|
| Status |
Public on Aug 26, 2016 |
| Title |
6Ar Untreated cells rep1 |
| Sample type |
SRA |
| |
|
| Source name |
K562 with B2M:tdTomato transgene
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: K562
|
| Treatment protocol |
K562 cells were treated with a cocktail of three plasmid each encoding for a different ATR. We used 1 ug of palsmid encoding for D3A-based ATR and then normalized the amount of the others plasmids to obtain a 1:1 molar ratio. For dCas9 based ATR treatment we used 250 ng of plasmid encoding for sgRNA.
|
| Growth protocol |
K562 cells were grown in IMDM (Sigma) 10% Fetal Bovine Serum (EuroClone) and 1% Pennicillin/Streptomycin (100 U/ml final concentration; EuroClone). Cells were routinely splitted every 3 days at a concentration of 10^5 cells/ml without allowing them to reach concentration higher than 8^105 cells/ml
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with Qiagen Kit (Cat. 74134, respectively) according to manifacturer's instructions.
Amplification of cDNA from total RNA was performed using the Ovation Human FFPE RNA-seq Library System (Nugen), cDNA was fragmented with E220 COVARIS ultrasonicator (Covaris).
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
6Ar
|
| Data processing |
Reads were aligned to reference genome using STAR v2.3.0
Features were counted using Rsubread; gencode v19 was used as gene model; reads were summarized at gene level
Genome_build: hg19
Supplementary_files_format_and_content: broadPeak. Features identified for MeDIP-seq samples
Supplementary_files_format_and_content: abundance measurements: raw read counts over merged features (meDIP-seq) or genes (RNA-seq)
|
| |
|
| Submission date |
May 24, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Davide Cittaro |
| E-mail(s) |
[email protected]
|
| Organization name |
Ospedale San Raffaele
|
| Department |
Center for Traslational Genomics and Bioinformatics
|
| Street address |
via Olgettina 58
|
| City |
Milano |
| ZIP/Postal code |
20138 |
| Country |
Italy |
| |
|
| Platform ID |
GPL16791 |
| Series (1) |
| GSE81826 |
Inheritable Silencing of Endogenous Genes by Hit-and-Run Targeted Epigenetic Editing |
|
| Relations |
| BioSample |
SAMN05171613 |
| SRA |
SRX1797755 |
