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| Status |
Public on Feb 19, 2019 |
| Title |
HepG2_RNASeq_CsA_Rep1 |
| Sample type |
SRA |
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| Source name |
hepatocarcinoma (HepG2) cell
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| Organism |
Homo sapiens |
| Characteristics |
tissue: HepG2 cells
cell type: hepatocarcinoma
treatment: CsA treatment
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| Treatment protocol |
HepG2 cells were either cultured as above under proliferating conditions, or cultured with 10 µM CsA (Sigma-Aldrich) for 72 h before harvesting for analyses.
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| Growth protocol |
HepG2 cells were cultured in DMEM/F12 with 10% fetal calf serum and 1% penicillin-streptomycin.
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| Extracted molecule |
total RNA |
| Extraction protocol |
RNA-Seq: Total RNA from 2 replicates of HepG2 treated and untreated cells were extracted using the RNeasy Mini Kit (Qiagen). DNase treatment was performed with RQ1 RNase-Free DNase (M101, Promega).
The ChIP-seq and RNA-seq sequencing libraries were prepared according to Illumina protocols for the HSeq2500 at the Norwegian Sequencing Center.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
RNA-seq was processed using the tuxedo protocol
Differential gene expression determined using cuffdiff v2.2.1 against the hg19 reference genome, (last update of RefGene.gtf july 2018)
processed data files format and content: fpkm_tracking files with 13 columns tracking_id, class_code, nearest_ref_id, gene_id, gene_short_name, tss_id, locus, length, coverage, FPKM, FPKM_conf_lo, FPKM_conf_hi, FPKM_status
Genome_build: hg19
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| Submission date |
Sep 07, 2018 |
| Last update date |
Feb 19, 2019 |
| Contact name |
Philippe Collas |
| Organization name |
University of Oslo
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| Department |
Institute of Basic Medical Sciences
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| Street address |
PO Box 1112 Blindern
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| City |
Oslo |
| ZIP/Postal code |
0317 |
| Country |
Norway |
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| Platform ID |
GPL16791 |
| Series (1) |
| GSE119631 |
Characterization of the dynamics of lamin A and lamin B LADs in HepG2 cells: impact of cyclosporin A |
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| Relations |
| BioSample |
SAMN09989370 |
| SRA |
SRX4654324 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3379702_HepG2_RNASeq_CsA_Rep1_Cufflink_genes.fpkm_tracking.gz |
766.2 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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