 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Aug 01, 2020 |
| Title |
2704Cont |
| Sample type |
SRA |
| |
|
| Source name |
ishikawa cells
|
| Organism |
Homo sapiens |
| Characteristics |
transfection: control
|
| Treatment protocol |
Ishikawa cells were plated in 6-well plates at a density of 200,000 cells per well in 2% (v/v) FBS, 0.25% L-Glutamine and 1% antibiotic/antimycotic solution . Ishikawa cells were transfected with plasmid DNA (11ng/ul) encoding human NFAT5 in pcDNA6V5-HisC vector or empty vector plasmid by using VIROMER RED (#230155, Biozym, Germany) according to the manufacturer’s protocol for 24h.
|
| Growth protocol |
A well differentiated endometrial carcinoma cell line (Ishikawa cells, ECACC #99040201, Sigma Aldrich) was cultured in a humidified atmosphere of 5% CO2 at 37 ºC in Dulbecco’s modified Eagle’s medium F-12 (DMEM: F12) phenol free supplemented with 10% (v/v) FBS, 1% antibiotic/antimycotic solution and 0.25% L-Glutamine (Invitrogen, Germany), which was replenished every 48h. Cells were passaged when the confluency reached at 80%. When performing experiments, cells were cultured in DMEM: F12 phenol free supplemented with 2% (v/v) FBS, 0.25% L-Glutamine and 1% antibiotic/antimycotic solution overnight. .
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA samples were extracted by using miRNeasy Mini kit (QIAGEN, Germany) according to the manufacturer’s protocol. RNA concentration and quality were measured by using a Nanodrop (Eppendorf µCuvette® G1.0, Microvolume measuring cell for Eppendorf BioPhotometer® and BioSpectrometer®, Eppendorf, Germany). RNA quality was assessed with an Agilent 2100 Bioanalyzer system. Samples with high RNA integrity number >8 were selected for library construction.
Sequencing libraries have been prepared with New England Biolabs NEBNext Ultra II Directional RNA Library Prep following the manufacturer's handbook.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Basecalling of raw sequencing output was performed with Illumina bcl2fast2 version 2.19.1.
For subsequent adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_06 was used.
Cleaned read sequences were aligned with STAR version 2.5.4a
Read counting for exonic regions was performed with subread featureCounts version 1.6.0.
Genome_build: GRCh37
Supplementary_files_format_and_content: Raw count data in featureCounts default output format, see description at http://bioinf.wehi.edu.au/subread-package/SubreadUsersGuide.pdf
|
| |
|
| Submission date |
Jul 15, 2019 |
| Last update date |
Aug 02, 2020 |
| Contact name |
Jakob Admard |
| Organization name |
Universitätsklinikum Tübingen
|
| Department |
Institut für Medizinische Genetik und Angewandte Genomik
|
| Street address |
Calwerstr. 7
|
| City |
Tübingen |
| ZIP/Postal code |
72076 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE134319 |
NFAT5-sensitive upregulation of COX2 in endometrial ishikawa cells |
|
| Relations |
| BioSample |
SAMN12280517 |
| SRA |
SRX6449319 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3942125_I18R031b01_01_counts_raw.tsv.gz |
4.8 Mb |
(ftp)(http) |
TSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
