|
| Status |
Public on Sep 19, 2012 |
| Title |
Control 48h - Adenoma 2 |
| Sample type |
SRA |
| |
|
| Source name |
Parathyroid adenoma
|
| Organism |
Homo sapiens |
| Characteristics |
patient: 2
tissue: Parathyroid tumor
agent: Control
time: 48h
|
| Treatment protocol |
cells were plated and treated with 100 nM DPN (Tocris Bioscience), or 100 nM OHT (Sigma-Aldrich, Stockholm, Sweden) for 24h or 48h, respectively. Untreated cells cultured in parallel were used as controls.
|
| Growth protocol |
Tissue for cell culturing was obtained from four parathyroid adenomas collected directly at surgery. All samples were from female, postmenopausal patients with chief cell adenoma with no preoperative signs of malignancy or kidney failure. Isolation of cells and cell culturing were performed essentially as previously described by Lu et al. In brief, tissues were cut and digested into cells with 1.5 mg/mL collagenase type II. About 1×106 cells were plated
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Illumina TruSeq RNA
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
Sample 8
|
| Data processing |
Base-calling was done with Illumina's Offline Base Caller (OLB) v.1.9.
Alignment to reference genome was done with TopHat v1.0.14.
Duplicates were removed using Picard (v. 1.29) MarkDuplicates.
Read counts per gene were calculated with HTSeq v. 0.5.1.
FPKM values for genes and transcripts were calculated with Cufflinks v. 1.0.3.
Differential expression analysis was performed using the edgeR package and subsequent custom filtering
Genome_build: hg19
Supplementary_files_format_and_content: count_table.txt: tab separated text file (read counts per ENSEMBL gene)
Supplementary_files_format_and_content: fpkm_table.txt: tab separated text file (FPKM per ENSEMBL gene)
|
| |
|
| Submission date |
Apr 12, 2012 |
| Last update date |
May 15, 2019 |
| Contact name |
Mikael Huss |
| E-mail(s) |
mikael.huss@scilifelab.se
|
| Organization name |
Science for Life Laboratory Stockholm
|
| Street address |
Tomtebodav. 23A
|
| City |
Solna |
| ZIP/Postal code |
17165 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL11154 |
| Series (1) |
| GSE37211 |
DPN and Tamoxifen treatments of parathyroid adenoma cells |
|
| Relations |
| SRA |
SRX140510 |
| BioSample |
SAMN00854916 |
