Experiment summary for ENCSR239BCO
doi:10.17989/ENCSR239BCO
Summary
- Status
- archived
- Assay
- shRNA knockdown followed by RNA-seq (shRNA RNA-seq)
- Target
- PTBP1
- Biosample summary
- Homo sapiens K562 expressing RNAi targeting H. sapiens PTBP1
- Biosample Type
- cell line
- Replication type
- isogenic
- Description
- shRNA knockdown against PTBP1 in K562 cells followed by RNA-seq
- Nucleic acid type
- RNA
- RNA integrity number
- 10
- Depleted in
- rRNA
- Size range
- >200
- Extraction method
- Trizol
- 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:K-PTBP1
- Date submitted
- May 14, 2014
- Date released
- June 30, 2014
- Gene Silencing Series
- ENCSR996MPK
- Submitter comment
- This dataset is superseded by ENCSR527IVX, which used a transduction protocol.
- Tags
Isogenic replicates
Isogenic replicate | Technical replicate | Summary | Biosample | Modifications | Library |
|---|---|---|---|---|---|
| 1 | 1 | Homo sapiens K562 cell line expressing RNAi targeting H. sapiens PTBP1 | ENCBS947VKK | ENCGM637CPI | ENCLB995SHP |
| 2 | 1 | Homo sapiens K562 cell line expressing RNAi targeting H. sapiens PTBP1 | ENCBS494YUP | ENCGM637CPI | ENCLB478LKK |