|
| Status |
Public on May 02, 2024 |
| Title |
TNBU1 |
| Sample type |
SRA |
| |
|
| Source name |
HK2 cells treated with butyrate (3mM) 24h after stimulation with TNF-α 5ng/ml 3h
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: HK2
|
| Treatment protocol |
Cell were stimulated with thapsigargin (4 μM) in absence or presence of JQ1 (500nM) for 24h
|
| Growth protocol |
human epithelial renal cell line (HK2) (CRL-2190; ATCC) were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% penicillin/ streptomycin, 1% insulin transferrin selenite and 5ng/ml hydrocortisone.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
PureLink TM RNA Mini kit (Invitrogen), with Dnase treatment. Total RNA was eluted in RNase-free water
Sequencing libraries were prepared following the protocol "TruSeq Stranded mRNA Sample Preparation Guide(Part#15031047Rev.E)" with the “TruSeq® Stranded mRNA Library Prep” kit (Illumina Inc. Cat. # 20020594) and TruSeq RNA Single Indexes (Illumina Inc. Cat. # 20020492 and 20020493)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Raw reads were analyzed for data quality using FastQC v0.11.5 (Babraham Bioinformatics) and filtered using skewer v0.2.2 (Jiang et al., 2014) for removing the low quality reads and trimming the Illumina adapter
Mapping of the reads were obtained using the STAR program (Dobin et al., 2013) (v2.6.1a_08-27) against human genome (GRCh38) and the quantification of genes and transcripts were done with the RSEM program using GENCODE.v26 database .
Assembly: GRCh38.94
|
| |
|
| Submission date |
Dec 21, 2022 |
| Last update date |
May 02, 2024 |
| Contact name |
Ana Maria Aransay |
| E-mail(s) |
amaransay@cicbiogune.es
|
| Phone |
0034944061325
|
| Organization name |
CIC bioGUNE
|
| Department |
Genome Analysis Platform
|
| Street address |
Parque tecnologico de Bizkaia, Building 801-A
|
| City |
Derio |
| State/province |
BIZKAIA |
| ZIP/Postal code |
48160 |
| Country |
Spain |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE221506 |
Propionate and butyrate counteract renal damage and progression to chronic kidney disease |
|
| Relations |
| BioSample |
SAMN32348523 |
| SRA |
SRX18804743 |
