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Sample GSM1521351 Query DataSets for GSM1521351
Status Public on Nov 24, 2014
Title chip 3991 replicate B sort S0
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 SAMN03100085
SRA SRX729375

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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