Cellecta Blog & News

We have started the Cellecta blog as a simple, unobtrusive conduit that enables us to talk directly to our customers, collaborators, and other interested researchers about new and interesting developments related to Cellecta’s technology and business. Check back here often for the latest news and events.

About Cellecta

Cellecta Inc., a custom and contract functional genomics solutions provider, focuses primarily on developing and implementing flexible and scalable broad-based screening and analysis approaches for drug target and biomarker discovery. Our high throughput functional genetic screening portfolio includes shRNA and CRISPR screening services, custom and off-the-shelf pooled libraries, and knockout/knockdown cell lines that facilitate genome-wide functional screening and the identification and validation of genes involved in critical biological and pathological responses.

With our new DriverMap™ Gene Expression and Molecular Profiling Service, Cellecta now offers a quantitative, multiplexed approach that allows simultaneous profiling of thousands of genes in one reaction, thereby providing the transcriptome profile of the tumor microenvironment.

Core Population of Cancer Stem Cells Mediates Therapeutic Resistance in Tumors

April 22, 2019

Researchers at MD Anderson Cancer Center recently used a Cellecta CloneTracker Barcode Library to label patient-derived xenograft (PDX) cells and establish a stable population of aggressive tumorigenic cells with a specific set of barcodes. With this population of barcoded tumorigenic clones, the investigators...
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DriverMap™ Targeted RNA Sequencing of Blood Finds Gene Signatures Linked to Labor

March 28, 2019

A recent article demonstrates the unique suitability of the DriverMap Expression Profiling Assay for blood biomarker analysis. In Scientific Reports, Tarca, et al. reported that DriverMap Targeted RNA sequencing identified more potential biomarkers associated with spontaneous labor than either standard Illumina...
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Cellecta Scribe™ Vectors Enable RNA-Seq Analysis of Pooled CRISPR and RNAi Screens

October 04, 2017

Earlier this year, 3 separate studies (Adamson, et al., Datlinger, et al., and Dixit, et al.) demonstrated an approach to combine pooled CRISPR genetic screening with RNA expression profiling at the single-cell level. Integrating these two approaches enables knockout-specific expression data to be generated for...
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Thy1.1 Gene as Marker in Cellecta Custom Constructs

September 05, 2017

Cellecta now offers the mouse Thy1.1 gene (Thymus Cell Antigen 1.1, CD90.1) as a marker in custom CRISPR, RNAi, and cDNA constructsThy1 genes express small, almost peptide-like T-cell glycooprotein expressed by thymocytes, hematopoietic stem cells, some fibroblast and muscle cells in most mammals. These...
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Cancer, the Human Mobilome, and LINE-1 Retrotransposons

July 03, 2017

Essentially half of human DNA consists of repeated transposable elements or "mobile" DNA. One type of long interspersed element—LINE-1—is one of the most prevalent variants and accounts for approximately 17% of the human genome. The LINE-1 sequence is a protein-coding transposable element that copies itself through...
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How to Make a Crappy CRISPR Library

June 01, 2017

In addition to the pooled CRISPR libraries we offer, there are a few other libraries that researchers can choose to use for gene knockout screens, such as the Broad Institute’s GeCKO and Brunello libraries available through Addgene. To conserve the limited stock of these libraries, many labs only distribute a...
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Loss-of-Function RNAi Screen in PDX Mouse Models

May 27, 2016

Using a Cellecta-made shRNA library, groups from the European Institute of Oncology and MD Anderson Cancer Center published the first in vivo pooled RNAi screen in patient-derived tumor xenograft PDX mouse models. The study published in June Cancer Discovery screened 236 epigenetic genes targeted with a pooled shRNA...
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Improved sgRNA Design Delivers Better CRISPR Knockout Screen Results

April 07, 2016

Last year, Cellecta received a Phase 1 NIH SBIR grant to develop validated single guide RNA (sgRNA). The initial study was designed to investigate an approach to optimize CRISPR sgRNA to improve the efficiency of CRISPR knockout.The 5'-end of the CRISPR sgRNA contains 20 nucleotides specific to the gene targeted...
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Cellecta Gets SBIR Grant to Develop Validated CRISPR Library

July 22, 2015

Cellecta received a Phase I NIH SBIR Grant to develop CRISPR guide RNAs (gRNAs or sgRNAs) for human and mouse genes and then use these to build a knockout library targeting 6,500 key disease-related genes in major signal transduction pathways.Targeting a gene for knockout using CRISPR requires a short strand of...
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Viral Barcode Library Used to Track Treatment Resistant Cancer Cells

