlin.de
|
| Organization name |
MDC-Berlin
|
| Street address |
Robert-Rössle Str. 10
|
| City |
Copenhagen |
| ZIP/Postal code |
13092 |
| Country |
Germany |
| |
|
| Platform ID |
GPL14761 |
| Series (1) |
| GSE56657 |
Alternative poladenylation of tumor suppressor genes in small intestinal neuroendocrine tumors |
|
| Relations |
| BioSample |
SAMN02724933 |
| SRA |
SRX514716 |
