GEO DataSets

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; unidentified plasmid

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

5 related Platforms

139 Samples

Download data: BW, PSI, TAB

(Submitter supplied) Although CRISPR-Cas technology has revolutionized functional genomics, the systematic exploration of the role of individual exons for critical cellular phenotypes is lagging, limiting our understanding of genome regulation. To overcome this constraint, we have optimized and applied massively parallel exon deletion and splice site mutation screens in human cell lines identifying thousands of exons required for cell fitness. more...

Organism:

Homo sapiens; unidentified plasmid

Type:

Other

5 related Platforms

85 Samples

Download data: TXT

(Submitter supplied) The development of all dendritic cells (DCs) including antigen-presenting conventional DCs (cDCs) and cytokine-producing plasmacytoid DCs (pDCs) is controlled by the growth factor Flt3 ligand (Flt3L) and its receptor Flt3. We genetically dissected this common Flt3L-driven pathway of DCs differentiation using CRISPR/Cas9-based dropout screening in a Flt3L-dependent progenitor cell line. Genome-wide screening identified multiple regulators of DC differentiation including the glycosylphosphatidylinositol transamidase complex and arginine methyltransferase Carm1, whose role was confirmed in vivo. more...

Organism:

Mus musculus; unidentified plasmid

Type:

Other

Platforms:

GPL32254 GPL21103

6 Samples

Download data: CSV

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; unidentified plasmid

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other

4 related Platforms

38 Samples

Download data: BW

(Submitter supplied) SAMOSA, a method previously developed in the Ramani Lab, was employed to reveal nucleosome patterns from remodeling reactions in vitro with the Imitation Switch (ISWI) ATP-Dependent Remodeler ATPase, SNF2h. SAMOSA was further employed to reveal single-molecule nucleosome patterns in vivo from SNF2h knockout and re-expression murine embryonic stem cells.

Organism:

Mus musculus; unidentified plasmid

Type:

Other

Platforms:

GPL29466 GPL29177

235 Samples

Download data: PICKLE

(Submitter supplied) Genome-wide CRISPR screens aid researchers in discovering genes that function across a broad range of cellular mechanisms. Loss-of-function screens are particularly useful for identifying essential genes through loss of cell fitness measurements. However, loss-of-function screens are more challenging compared to gain-of-function screens due to the limited dynamic range of decreased sgRNA sequence detection. more...

Organism:

Homo sapiens; unidentified plasmid

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL21697 GPL28513

13 Samples

Download data: CSV

(Submitter supplied) We use stable expression of a cystathionine-beta synthase (CBS) variant library in HEK293T cells to identify CBS coding sequence variants that alter mRNA abundance

Organism:

unidentified plasmid; Homo sapiens

Type:

Other

6 related Platforms

22 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Drosophila melanogaster; unidentified plasmid

Type:

Other

Platforms:

GPL21376 GPL19132

19 Samples

Download data: FASTA, TSV, TXT

(Submitter supplied) Activity of enhancers in Drosophila embryos was measured by highly parallel reporter assay. We examined the results of mutating binding sites for 4 poorly studied TFs individually or in combination, and characterized complex genetic interactions among the different classes of motif mutant.

Organism:

unidentified plasmid

Type:

Other

Platform:

GPL21376

1 Sample

Download data: FASTA, TSV, TXT

(Submitter supplied) Human Accelerated Regions (HARs) are the fastest-evolving regions of the human genome and many are hypothesized to function as regulatory elements that drive human-specific gene regulatory programs. We interrogate the in vitro enhancer activity of >3,100 HARs in massively parallel reporter assays (MPRAs), demonstrating that many HARs appear to act as neural enhancers and that sequence divergence at HARs has largely augmented their neuronal enhancer activity.

Organism:

Homo sapiens; Mus musculus; unidentified plasmid

Type:

Other

Platforms:

GPL30428 GPL21273 GPL20795

14 Samples

Download data: BED, TXT

(Submitter supplied) Numerous rationally-designed and directed-evolution variants of SpCas9 have been reported to expand the utility of CRISPR technology. Here, we benchmark PAM preferences, on-target activity, and off-target susceptibility of 11 variants of SpCas9 in cell culture assays with thousands of guides targeting endogenous genes. To enhance the coverage and thus utility of base editing screens, we demonstrate that the SpCas9-NG and SpG variants are compatible with both A>G and C>T base editors, more than tripling the number of guides and assayable residues. more...

Organism:

unidentified plasmid; Homo sapiens

Type:

Other

Platforms:

GPL25362 GPL16791

67 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

unidentified plasmid; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL28010 GPL18573

68 Samples

Download data

(Submitter supplied) Regulation of cytokine production in stimulated T cells can be disrupted in autoimmunity, immunodeficiencies, and cancer. Systematic discovery of stimulation-dependent cytokine regulators requires both loss-of-function and gain-of-function studies, which have been challenging in primary human cells. We now report genome-wide CRISPR activation (CRISPRa) and interference (CRISPRi) screens in primary human T cells to identify gene networks controlling interleukin 2 and interferon gamma production. more...

Organism:

Homo sapiens; unidentified plasmid

Type:

Other

Platforms:

GPL18573 GPL28010

52 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Mus musculus; unidentified plasmid; Suid alphaherpesvirus 1

Type:

Other; Expression profiling by high throughput sequencing

6 related Platforms

128 Samples

Download data: CSV, TAR, TSV, TXT, ZIP

(Submitter supplied) Validating plasmid barcode diversity

Organism:

unidentified plasmid

Type:

Other

Platform:

GPL28010

1 Sample

Download data: TXT

(Submitter supplied) Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3,073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we constructed a massively parallel reporter assays (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into Epstein-Barr virus-transformed B cell line GM12878 revealed 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. more...

Organism:

unidentified plasmid; Homo sapiens

Type:

Expression profiling by high throughput sequencing; Other

Platforms:

GPL28010 GPL24676 GPL18573

25 Samples

Download data: TXT, XLSX

(Submitter supplied) SAMOSA is a single-molecule oligonucleosome footprinting technology, which can be employed to reveal nucleosome patterns (nucleosome positioning, nucleosome repeat length) at transcription factor binding sites and epigenomic domains.

Organism:

unidentified plasmid; Homo sapiens

Type:

Other

Platforms:

GPL29466 GPL28352 GPL29465

22 Samples

Download data: NPY, PICKLE

(Submitter supplied) We screened the genome of OCI-Ly-7, a Diffuse Large B-cell Lymphoma cell line, for genes mediating the response to rituximab treatment. We utilized the genome-wide library GeCKO v2 (A+B) from Feng Zhang. (Addgene#1000000049)

Organism:

Homo sapiens; unidentified plasmid

Type:

Other

Platforms:

GPL23227 GPL27656

5 Samples

Download data: TXT

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Homo sapiens; unidentified plasmid

Type:

Genome binding/occupancy profiling by high throughput sequencing; Other

5 related Platforms

210 Samples

Download data: BED, BW

(Submitter supplied) Genome-wide association studies have associated thousands of genetic variants with complex traits and diseases, but pinpointing the causal variant(s) among those in tight linkage disequilibrium with each associated variant remains a major challenge. Here, we used seven experimental assays to characterize all common variants at the multiple disease-associated TNFAIP3 locus in three disease-relevant immune cell types, based on a set of features related to regulatory potential. more...

Organism:

Homo sapiens; unidentified plasmid

Type:

Other

Platforms:

GPL25362 GPL24676 GPL16791

33 Samples

Download data: FASTA, MAP, TXT