GSM1521360: chip 4001 replicate B sort S1; synthetic construct; OTHER - SRA

SRX729384: GSM1521360: chip 4001 replicate B sort S1; synthetic construct; OTHER
1 ILLUMINA (Illumina Genome Analyzer II) run: 19.8M spots, 991.4M bases, 632.9Mb downloads

Submitted by: Gene Expression Omnibus (GEO)

Study: shRNA Sensor Analysis of DSIR Selected shRNAs

PRJNA263390 • SRP048751 • All experiments • All runs

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Purpose: Generate a large, high quality database of paired shRNA efficacy/sequence datapoints. Overall design: Methods:Twelve shRNAs for each Refseq annotated human gene were selected based on the DSIR algorithm. Twelve batches of ~22K shRNAs (corresponding to 12 agilent chips) were then assessed for efficacy via the sensor method outlined in Fellmann et al, Mol Cell, 2011. Conclusions: Neighboring nucleotide combinations are best at predicting shRNA efficacy.

Sample: chip 4001 replicate B sort S1

SAMN03100094 • SRS718822 • All experiments • All runs

Organism: synthetic construct

Library:

Instrument: Illumina Genome Analyzer II

Strategy: OTHER

Source: GENOMIC

Selection: other

Layout: SINGLE

Construction 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.

Experiment attributes:

GEO Accession: GSM1521360

Links:

External link: GEO Sample GSM1521360

NCBI link: NCBI Entrez (gds)

Runs: 1 run, 19.8M spots, 991.4M bases, 632.9Mb

Run	# of Spots	# of Bases	Size	Published
SRR1608323	19,828,329	991.4M	632.9Mb	2015-07-22

ID:: 1052759

SRA

Sequence Read Archive

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