title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M, PE3, rep2

description:
6588
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-33-5-M, PE3, rep2

status: Public on Nov 17 2025

type: SRA

city: Hangzhou

first: Lijia

last: Ma

state: Zhejiang

address: Shilongshan Road No.18, Cloud Town, Xihu District

department: School of Life Sciences

country: China

institute: Westlake university

description:
6597
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

growth_protocol: The culture conditions for HEK293T cells typically involve maintaining the cells in a high-glucose Dulbecco's Modified Eagle Medium (DMEM) supplemented with 10% fetal bovine serum (FBS) and 1% penicillin-streptomycin antibiotic solution. The medium is further enriched with 2 mM L-glutamine for optimal cell growth and health. Cells should be cultured at 37°C in a humidified atmosphere with 5% CO2. Regular media replacement is essential, usually every 2-3 days, to prevent the accumulation of metabolic waste and to supply fresh nutrients. When the cell confluence reaches about 80-90%, subculturing is recommended to avoid overgrowth, commonly achieved by detaching the cells using trypsin and splitting them into fresh culture flasks at a suitable dilution ratio, typically around 1:10.

extract_protocol:
Genomic DNA was extracted by the addition of 20 µl of freshly prepared lysis buffer (10 mM Tris-HCl, pH 7.5; 0.05% SDS (ThermoFisher Scientific); 25 µg/ml proteinase K (Tiangen)) directly into each tube which 30,000 cells were sorted from each sample. The genomic DNA mixture was incubated at 37 °C for 1.5 h, followed by an 80 °C enzyme inactivation step for 30 min.
Use site-specific primers with second-generation sequencing adapters to amplify target sites via PCR for library construction.

treatment_protocol: HEK293T cells were seeded on 12-well poly-d-lysine coated plates (Corning). Between 16 and 24 h after seeding, cells were transfected at approximately 70% confluency with lipofectamine 3000 (ThermoFisher Scientific) according to the manufacturer’s protocols and 3249 ng All in one(PE2) plasmid, and 1083 ng sgRNA plasmid (for PE2 and PE3). Unless otherwise stated, cells were cultured for 2 days following transfection, after which the medium was removed, the cells were washed with 1 ml 1×PBS (ThermoFisher Scientific), then digested with 0.25% Trypsin-EDTA (1X) (Gibco) for 1 min, 1 ml DMEM complete medium was added to terminate the reaction. Centrifugation at 300 g for 5 min, discard supernatant and resuspended with 150 ul 1×PBS (ThermoFisher Scientific). After resuspended, all positive cells (single or double fluorescence positive) were sorted and collected into a 1.5 ml low adsorption centrifuge tube (ThermoFisher Scientific) by MULTI-APPLICATION CELL SORTER MA900 (Sony). Centrifugation at 11,200 g for 1 min, discard supernatant and store at -20°C for a long time.

tag: cell line

tag: treatment

value: base editing by prime editing


title: HEK293T cell, RNF2, A4C, loop2-26-39-5-M, PE3, rep2

description:
6585
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA, PE3, rep3

description:
6583
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-33-5-M, PE3, rep2

description:
6594
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M, PE3, rep1

description:
6587
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA, PE3, rep2

description:
6591
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-39-5-M, PE3, rep1

description:
6584
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, loop2-23-43-5-M, PE2, rep2

description:
6638
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-44-5-M, PE3, rep1

description:
6579
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-44-5-M, PE3, rep2

description:
6576
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-44-5-M, PE3, rep1

description:
6575
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA, PE3, rep3

description:
6574
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA, PE3, rep2

description:
6573
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-44-5-M, PE3, rep3

description:
6577
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-43-5, PE2, rep3

description:
6562
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-39-5-M, PE3, rep3

description:
6586
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-43-5-M, PE2, rep3

description:
6565
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA, PE3, rep1

description:
6572
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-37-5-M, PE2, rep3

description:
6559
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-37-5, PE2, rep3

description:
6556
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-37-5-M, PE2, rep1

description:
6557
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-43-5-M, PE2, rep1

description:
6563
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-43-5, PE2, rep1

description:
6560
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M, PE3, rep3

description:
6589
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-37-5, PE2, rep1

description:
6554
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-5-M, PE2, rep3

