Experiment summary for ENCSR067AUG
doi:10.17989/ENCSR067AUG
Superseded by ENCSR598GKQ
Summary
- Status
- archived
- Assay
- shRNA knockdown followed by RNA-seq (shRNA RNA-seq)
- Target
- DDX59
- Biosample summary
- Homo sapiens HepG2 expressing RNAi targeting H. sapiens DDX59
- Biosample Type
- cell line
- Replication type
- isogenic
- Description
- shRNA knockdown against DDX59 in HepG2 cells followed by RNA-seq. (DDX59_BGHLV18)
- Nucleic acid type
- polyadenylated mRNA
- RNA integrity number
- 9.3 [1-1]9.5 [2-1]
- Size range
- >200
- Extraction method
- Maxwell 16 LEV simpleRNA Cells Kit (Promega cat#: AS1270)
- Fragmentation methods
- chemical (Illumina TruSeq)
- Size selection method
- SPRI beads
- Strand specificity
- Strand-specific (reverse)
- Spike-ins datasets
- ENCSR449DXG
- Platform
- Illumina HiSeq 2000
- Controls
Attribution
ENCODE3 project
- Lab
- Brenton Graveley, UConn
- Award
- U54HG007005 (Brenton Graveley, UConn)
- Project
- ENCODE
- External resources
- References
- Aliases
- brenton-graveley:DDX59_BGHLV18
- Date submitted
- December 11, 2014
- Date released
- December 17, 2014
- Submitter comment
- KD% too low (27, 39.3) and a better KD experiment has been submitted (ENCSR598GKQ, brenton-graveley:DDX59_BGHLV35)
- Tags
Isogenic replicates
Isogenic replicate | Technical replicate | Summary | Biosample | Modifications | Library |
|---|---|---|---|---|---|
| 1 | 1 | Homo sapiens HepG2 cell line expressing RNAi targeting H. sapiens DDX59 | ENCBS542DRS | ENCGM115OVT | ENCLB641COQ |
| 2 | 1 | Homo sapiens HepG2 cell line expressing RNAi targeting H. sapiens DDX59 | ENCBS157CAN | ENCGM115OVT | ENCLB347AZD |