|
| Status |
Public on Feb 26, 2019 |
| Title |
ATP7B KO Hep G2 cells treated with Cu, biological rep3 |
| Sample type |
SRA |
| |
|
| Source name |
ATP7B KO Hep G2 cells
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: Hep G2
genotype/variation: ATP7B KO
treatment: treated with Cu
|
| Treatment protocol |
Both ATP7B KO Hep G2 cells and control HepG2 cells were incubated with Cu for 24h and then total RNA was extracted
|
| Growth protocol |
ATP7B-KO and control HepG2 cells were incubated with Cu for 24h and their transcriptional responses to the metal were analyzed using QuantSeq 3’ mRNA sequencing
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Extraction of total RNA was performed according to the manufacturer's instructions (Qiagen).
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Transcriptome profile of ATP7B KO Hep G2 cells treated with Cu, biological rep3
|
| Data processing |
Reads were aligned and assigned to Human Gencode release 19 transcripts and genes by using STAR 2.3.0 with Htseq-count
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample
|
| |
|
| Submission date |
Nov 24, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Annamaria Carissimo |
| E-mail(s) |
carissimo@tigem.it
|
| Organization name |
Tigem
|
| Street address |
via Castellino
|
| City |
Napoli |
| ZIP/Postal code |
80131 |
| Country |
Italy |
| |
|
| Platform ID |
GPL18573 |
| Series (1) |
| GSE107323 |
Transcriptome profile of ATP7B KO cells and WT cells treated with Copper (Cu) to study Autophagy as a pro-survival mechanism in Wilson disease |
|
| Relations |
| BioSample |
SAMN08097622 |
| SRA |
SRX3421807 |