description:
6553
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-37-5, PE2, rep2

description:
6555
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-43-5, PE2, rep2

description:
6561
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-5-M, PE2, rep2

description:
6552
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-5-M, PE2, rep1

description:
6551
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA, PE3, rep2

description:
6582
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-5, PE2, rep3

description:
6550
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-5, PE2, rep1

description:
6548
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-25-5-M, PE2, rep3

description:
6547
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-43-5-M, PE2, rep2

description:
6564
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA, PE3, rep1

description:
6581
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-25-5-M, PE2, rep2

description:
6546
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-37-5-M, PE2, rep2

description:
6558
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-25-5, PE2, rep3

description:
6544
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-25-5-M, PE2, rep1

description:
6545
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-25-5, PE2, rep1

description:
6542
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-25-5, PE2, rep2

description:
6543
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-37-5-M-PE, PE2, rep3

description:
6541
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-37-5-M-PE, PE2, rep2

description:
6540
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-37-5-M-PE, PE2, rep1

description:
6539
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-37-5-M, PE2, rep2

description:
6538
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-31-5-M, PE2, rep1

description:
6530
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-25-5-M, PE2, rep3

description:
6526
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA, PE2, rep2

description:
6522
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, loop2-27-45-5-M, PE2, rep1

description:
6512
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-37-5-M, PE2, rep3

description:
6536
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-25-5-M, PE2, rep1

description:
6524
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA, PE2, rep3

description:
6523
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, loop2-27-45-5-M, PE2, rep3

description:
6514
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, epegRNA+loop2-27-39-5-M-PE, PE2, rep3

description:
6511
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-5, PE2, rep2

description:
6549
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-25-5-M, PE2, rep2

description:
6525
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, epegRNA+loop2-27-39-5-M-PE, PE2, rep1

description:
6509
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-45-5-M, PE2, rep3

description:
6496
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, epegRNA+loop2-27-39-5-M-PE, PE2, rep2

description:
6510
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA, PE2, rep1

description:
6521
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-45-5-M, PE2, rep3

description:
6493
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-45-5-M, PE2, rep1

description:
6494
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-45-5-M, PE2, rep2

description:
6495
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-45-5-M, PE2, rep2

description:
6492
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M-PE, PE2, rep3

description:
6490
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-45-5-M, PE2, rep1

description:
6491
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M-PE, PE2, rep1

description:
6488
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M, PE2, rep3

description:
6487
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M, PE2, rep2

description:
6486
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-39-5-M, PE2, rep1

description:
6482
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-44-5-M, PE2, rep1

description:
6474
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-44-5-M, PE2, rep3

description:
6472
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-39-5-M, PE2, rep3

description:
6484
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-38-5-M-PE, PE2, rep3

description:
6469
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-38-5-M-PE, PE2, rep1

description:
6467
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-39-5-M, PE2, rep2

description:
6483
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-38-5-M, PE2, rep1

description:
6464
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-38-5-M, PE2, rep3

description:
6463
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-38-5-M, PE2, rep3

description:
6466
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-38-5-M-PE, PE2, rep2

description:
6468
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-38-5-M, PE2, rep2

description:
6465
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-38-5-M, PE2, rep1

description:
6461
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M-PE, PE2, rep2

description:
6489
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-38-5-M, PE2, rep2

description:
6462
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+tetraloop-25-45-5-M, PE2, rep3

description:
6433
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RUNX1, C1A, loop2-27-45-5-M, PE2, rep2

description:
6513
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+tetraloop-25-45-5-M, PE2, rep2

description:
6432
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+tetraloop-25-45-5, PE2, rep1

description:
6428
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+tetraloop-25-45-5-M, PE2, rep1

description:
6431
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-45-5, PE2, rep3

description:
6424
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-39-5-M, PE2, rep1

description:
6485
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-44-5-M, PE2, rep2

description:
6471
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+tetraloop-25-45-5, PE2, rep3

description:
6430
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+tetraloop-25-45-5, PE2, rep2

description:
6429
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-39-5, PE2, rep3

description:
6418
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-39-5-M, PE2, rep1

description:
6419
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, FANCF, A7C, loop2-29-44-5-M, PE2, rep1

