Experiment summary for ENCSR047QHX
doi:10.17989/ENCSR047QHX
Superseded by ENCSR544ZCR
Summary
- Status
- archived
- Assay
- shRNA knockdown followed by RNA-seq (shRNA RNA-seq)
- Target
- SF3B1
- Biosample summary
- Homo sapiens K562 expressing RNAi targeting H. sapiens SF3B1
- Biosample Type
- cell line
- Replication type
- isogenic
- Description
- RNA-seq on K562 cells treated with an shRNA knockdown against SF3B1. (SF3B1_BGKLV36)
- Nucleic acid type
- polyadenylated mRNA
- RNA integrity number
- 9.7
- 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
- ENCSR358OMW
- Platform
- Illumina HiSeq 2500
- Controls
Attribution
ENCODE3 project
- Lab
- Brenton Graveley, UConn
- Award
- U54HG007005 (Brenton Graveley, UConn)
- Project
- ENCODE
- External resources
- References
- Aliases
- brenton-graveley:SF3B1_BGKLV36
- Date submitted
- December 12, 2016
- Date released
- January 4, 2017
- Gene Silencing Series
- ENCSR406ZEB
- Submitter comment
- As of November 2022, this dataset is superseded by ENCSR544ZCR, which has a better knockdown rate.
- Tags
Isogenic replicates
Isogenic replicate | Technical replicate | Summary | Biosample | Modifications | Library |
|---|---|---|---|---|---|
| 1 | 1 | Homo sapiens K562 cell line expressing RNAi targeting H. sapiens SF3B1 | ENCBS389KTJ | ENCGM914QKZ | ENCLB240VJU |
| 2 | 1 | Homo sapiens K562 cell line expressing RNAi targeting H. sapiens SF3B1 | ENCBS357WVC | ENCGM914QKZ | ENCLB835DSY |