|
| Status |
Public on Oct 01, 2018 |
| Title |
A_mk12 (rna-seq) |
| Sample type |
SRA |
| |
|
| Source name |
ATRX mutated PanNET
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Pancreatic Neuroendocrine Tumors
genotype: ATRX
tumor in specimen: Lymph Node
pannet subtype: A-D-M Mutant PanNETs
phenotype: Well Differentiated PanNETs
cell type: pancreatic neuroendocrine Islet cells
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted with TRIzol reagent following the recommendations of the manufacturer.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
2 x 76 paired end sequence reads
|
| Data processing |
Raw fastq files were probed for sequencing quality control using FastQC. Sequencing reads were mapped to human transcripts corresponding to Genepattern genome (hg19 version) GTF annotations using RSEM with default parameters. RSEM package was used to prepare the reference genome with given GTF and calculated expression from mapped BAM files. STAR aligner was used to map reads in RSEM algorithm. Transcripts mapped data were normalized to TPM (Transcript Per Million) from RSEM and log2 transformed (Supplementary file). This log2 (x+1) TPM normalized values were used for all downstream analysis.
Genome_build: UCSC hg19
Supplementary_files_format_and_content: log2 (x+1) TPM normalized values for each sample using RSEM and STAR
|
| |
|
| Submission date |
Aug 01, 2018 |
| Last update date |
Oct 01, 2018 |
| Contact name |
SAURABH V LADDHA |
| E-mail(s) |
[email protected]
|
| Organization name |
Rutgers Cancer Institute of New Jersey
|
| Department |
Center for Systems and Computational Biology
|
| Street address |
195 Little Albany Street
|
| City |
New Brunswick |
| State/province |
NEW JERSEY |
| ZIP/Postal code |
08901-1914 |
| Country |
USA |
| |
|
| Platform ID |
GPL11154 |
| Series (2) |
| GSE117853 |
Gene expression and methylation profile of Human non-functional Pancreatic neuroendocrine tumors (PanNETs) |
| GSE118014 |
Transcriptome of human non-functional pancreatic neuroendocrine tumors (PanNETs) |
|
| Relations |
| BioSample |
SAMN09755745 |
| SRA |
SRX4498235 |