June 06, 2015

Researchers at Novartis recently published a study using a lentiviral based library containing many millions of unique sequences (barcodes) to label and track erlotinib-resistant non-small lung cancer cells. The approach provided a way to differentiate whether these resistant cells were already present in...
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A New GFP CRISPR for Primary and Non-Dividing Cells

April 29, 2015

Use of antibiotic resistance markers with CRISPR is an effective tool for cells that proliferate.  However, for primary cells and non-dividing cells, all-in-one sgRNA-Cas9 lentiviral vector that contains a fluorescence marker (GFP-CRISPR) could be a better option.Our standard, Single-Vector CRISPR-Cas9 System...
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shRNA Loss-of-Function Screen Identifies Alternate Pathway for BCR-ABL1 Kinase-independent Resistance in Chronic Myeloid Leukemia

March 30, 2015

Chronic Myeloid Leukemia (CML) is characterized by increased and unregulated growth of myeloid cells in the bone marrow and accumulation of these cells in the blood. Most CML is caused by a chromosomal abnormality that results in a fusion between Abl tyrosine kinase and BCR gene on chromosome 2, which results in a constitutively active tyrosine kinase. Most CMLs are treated with tyrosine kinase inhibitors...
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CRISPR Knockout Screens with Optimal Cas9 to sgRNA Ratios

March 12, 2015

The previous blog post " Two-Vector CRISPR System Is Better Approach for Knockout Screens" discussed the advantages of expressing the Cas9 nuclease on a vector separate from the one used for the guide RNAs (sgRNA)—a two-vector CRISPR system—when using the system for complex pooled loss-of-function screens.  In...
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Two-Vector CRISPR System Is Better Approach for Knockout Screens

November 26, 2014

Since our introduction of the All-in-One CRISPR-Cas9 lentiviral system in the Spring, we have done a bit more work and moved forward with a two-vector system for our pooled libraries of sgRNA expression constructs. If the All-in-One CRISPR-Cas9 vector works well—which it does—why, you might wonder, would we...
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Get Pure High-Titer Virus with Every Packaging Prep with LentiFuge™

October 16, 2014

Most experiments that rely on lentiviral technology to deliver genetic elements benefit greatly by starting with pure high-titer virus. With some easy-to-transduce cell systems grown in routine medium, such as DMEM, it may be possible to squeak by with a dilute viral supernatant containing proteins and factors from the packaging cell culture. However, protocols involving cells that require different media...
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CRISPR Knockout Rate Dependent on Cas9 Expression Levels

May 28, 2014

Cellecta recently developed a one-plasmid CRISPR lentiviral vector that expresses both the sgRNA and Cas9 protein. CRISPR enables convenient of a target gene at the genomic level, as opposed to shRNA which knocks down the level of the RNA transcript for the target gene.Due to the differences between the shRNA...
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Cellecta's Lentiviral Packaging Mix Outperforms Competitors'!

March 25, 2014

Recently, one of our customers compared our lentiviral packaging mix with packaging mixes from two competitors. The same lentiviral vector that expresses firefly luciferase was used in all three packaging protocols. Each lentivector was packaged according to the manufacturer's instructions in 293T cells....
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Custom Library from Cellecta Helps Identify BRM/SMARCA2 as a Critical Target in Cancers

March 12, 2014

Dr. Gregory Hoffman's group from Novartis recently used a custom library from Cellecta that identified BRM/SMARCA2 as a critical target in BRG1-deficient cancers (PMID: 24520176). The shRNA library consisted of 6500 shRNAs (380 genes with 17 shRNAs per gene) involved in epigenetic regulation. These genes represented...
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Millions of Defined Sequenceable Barcodes for Clonal Cell Tracking

February 26, 2014

The ability to identify and quantify the size of clonal cell populations produced by each cell in a founder population offers researchers a powerful tool for understanding how groups cells grow and proliferate in all sorts of conditions. This sort of clonal cell tracking enables cell biologists,...
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Researchers Identify SALL1 as a Tumor Suppressor in Breast Cancer with a Role in E-Cadherin Regulation

January 17, 2014

Researchers at the German Cancer Research Center (DKFZ) and the MD Anderson Cancer Center used Cellecta's shRNA DECIPHER Libraries for an in vivo genetic screen that identified SALL1 as a breast cancer tumor suppressor that plays a role in E-cadherin regulation (Article)E-cadherin (CDH1) has been shown to have a...
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German Researchers Find Sensitizer for Gemcitabine Using DECIPHER RNAi Libraries

