single-nucleus RNA sequencing assay (10x multiome with MULTI-seq)
Ansuman Satpathy, Stanford
Sample Summary
multiplexed sample: Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 11 days; Homo sapiens (mixed sex) induced pluripotent stem differentiated cell specimen induced to islet of Langerhans for 3 days; ... and 6 more samples
released
MeasurementSet
IGVFDS6464SOVZ
CRISPR base editing FACS screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide
Richard Sherwood, Brigham and Women's Hospital
Sample Summary
Homo sapiens (male) HepG2 cell line (sorting details: Sorted for Bottom 20% LDL-C uptake) modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5)
Homo sapiens HUDEP-2 cell line modified with CRISPR cutting SpRY, transduced (lentivirus) with a guide library
released
MeasurementSet
IGVFDS2333QYKL
CRISPR base editing FACS screen integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide
Richard Sherwood, Brigham and Women's Hospital
Sample Summary
Homo sapiens (male) HepG2 cell line (sorting details: Sorted for Top 20% LDL-C uptake) modified with CRISPR base editing SpRY-ABE8e, transduced (lentivirus) with a guide library (MOI of 0.5)
released
AuxiliarySet
IGVFDS3265EOGA
lipid-conjugated oligo sequencing
Ansuman Satpathy, Stanford
Summary
lipid-conjugated oligo sequencing for single-nucleus RNA sequencing assay (10x multiome with MULTI-seq), single-nucleus ATAC-seq (10x multiome with MULTI-seq)
CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus
Jesse Engreitz, Stanford
Sample Summary
Homo sapiens (male) Jurkat cell line (sorting details: FACS bin for 11-20% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
released
intermediate
AnalysisSet
IGVFDS7903FOXV
10x multiome with MULTI-seq: cell hashing barcodes, fragments, index, peaks, raw feature barcode matrix
Ansuman Satpathy, Stanford
Samples
Homo sapiens multiplexed sample of GM25256 (WTC-11), H7-hESC
released
MeasurementSet
IGVFDS2606PSFA
CRISPR interference FlowFISH screen sorted on the expression of NFKBIA integrating a guide (sgRNA) library targeting phenotype-associated variants genome-wide associated with blood pressure
Guillaume Lettre, MHI
Sample Summary
Homo sapiens (female) TeloHAEC cell line (sorting details: FACS 60-80% expression of NFKBIA) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transduced (lentivirus) with a guide library
released
MeasurementSet
IGVFDS4363PDBQ
CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus
Jesse Engreitz, Stanford
Sample Summary
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 0-25% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
released
MeasurementSet
IGVFDS2419JZMR
CRISPR interference FlowFISH screen sorted on the expression of TLNRD1 integrating a guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus
Jesse Engreitz, Stanford
Sample Summary
Homo sapiens (female) TeloHAEC cell line (sorting details: FACS bin for 76-100% expression of TLNRD1) modified with CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library
released
MeasurementSet
IGVFDS4736IKQS
unsorted FACS input CRISPR prime editing Variant-EFFECTS integrating a guide (sgRNA) library targeting sequence variants in a genomic locus
Jesse Engreitz, Stanford
Sample Summary
Homo sapiens (male) THP-1 cell line modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
released
MeasurementSet
IGVFDS3969UCCQ
CRISPR knockout RNA-seq integrating a guide (sgRNA) library targeting transcription start sites in GATA3
Charles Gersbach, Duke
Sample Summary
Homo sapiens CD8-positive, alpha-beta memory T cell modified with CRISPRko Sp-Cas9, transduced (lentivirus) with a guide library (MOI of 0.4)
released
MeasurementSet
IGVFDS5041NPBP
mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci
Jesse Engreitz, Stanford
Sample Summary
Homo sapiens (male) HCT116 cell line (sorting details: FACS bin F for 80-100% expression of KITLG) modified with CRISPRi Sp-dCas9-KOX1-KRAB, inactive AID system targeting RAD21, transfected with a guide library
released
AuxiliarySet
IGVFDS8473JDSO
quantification DNA barcode sequencing
Jay Shendure, UW
Summary
quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci
released
MeasurementSet
IGVFDS5601DSMT
CRISPR prime editing Variant-EFFECTS sorted on the expression of PPIF integrating a guide (sgRNA) library targeting sequence variants in a genomic locus
Jesse Engreitz, Stanford
Sample Summary
Homo sapiens (male) THP-1 cell line (sorting details: FACS bin for 26-50% expression of PPIF) modified with CRISPR prime editing Sp-nCas9-M-MLV RT (PE2), transduced (lentivirus) with a guide library
released
CuratedSet
IGVFDS3190PUWD
10X Multiome ATAC cell barcode inclusion list
External Lab, Community
Summary
barcodes
released
MeasurementSet
IGVFDS2160ZTSJ
CRISPR knockout FACS screen sorted on the expression of IL7R integrating an expression vector library of BATF3 and a guide (sgRNA) library targeting transcription start sites in many genes
Charles Gersbach, Duke
Sample Summary
Homo sapiens CD8-positive, alpha-beta memory T cell (sorting details: FACS bin for 90-100% expression of IL7R in cells overexpressing BATF3) modified with CRISPRko Sp-Cas9, transduced (lentivirus) with multiple libraries (MOI of 0.4)
released
principal
AnalysisSet
IGVFDS5394QLIN
lentiMPRA: reporter genomic variant effects
Nadav Ahituv, UCSF
Samples
Homo sapiens H1-hESC pooled differentiated cell specimen induced to glutamatergic neuron, at 7 day(s) post change, transfected with a reporter library
released
intermediate
AnalysisSet
IGVFDS2296EFNK
HiCAR: contact matrix
Charles Gersbach, Duke
Samples
GM25256 (WTC-11) differentiated cell specimen induced to cardiac muscle cell, at 42 day(s) post change, perturbed with 1 μM Endothelin-1 for 3 days, transfected with a guide library
released
MeasurementSet
IGVFDS5523WWKM
single-cell RNA sequencing assay (SHARE-seq)
Jason Buenrostro, Broad
Sample Summary
Mus musculus C57BL/6J colon tissue
released
MeasurementSet
IGVFDS5674PNNL
single-cell RNA sequencing assay (SHARE-seq)
Jason Buenrostro, Broad
Sample Summary
Homo sapiens (male, 37 years) bone marrow cell (cellular sub pool: SS-PKR 1)
released
principal
AnalysisSet
IGVFDS6344XBAV
ATAC-seq: alignments, fold change over control, peak quantifications
Charles Gersbach, Duke
Samples
CD8-positive, alpha-beta memory T primary cell primary cell, transfected with a expression vector library
released
MeasurementSet
IGVFDS3304YLTM
snMCT-seq
Chongyuan Luo, UCLA
Sample Summary
Homo sapiens fibroblast reprogrammed cell specimen induced to induced pluripotent stem cell for 3 days
released
MeasurementSet
IGVFDS8710ZSOZ
mixed CRISPR FlowFISH screen sorted on the expression of KITLG integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci
Jesse Engreitz, Stanford
Sample Summary
Homo sapiens (male) HCT116 cell line (sorting details: FACS bin C for 35-45% expression of KITLG) treated with 1 μM 5-Phenyl-1H-indole-3-acetic acid for 6 hours, modified with AID system targeting RAD21, CRISPRi Sp-dCas9-KOX1-KRAB, transfected with a guide library