IGVF

/human-donors/IGVFDO1080XFGV/

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

Variant FlowFISH

/in-vitro-systems/IGVFSM8601WYGY/

released

prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

Homo sapiens

feb7d08a-1287-4cac-b362-f81fd5ba1f81

/measurement-sets/IGVFDS4363PDBQ/

IGVFDS4363PDBQ

jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-BioRep2-FFrep2-BinA_AmpliconSequencing

PPIF

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

Variant FlowFISH

/in-vitro-systems/IGVFSM7022AZSZ/

released

prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

Homo sapiens

fe739718-a398-4e5c-b7b5-4d95497c90ad

/measurement-sets/IGVFDS2419JZMR/

IGVFDS2419JZMR

jesse-engreitz:measurement_set_eRZ10_teloHAEC_TLNRD1_enhancer_CRISPRi_FlowFISH_Rep4_bin4

/human-donors/IGVFDO3459DFTW/

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

CRISPR FlowFISH screen

/in-vitro-systems/IGVFSM5826EWDE/

released

CRISPR interference FlowFISH screen integrating a guide (sgRNA) library targeting candidate cis-regulatory elements in a genomic locus

Homo sapiens

fe738818-a459-4367-8223-af72aa6bca96

/measurement-sets/IGVFDS4736IKQS/

IGVFDS4736IKQS

jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep4-FACS_Input_AmpliconSequencing

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

Variant FlowFISH

/in-vitro-systems/IGVFSM0906STHP/

released

prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

Homo sapiens

fe6d143f-dbd2-40a5-b72b-55021f81951f

/measurement-sets/IGVFDS3969UCCQ/

IGVFDS3969UCCQ

charles-gersbach:cd8-tcells-rna-seq-cas-ko-gata3-rep3

/assay-terms/OBI_0003090/

/human-donors/IGVFDO4048LCOU/

experimental data

https://www.protocols.io/view/tfome-crisprko-screens-81wgbxk8olpk/v1, https://www.protocols.io/view/rnaseq-of-primary-human-t-cells-overexpressing-bat-c5pdy5i6

RNA-seq

/primary-cells/IGVFSM7117ATUZ/

released

knockout RNA-seq integrating a guide (sgRNA) library targeting transcription start sites in GATA3

Homo sapiens

fe29fcd6-36dd-4bba-acde-cc30fbb5ebc7

/measurement-sets/IGVFDS5041NPBP/

IGVFDS5041NPBP

jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR1_S42
jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR2_S48
jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR3_S138
jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF4-BinF-PCR4_S144

KITLG

experimental data

https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1

CRISPR FlowFISH screen

/in-vitro-systems/IGVFSM1131LTFK/

released

mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

Homo sapiens

fe1a8271-fd7e-454e-ae2c-187f1d46d77d

/auxiliary-sets/IGVFDS8473JDSO/

IGVFDS8473JDSO

jay-shendure:dev_CRE_mEBs_repB_bulk_DNA_day4_reads

/awards/HG011966/

/rodent-donors/IGVFDO3898MNLZ/

quantification DNA barcode sequencing

/labs/jay-shendure/

/measurement-sets/IGVFDS6355YALJ/

/in-vitro-systems/IGVFSM5978TPKG/

released

quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci

Mus musculus

fdfabd72-0a73-454b-bf93-f598df360118

/analysis-sets/IGVFDS9202ZPBI/

IGVFDS9202ZPBI

charles-gersbach:cd8-tcells-intermediate-set-atac-seq-chronic-activation-batf3

/human-donors/IGVFDO9588OERW/, /human-donors/IGVFDO1522NSLA/

intermediate analysis

/measurement-sets/IGVFDS0986HRDF/, /measurement-sets/IGVFDS5328ZNKL/

https://www.protocols.io/view/atac-seq-primary-human-t-cells-overexpressing-batf-c5pfy5jn

CD8-positive, alpha-beta memory T cell primary cell, transfected with a expression vector library

/primary-cells/IGVFSM7232YAVV/, /primary-cells/IGVFSM8821YQXI/

released

ATAC-seq: alignments

Homo sapiens

fdbe1d71-d4b0-4025-a01e-46b963a45785

/measurement-sets/IGVFDS5601DSMT/

IGVFDS5601DSMT

jesse-engreitz:230531S019-THP1-P151-Amp_PPIF_enhancer-BioRep2-FFrep2-BinB_AmpliconSequencing

