|
| Status |
Public on Nov 24, 2014 |
| Title |
chip 3991 replicate A sort S1 |
| Sample type |
SRA |
| |
|
| Source name |
ERC Cell Line Infected with Chip 3991
|
| Organism |
synthetic construct |
| Characteristics |
host organism: Gallus gallus
host cell line: ERC
shRNA type: shRNA Guide Sequences
|
| Treatment protocol |
From Fellmann et al Mol Cell 2011: ERC reporter cells were infected with pSENSOR libraries at singly copy and sorted in iterative cycles, either after treatment with Dox and G418 (500 μg/ml) for 6–7 days (OnDox) or after Dox and G418 withdrawal for 6–7 days (OffDox). The gating was guided by reference cells transduced with small pools of potent (Top5) and weak (Bottom5) control shRNA-Sensor constructs.
|
| Growth protocol |
DMEM supplemented with 10% FBS, 1 mM sodium pyruvate, 100 U/ml penicillin, and 100 μg/ml streptomycin
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was isolated using the QIAamp DNA Blood Maxi Kit (Qiagen)
Libraries were constructed by PCR of the shRNA guides from the infected cells genomes. PCR primers were tailed with illumina addapter sequences.
|
| |
|
| Library strategy |
OTHER |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina Genome Analyzer II |
| |
|
| Data processing |
1: Reads were aligned to sensor construct target sequences using bowtie (allowing zero mismatches)
2: Reads were quantified with unix command uniq -c
3: Reads were normalized to have a sum of 1 for each sample.
4: Samples corresponding to sorts S1,S3 and S5 were log2 normalize by their corresopnding S0 reads.
5: Corresponding sorts were averaged across replicates
6: For each chip a matrix was constructed where rows correspond to shRNAs/targets and columns to the normalized values of sorts S1, S3 and S5. This is taken as the shRNA efficacy measurment.
Supplementary_files_format_and_content: Initial_Sensor_Summary has three fields for every construct assayed. Field 1: Human gene the shRNA is targeting. Field 2: The shRNA guide sequence. Field 3: The shRNA target sequence. Field 4: The calculated shRNA efficacy score
|
| |
|
| Submission date |
Oct 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Simon Robert Vincent Knott |
| Organization name |
Cold Spring Harbor Laboratory
|
| Department |
Biology
|
| Lab |
Hannon
|
| Street address |
1 Bungtown Rd
|
| City |
Cold Spring Harbor |
| State/province |
NY |
| ZIP/Postal code |
11724 |
| Country |
USA |
| |
|
| Platform ID |
GPL9423 |
| Series (2) |
| GSE62183 |
shRNA Sensor Analysis of DSIR Selected shRNAs |
| GSE62189 |
A computational algorithm to predict shRNA potency |
|
| Relations |
| BioSample |
SAMN03100082 |
| SRA |
SRX729372 |