description:
6470
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-39-5, PE2, rep1

description:
6416
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-33-5, PE2, rep1

description:
6411
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-39-5-M, PE2, rep3

description:
6400
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-39-5-M, PE2, rep2

description:
6399
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-27-5-M-PE, PE2, rep3

description:
6391
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-27-5-M-PE, PE2, rep1

description:
6389
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-27-5-M-PE, PE2, rep2

description:
6390
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-27-5-M, PE2, rep3

description:
6388
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-27-5, PE2, rep1

description:
6406
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-27-5-M, PE2, rep1

description:
6386
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-39-5-M, PE2, rep1

description:
6398
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA, PE2, rep2

description:
6384
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-45-5-M, PE2, rep1

description:
6427
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, tetraloop-22-39-5-M, PE2, rep3

description:
6376
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA, PE2, rep3

description:
6385
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA, PE2, rep1

description:
6383
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA+loop2-25-27-5-M, PE2, rep2

description:
6387
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, tetraloop-22-39-5-M, PE2, rep1

description:
6374
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-33-5-M-PE, PE2, rep2

description:
6351
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-33-5-M-PE, PE2, rep3

description:
6352
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, tetraloop-22-39-5-M, PE2, rep2

description:
6375
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-39-5, PE2, rep2

description:
6417
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-33-5-M, PE2, rep1

description:
6347
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-27-5-M, PE2, rep3

description:
6343
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, tetraloop-25-33-5-M, PE2, rep1

description:
6414
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-21-5-M, PE2, rep3

description:
6337
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-21-5-M, PE2, rep2

description:
6336
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-21-5-M, PE2, rep1

description:
6335
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-27-5-M, PE2, rep1

description:
6341
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA, PE2, rep3

description:
6334
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA, PE2, rep2

description:
6333
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA, PE2, rep1

description:
6332
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-37-5-M-PE, PE2, rep2

description:
6321
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-43-5-M, PE2, rep1

description:
6326
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, loop2-23-43-5-M, PE2, rep1

description:
6325
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-37-5-M-PE, PE2, rep1

description:
6320
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-37-5-M, PE2, rep3

description:
6319
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-37-5-M, PE2, rep1

description:
6317
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-37-5-M, PE2, rep2

description:
6318
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-43-5-M-PE, PE2, rep3

description:
6310
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, loop2-23-37-5-M, PE2, rep3

description:
6316
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-43-5-M-PE, PE2, rep1

description:
6308
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, loop2-23-37-5-M, PE2, rep1

description:
6314
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-43-5-M, PE2, rep3

description:
6307
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, loop2-23-37-5-M, PE2, rep2

description:
6315
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-43-5-M, PE2, rep2

description:
6306
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, loop2-22-43-5-M, PE2, rep3

description:
6304
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, epegRNA+loop2-22-27-5-M, PE2, rep2

description:
6342
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-43-5-M, PE2, rep1

description:
6305
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-37-5-M, PE2, rep3

description:
6298
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-37-5-M, PE2, rep2

description:
6297
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-37-5-M, PE2, rep1

description:
6296
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, loop2-22-43-5-M, PE2, rep2

description:
6303
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, loop2-22-43-5-M, PE2, rep1

description:
6302
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, loop2-22-37-5-M, PE2, rep3

description:
6295
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, loop2-22-37-5-M, PE2, rep1

description:
6293
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA, PE2, rep3

description:
6292
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA, PE2, rep2

description:
6291
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, DNMT1, C2A, epegRNA+loop2-23-37-5-M-PE, PE2, rep3

description:
6322
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA, PE2, rep1

description:
6290
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA(6xPBS-RTT), PE2, rep3

description:
6211
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA(6xPBS-RTT), PE2, rep2

description:
6210
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, epegRNA(6xPBS-RTT), PE2, rep1

description:
6209
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-34-18-1-M, PE2, rep2

description:
6196
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-34-18-1-M, PE2, rep3

description:
6197
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-43-5-M-PE, PE2, rep2

description:
6309
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-34-18-1-M, PE2, rep1

description:
6187
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-18-5-M, PE2, rep4

description:
6119
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA(6xPBS-RTT), PE2, rep3

description:
6117
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-34-31-5-M, PE2, rep3