PPIF

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

Variant FlowFISH

/in-vitro-systems/IGVFSM1683OFWB/

released

prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

Homo sapiens

fd6e5d84-173b-4f03-8de0-67bbec8d433f

/curated-sets/IGVFDS3190PUWD/

IGVFDS3190PUWD

igvf:10X_Multiome_ATAC_cell_barcode_inclusion_list_fileset

/awards/Community/

10X Multiome ATAC cell barcode inclusion list

barcodes

/labs/community/

released

barcodes

fd60d197-3dd4-49bb-9493-0d237ec82007

/measurement-sets/IGVFDS2160ZTSJ/

IGVFDS2160ZTSJ

charles-gersbach:cd8-tcells-measurement-set-crispr-ko-tfome-batf3-over-high-bin-rep1

IL7R

/human-donors/IGVFDO8306NDTY/

experimental data

https://www.protocols.io/view/tfome-crisprko-screens-81wgbxk8olpk/v1

CRISPR FACS screen

/primary-cells/IGVFSM8084QKPW/

released

CRISPR knockout FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes

Homo sapiens

fd5cf966-33dd-44fe-a22a-8bde46de6152

/analysis-sets/IGVFDS6344XBAV/

IGVFDS6344XBAV

charles-gersbach:cd8-tcells-analysis-set-atac-seq-chronic-activation-batf3

/human-donors/IGVFDO9588OERW/, /human-donors/IGVFDO1522NSLA/

principal analysis

/analysis-sets/IGVFDS9202ZPBI/, /analysis-sets/IGVFDS3609QWUZ/

/primary-cells/IGVFSM6508DFUL/, /primary-cells/IGVFSM7232YAVV/, /primary-cells/IGVFSM3805WZUU/, /primary-cells/IGVFSM8821YQXI/

CD8-positive, alpha-beta memory T cell primary cell, transfected with a expression vector library

released

ATAC-seq: fold change over control, peak quantifications

Homo sapiens

fcdc0263-c1e7-4ba0-87ba-5bcbfef7461c

/measurement-sets/IGVFDS8710ZSOZ/

IGVFDS8710ZSOZ

jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR1_S63
jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR2_S69
jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR3_S159
jesse-engreitz:measurement_CRUDO_KITLG-Auxin6hrs-FF2-BinC-PCR4_S165

KITLG

experimental data

https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1

CRISPR FlowFISH screen

/in-vitro-systems/IGVFSM7299CMAO/

released

mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

Homo sapiens

fcaeb9d7-e1f4-4136-9ce7-e43a1f35ee3c

/measurement-sets/IGVFDS7147ANAC/

IGVFDS7147ANAC

jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR1_S14
jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR2_S20
jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR3_S110
jesse-engreitz:measurement_CRUDO_KITLG-Auxin0hrs-FF2-BinB-PCR4_S116

KITLG

experimental data

https://www.protocols.io/view/crispri-of-regulatory-elements-upon-degron-operati-5jyl82d59l2w/v1

CRISPR FlowFISH screen

/in-vitro-systems/IGVFSM3263KXLP/

released

mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

Homo sapiens

fc9ab042-6677-4c24-9a08-261355a7f363

/auxiliary-sets/IGVFDS3120IRAP/

IGVFDS3120IRAP

jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR1-Rep1_S243
jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR2-Rep1_S249
jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR3-Rep1_S285
jesse-engreitz:auxiliary_CRUDO_CCND1_Auxin6hrs-FF1-BinC-PCR4-Rep1_S291

gRNA sequencing

/measurement-sets/IGVFDS6865SDZA/

/in-vitro-systems/IGVFSM2025NTWT/

released

gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

Homo sapiens

fc23e237-cefd-4218-9b9a-817a676d5b8d

/auxiliary-sets/IGVFDS5688OXJC/

IGVFDS5688OXJC

jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR1_S15
jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR2_S21
jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR3_S111
jesse-engreitz:auxiliary_CRUDO_KITLG-Auxin0hrs-FF2-BinC-PCR4_S117

gRNA sequencing

/measurement-sets/IGVFDS9308CBBI/

/in-vitro-systems/IGVFSM7071BULA/

released

gRNA sequencing for mixed CRISPR FlowFISH screen integrating a guide (sgRNA) library targeting accessible genome regions in many genomic loci

Homo sapiens

fbb50ae3-0460-48a0-9414-7ff400219b33

/measurement-sets/IGVFDS0885VFHW/

IGVFDS0885VFHW

jay-shendure:dev_CRE_mEBs_repB_bulk_RNA_day14_reads

/assay-terms/OBI_0002675/

/awards/HG011966/

/rodent-donors/IGVFDO3898MNLZ/

experimental data

/labs/jay-shendure/

MPRA

https://www.protocols.io/file/n92rb7r27.pdf

/in-vitro-systems/IGVFSM3546ITTD/

released

MPRA integrating a reporter library targeting accessible genome regions in many genomic loci

