 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jun 26, 2018 |
| Title |
OFAI-D8-02 |
| Sample type |
SRA |
| |
|
| Source name |
Adipocytes
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: SGBS
cell type: Simpson-Golabi-Behmel syndrome pre-adipocyte cell line
agonist treatment: (7E)-9-oxohexadec-7-enoic acid
differentiation day: Day 8
|
| Treatment protocol |
Human Simpson-Golabi-Behmel syndrome (SGBS) cells were differentiated into adipocytes essentially as described by Wabitsch et al., Int J Obes Relat Metab Disord 25:8-15, 2001. Briefly, cells were seeded at low passage (P6-P8) at 0.8×10e5 cells/well in 12-well plates and grown to confluence (day 0). From day 0 to day 4, the cells were exposed to adipogenic medium (Quickdiff; 3FC supplemented with 25 nM dexamethazone, 0.5 mM isobutylmethylxanthine, and 2 μM rosiglitazone, 25 μM (7E)-9-oxohexadec-7-enoic acid:BSA, or 25 μM (10E)-9-oxohexadec-10-enoic acid:BSA, followed by continuous culturing in 3FC (basal medium supplemented with 10 μg/mL human transferrin, 20 nM human insulin, 100 nM cortisol, and 0.2 nM triiodothyronine). Medium was renewed every fourth day.
|
| Growth protocol |
The SGBS cells were maintained in basal medium (DMEM/nutrient mix F-12; D6421, Sigma-Aldrich) supplemented with 2 mg/L of biotin, 1 mg/L of D-pantothenate, 4 mM L-glutamine, penicillin/streptomycin (50 U/mL; 50 μg/mL), and 10% non-inactivated fetal calf serum (F7524; Sigma-Aldrich).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated using the RNeasy Mini kit (#74104, Qiagen) with the following modifications: Lysates from cells with high-fat content, such as SGBS cells on day 8, were mixed 1:1 in 70% ethanol in high salt solution (0.45 M NaCl/0.24 M Na-acetate), before applied to the columns. RNA quality was assessed on a BioAnalyzer 2100, using the Agilent RNA 6000 Nano Kit (#5067-1511; Agilent Technologies Inc, Santa Clara, CA). The RIN values (RNA integrity number) varied between 9.80 and 10.00, with an average of 9.95.
Illumina sequencing libraries were prepared according to the strand-specific TruSeq RNA Sample Preparation Guide (revision D).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
processed data file: Sample RPKM data.xlsx
|
| Data processing |
For pre-alignment quality control the software FastQC v0.10.1 was used. The mean library size was ~18 million read pairs, with no difference between groups or time points.
Alignment of cDNA sequenced reads was done using Tophat v2.0.8, Samtools v0.1.18, and Bowtie v2.1.0 with default settings.
Reads were counted by Cufflinks v2.1.1 and presented as Reads Per Kilobase of transcript per Million mapped reads (RPKM).
Differentially expressed genes were identified using one-way ANOVA and an RPKM cut-off set to 5.
Genome_build: UCSC hg19 (GRCh37)
Supplementary_files_format_and_content: Sample_RPKM_data.xlsx: Excel file includes gene RPKM values for all samples.
Supplementary_files_format_and_content: QC_table.xlsx: Excel file includes quality control data for all samples.
|
| |
|
| Submission date |
Jun 14, 2018 |
| Last update date |
Jun 27, 2018 |
| Contact name |
Thomas Sæther |
| E-mail(s) |
thomas.sather@medisin.uio.no
|
| Organization name |
University of Oslo
|
| Department |
Dept. of Molecular Medicine
|
| Street address |
Sognsvannsveien 9
|
| City |
Oslo |
| State/province |
Oslo |
| ZIP/Postal code |
NO-0372 |
| Country |
Norway |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE115827 |
RNA-seq data from human SGBS adipocytes differentiated with marine oxohexadecenoic acids |
|
| Relations |
| BioSample |
SAMN09427496 |
| SRA |
SRX4218926 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
|
|
|
|
 |