description:
6115
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-34-31-5-M, PE2, rep2

description:
6114
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA(6xPBS-RTT), PE2, rep2

description:
6116
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-22-16-7-M, PE2, rep2

description:
6112
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-22-16-7-M, PE2, rep3

description:
6113
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-12-5-M, PE2, rep3

description:
6109
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-14-1-M, PE2, rep1

description:
6111
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-18-5-M, PE2, rep2

description:
6099
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-12-5-M, PE2, rep2

description:
6108
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, epegRNA(6xPBS-RTT), PE2, rep1

description:
6098
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-34-31-5-M, PE2, rep1

description:
6097
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, loop2-22-16-7-M, PE2, rep1

description:
6096
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-12-5-M, PE2, rep1

description:
6093
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-24-1-M, PE2, rep1

description:
6080
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, loop2-22-37-5-M, PE2, rep2

description:
6294
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-20-1-M, PE2, rep1

description:
6071
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-33-1-M, PE2, rep1

description:
6082
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-24-3-M, PE2, rep1

description:
6066
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-27-3-M, PE2, rep2

description:
6061
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-18-3-M, PE2, rep3

description:
6064
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-20-3-M, PE2, rep1

description:
6058
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-27-3-M, PE2, rep1

description:
6067
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-39-5-M, PE2, rep3

description:
6057
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-20-5-M, PE2, rep3

description:
6052
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-33-5-M, PE2, rep2

description:
6056
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-33-5-M, PE2, rep1

description:
6049
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-24-5-M, PE2, rep1

description:
6047
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-18-5-M, PE2, rep3

description:
6051
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-20-5-M, PE2, rep2

description:
6046
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-18-5-M, PE2, rep1

description:
6045
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-27-5-M, PE2, rep1

description:
6048
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-39-7-M, PE2, rep2

description:
6044
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-24-7-M, PE2, rep1

description:
6041
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-20-1-M, PE2, rep3

description:
6078
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-27-7-M, PE2, rep1

description:
6042
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-22-7-M, PE2, rep1

description:
6040
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-39-7-M, PE2, rep1

description:
6037
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-24-7-M, PE2, rep1

description:
6034
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-18-1-M, PE2, rep1

description:
6077
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-22-7-M, PE2, rep2

description:
6033
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-33-7-M, PE2, rep1

description:
6036
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-20-7-M, PE2, rep3

description:
6039
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-18-7-M, PE2, rep1

description:
6031
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-20-7-M, PE2, rep1

description:
6032
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-33-3-M, PE2, rep1

description:
6062
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-33-1-M, PE2, rep2

description:
6029
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-21-1-M, PE2, rep2

description:
6027
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-22-3-M, PE2, rep1

description:
6059
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-27-1-M, PE2, rep1

description:
6028
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-27-1-M, PE2, rep2

description:
6022
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-16-1-M, PE2, rep2

description:
6019
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-21-1-M, PE2, rep1

description:
6021
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-14-1-M, PE2, rep2

description:
6018
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-33-3-M, PE2, rep2

description:
6016
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-21-3-M, PE2, rep2

description:
6014
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-12-1-M, PE2, rep2

description:
6017
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-27-3-M, PE2, rep2

description:
6015
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-18-3-M, PE2, rep2

description:
6013
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-12-3-M, PE2, rep2

description:
6010
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-14-3-M, PE2, rep2

description:
6011
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-21-3-M, PE2, rep2

description:
6007
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-18-3-M, PE2, rep2

description:
6006
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-33-3-M, PE2, rep2

description:
6009
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-16-3-M, PE2, rep1

description:
6012
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-16-3-M, PE2, rep2

description:
6005
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-27-3-M, PE2, rep2

description:
6008
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-18-1-M, PE2, rep2

description:
6026
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-33-5-M, PE2, rep2

description:
6002
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-27-5-M, PE2, rep2

description:
6001
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-14-3-M, PE2, rep2

description:
6004
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-16-5-M, PE2, rep2

description:
5998
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-16-1-M, PE2, rep2

description:
6025
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-18-5-M, PE2, rep2

description:
5999
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-14-5-M, PE2, rep1

description:
5997
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-21-5-M, PE2, rep2