June 10, 2013

Researchers at the German Cancer Research Center (DKFZ) used Cellecta's shRNA DECIPHER libraries to identify genes that sensitize pancreatic cells to gemcitabine.Pancreatic cancer has only a 6% 5-year survival rate. Gemcitabine is the standard treatment in conjunction with surgery to remove cancerous...
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An MSCV-Based shRNA Expression Vector for Mouse Hematopoietic Cells

February 11, 2013

At Cellecta, we have relied primarily on lentiviral vectors to develop our RNAi genetic screening technology. The broad tropism of lentivirus-based plasmids packaged into VSV-g pseudotyped viral particles provides a very convenient vector system to introduce and stably express shRNA expression...
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The 2012 Cell Biology Meeting: A Good Finish to the Year

January 05, 2013

2013 seems to have started at a full sprint. It feels as though the annual meeting of the American Society of Cell Biology in San Francisco just finished. We exhibited and presented a tutorial there entitled, Find Functionally Important Driver Genes with RNAi Genetic ScreeningUsing Pooled shRNA Libraries on December...
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Second Phase SBIR Contract from the National Cancer Institute (NCI) to Identify Lethal Gene Combinations in Cancer Cell Models

October 23, 2012

It's been a while since the last post to this blog. It is not that nothing has been going on, in fact, quite the opposite. It has been quite busy the past several months and, unfortunately, blog postings have suffered. However, I thought I would get things started again with short post about our recent SBIR...
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Another Group Finds Similar Keys to Optimal Pooled shRNA Library Screens

March 20, 2012

Our group recently ran across an article describing an independent RNAi screen with a non-Cellecta pooled shRNA expression library that piqued our interest. In the October 2011 online Genome Biology Journal, Sims, et al. comprehensively described how to run a rigorous genome-wide pooled RNA interference screen...
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The Need for RNAi Screening Standards

February 03, 2012

A couple of months ago at the CHI Discovery on Target Conference, Hakim Djaballah, Director of the HTS Core Facility at the Memorial Sloan Kettering Cancer Center, gave a unique and insightful presentation highlighting the challenges RNAi screening to identify lethal loss of function interaction in oncogenic...
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Tissue Targeting May Offer an Alternative Therapeutic Approach for Difficult-to-Treat Diseases

October 14, 2011

We recently received a phase II of our SBIR grant Exploiting Synthetic Lethality of Hematopoietic Lineage Cells to Develop Novel Targets from the NIH. Rather than trying to identify potential drug targets in oncogenic hematopoietic cells, much of the effort for this project focuses on trying to develop a...
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Screening for Synergistically Lethal Knockdown Combinations in Cancer Cells

August 31, 2011

Therapeutic approaches using multiple drug combinations have become a standard treatment model for many types of cancer. Due to the tremendous genetic complexity and adaptive nature of most human malignancies, the use of multiple drugs acting on different targets increases the efficacy and helps thwart the...
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shRNA Design Results – How good is your algorithm?

August 03, 2011

The last blog entry discussed how hairpin structural features affect representation and effectiveness of shRNA sequences in pooled libraries. However, it is clear that the nucleotide sequence is possibly the major factor that determines the efficiency at which a particular siRNA or shRNA knocks down a...
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The Importance of shRNA Structural Design for Pooled Libraries

June 23, 2011

We have done a significant amount of evaluation to identify features of the optimal shRNA structure necessary to ensure our complex libraries maintain and express representative and effective shRNA. Independent from particular targeting sequences, structural variations such as defined mismatches, loop...
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RNAi Screening with An Inducible Promoter: Is There an Advantage?

May 13, 2011

Inducible expression is often desirable for functional genetic testing to establish clear cause and effect for a specific phenotype. A particular phenotype can be demonstrably linked to expression of a specific cDNA by showing it disappears when transcription is suppressed. Although less direct, similar logic...
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Ensuring Comprehensive Screening with Pooled shRNA Expression Libraries

April 03, 2011

Researchers are often interested in using a pooled shRNA library for genome-wide RNAi screening to cast a very “wide and unbiased net to identify any and all genes functionally involved in some pathway”. Although it is not difficult to make an shRNA library targeting all human or mouse genes, it is practically very...
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