Mus musculus

fb95a9da-2dd1-4f85-b7b7-4604eea3838f

/measurement-sets/IGVFDS3899ANMJ/

IGVFDS3899ANMJ

jesse-engreitz:220228_8merInsertion-THP1-Amp_PPIF_promoter-BioRep3-FFrep3-BinF_AmpliconSequencing

PPIF

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

Variant FlowFISH

/in-vitro-systems/IGVFSM1757XEWZ/

released

prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

Homo sapiens

fb676008-1191-4fbf-b590-6e868e8a197f

/measurement-sets/IGVFDS5128CXIS/

IGVFDS5128CXIS

jesse-engreitz:230523pPPIFEnformer-THP1-Amp_PPIF_promoter-THP1-PE2_Exp4_NegControl_AmpliconSequencing

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

Variant FlowFISH

/in-vitro-systems/IGVFSM3211UEWZ/

released

prime editing Variant FlowFISH

Homo sapiens

fb47792f-c0be-488b-84bd-c23a65c154a1

/measurement-sets/IGVFDS9738RCWL/

IGVFDS9738RCWL

jesse-engreitz:220829_8merInsertion-Jurkat_Stimulation-Amp_PPIF_promoter-BioRep3-FFrep2-BinF_AmpliconSequencing

PPIF

/human-donors/IGVFDO1080XFGV/

experimental data

https://www.protocols.io/view/flowfish-with-primeflow-36wgq3q4olk5/v1

Variant FlowFISH

/in-vitro-systems/IGVFSM8638GWPD/

released

prime editing Variant FlowFISH integrating a guide (sgRNA) library targeting sequence variants in a genomic locus

Homo sapiens

fb30f5f3-a7fc-435a-8ec3-890a56d9703f

/auxiliary-sets/IGVFDS9693EKGR/

IGVFDS9693EKGR

charles-gersbach:cd8-tcells-auxiliary-set-crispri-ccr7-low-bin-rep1

/human-donors/IGVFDO3231VPAA/

gRNA sequencing

/measurement-sets/IGVFDS4930BLTW/

/primary-cells/IGVFSM7413JCSK/

released

gRNA sequencing for CRISPR interference FACS screen integrating a guide (sgRNA) library targeting transcription start sites in many genes

Homo sapiens

fb19e037-5dec-45bc-9a68-cf959a8281ea

/auxiliary-sets/IGVFDS8746LSXO/

IGVFDS8746LSXO

jay-shendure:dev_CRE_mEBs_rep2B_part1_bulk_DNA_day4_reads

/awards/HG011966/

/rodent-donors/IGVFDO3898MNLZ/

quantification DNA barcode sequencing

/labs/jay-shendure/

/measurement-sets/IGVFDS8540VFIL/

/in-vitro-systems/IGVFSM3811HZXX/

released

quantification DNA barcode sequencing for MPRA integrating a reporter library targeting accessible genome regions in many genomic loci

Mus musculus

faf19294-71cd-4e7c-95ac-c84244c19f8d

/measurement-sets/IGVFDS1619VKNB/

IGVFDS1619VKNB

charles-gersbach:cd8-tcells-atac-seq-acute-activation-batf3-rep1

/assay-terms/OBI_0003089/

/human-donors/IGVFDO9588OERW/

experimental data

https://www.protocols.io/view/atac-seq-primary-human-t-cells-overexpressing-batf-c5pfy5jn

ATAC-seq

/primary-cells/IGVFSM0066TACG/

released

ATAC-seq integrating a expression vector library of BATF3

Homo sapiens

fac6ae1a-55ce-44cc-879c-2b167fb2ff8d

/construct-library-sets/IGVFDS2398ZXBQ/

IGVFDS2398ZXBQ

charles-gersbach:cd8-tcell-ko-gata3-grna-construct-lib-set

guide library

GATA3

/auxiliary-sets/IGVFDS6678UHIV/

genes

transcription start sites

released

Guide (sgRNA) library targeting transcription start sites in GATA3

fab6e354-151b-47c0-9d2a-e229104f3a23

IGVFDS6678UHIV

jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep1_S138
jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR1_Rep2_S193
jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep1_S144
jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR2_Rep2_S199
jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep1_S150
jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR3_Rep2_S205
jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep1_S156
jesse-engreitz:auxiliary_CRUDO_MYC-Auxin6hrs-FF2-BinD-PCR4_Rep2_S211

gRNA sequencing