description:
6000
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-33-5-M, PE2, rep2

description:
5996
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-21-5-M, PE2, rep2

description:
5994
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: m005 cells, GSK620_1

city: San Diego

first: raghavendra

last: vadla

state: CA

address: sanford consortium for regenerative medicine, 2880 Torrey Pines Scenic Drive

country: USA

institute: UCSD

description:
Library name: Sample 55
raw_counts_3.txt
m005_GSK620_1

library_source: transcriptomic

data_processing:
Fastq file quality was ensured with FastQC, and reads were aligned to the hg38 index using STAR. Alignment quality was confirmed by assessing the final STAR logs. Index and bigwig files were generated from the BAM files with samtools and bamCoverage, respectively. Each BAM file was viewed in IGV to assess the quality and features of mapped reads. The Subread package was used to generate count files
Assembly: GRCh38 (GENCODE v39)
Supplementary files format and content: tab-delimited text includes raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
RNA was extracted using Rneasy mini kit (Qiagen)
Novogene sequencing

tag: tissue

value: Brain

tag: cell type

value: Glioma stem cells


title: m005 cells, GSK620_3

description:
Library name: Sample 57
raw_counts_3.txt
m005_GSK620_3


title: m005 cells, DMSO_3

description:
Library name: Sample 54
raw_counts_3.txt
m005_DMSO_3

value: DMSO


title: HEK293T cell, HEK4, G2T, loop2-10-12-3-M, PE2, rep2

description:
6003
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: m005 cells, DMSO_2

description:
Library name: Sample 53
raw_counts_3.txt
m005_DMSO_2


title: HEK293T cell, HEK4, G2T, loop2-10-27-5-M, PE2, rep2

description:
5995
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: m005 cells, DMSO_1

description:
Library name: Sample 52
raw_counts_3.txt
m005_DMSO_1


title: HEK293T cell, HEK4, G2T, loop2-22-12-7-M, PE2, rep2

description:
5983
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-27-7-M, PE2, rep2

description:
5988
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-14-5-M, PE2, rep2

description:
5991
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-12-5-M, PE2, rep2

description:
5990
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-18-7-M, PE2, rep2

description:
5986
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-27-7-M, PE2, rep2

description:
5981
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-14-7-M, PE2, rep2

description:
5984
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-12-1-M, PE2, rep1

description:
6024
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-33-7-M, PE2, rep2

description:
5989
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-21-7-M, PE2, rep2

description:
5987
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_multi-omics_seq_GEX_baseline-Control_Ezh2_KO_Female_KSL_Cells

city: St Louis

first: Grant

middle: A

last: Challen

state: MO

address: 660 Euclid Avenue

department: Medicine

institute: Washington University School of Medicine

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_GEX_baseline-Ezh2_KO_Female
10X_Genomics

data_processing:
For Single Cell RNA Seq experiment: FastQ files were demultiplexed, aligned to the mouse reference genome (mm10), and processed using Cell Ranger v3.1.0. After generation of the gene-barcode matrix, low-quality cells were filtered out based on quality control metrics: cells with >10% mitochondrial gene expression (indicative of stress or apoptosis) and cells in the top 5% of total UMI or feature counts (to exclude potential multiplets or doublets) were excluded from downstream analysis. Further analysis was performed using Seurat v3.0 in R and Partek Flow® software. Dimensionality reduction was conducted via principal component analysis (PCA), and clusters were visualized using both t-distributed stochastic neighbor embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP). Marker genes for each cluster were identified using a Wilcoxon rank-sum test, with significance set at p < 0.01 and absolute log2 fold change >1.5. Clusters were annotated based on known hematopoietic stem and progenitor cell (HSPC) gene markers. Differential gene expression analysis within clusters was performed to compare cells from control, Jarid2Δ/Δ, and Ezh2Δ/Δ mice. Enriched pathways were identified using the Gene Set Enrichment Analysis (GSEA) software package.
For Single Cell CITE Seq experiment: FastQ files were demultiplexed and processed using Cell Ranger v3.1.0. Gene expression and antibody capture reads were analyzed simultaneously using the cellranger count pipeline with a custom reference genome built from the mm10 genome assembly and the appropriate Feature Barcode reference file. Cells with >10% mitochondrial transcript content and those within the top 5% of UMI counts (potential doublets) were excluded from downstream analysis. Further analysis of the single-cell CITE-seq data was performed using Seurat v3.0 (R package) and Partek Flow® software. Dimensionality reduction was first conducted using principal component analysis (PCA) on the integrated gene expression and antibody-derived tag (ADT) matrices. Clustering was performed using graph-based algorithms and visualized via t-SNE and UMAP. Cluster-specific gene and protein surface markers were identified using the Wilcoxon rank-sum test, with a significance threshold of p < 0.01 and an absolute log2 fold change >2. Cluster annotation was guided by the expression patterns of well-established hematopoietic stem and progenitor cell (HSPC) transcriptomic and surface protein markers. Differential gene expression analysis within clusters was performed to compare cells from control, Jarid2Δ/Δ, and Ezh2Δ/Δ mice. Enriched pathways were identified using the Gene Set Enrichment Analysis (GSEA) software package. Antibodies used: TotalSeq B0952 PE Streptavidin Cat: 405287, TotalSeq B0203 anti-mouse CD150 (SLAM) Cat: 115951, TotalSeq B0012 anti-mouse CD117 (c-Kit), totalSeq B0429 anti-mouse CD48 Cat: 103457, TotalSeq B0439 anti-mouse CD201 (EPCR), TotalSeq B0098 anti-mouse CD135 Cat: 135319.
Assembly: Mus Musculus 10 (mm10)
Supplementary files format and content: The processed data files submitted to GEO include outputs generated by the Cell Ranger count pipeline for both single-cell RNA-seq and CITE-seq data. These files consist of the filtered gene and protein expression matrices in Matrix Market format (matrix.mtx), along with corresponding cell barcodes (barcodes.tsv) and feature annotations (features.tsv) that include both gene expression and antibody-derived tags. Additionally, the combined expression matrix is provided in HDF5 format (filtered_feature_bc_matrix.h5). These processed files were used for downstream analyses in Seurat, including normalization, dimensionality reduction (PCA, UMAP), clustering, and cell type annotation based on both gene and surface protein markers. Pseudobulk differential expression analysis was performed by aggregating UMI counts across cell populations, followed by statistical testing, and gene set enrichment analysis (GSEA) was conducted using clusterProfiler. Similar analyses were performed in Partek Flow, which was also used for quality control, clustering, marker detection, and pathway enrichment.
Library strategy: CITE-seq

molecule: polyA RNA

source_name: Baseline mice

growth_protocol: To investigate mechanistic differences between genotypes, we performed competitive bone marrow transplantation by co-administering 500,000 CD45.2 donor cells (experimental genotypes) with 500,000 CD45.1 competitor cells into lethally irradiated recipients. Following engraftment, CD45.2⁺ c‑Kit⁺ Sca1⁺ Lineage⁻ cells were isolated from the primary recipients’ bone marrow for downstream single-cell RNA‑Seq analysis. For the Single-Cell CITE Seq experiment, we enriched for c‑Kit⁺ cells from whole bone marrow of age- and sex-matched baseline donor mice of the same genotypes. Post-enrichment, we further sorted c‑Kit⁺ Sca1⁺ Lineage⁻ cells for CITE Seq profiling.

extract_protocol:
For Single Cell RNA Seq experiment: C-kit+ cells were enriched from the bone marrow of 18-week post-transplant recipient mice (5 × 10⁵ CD45.2/CD45.1 whole bone marrow primary transplant). Donor-derived (CD45.2) KSL (c-Kit+ Sca1+ Lineage–) cells were subsequently sorted from the enriched population and resuspended at a concentration of 1,200 cells/μL in PBS supplemented with 0.04% BSA. For Single Cell CITE Seq Experiment, C-kit+ cells were enriched from bone marrow of untransplanted control, Jarid2Δ/Δ, and Ezh2Δ/Δ mice. Following enrichment, c-Kit+ Sca1+ Lineage– (KSL) cells were subsequently sorted by FACS (Beckman Coulter MoFlo). Cells were first stained with biotin-conjugated anti-Sca1 (Ly-6A/E) antibody (Supp Table 2) for 20 minutes at 4 °C, then washed and incubated with a panel of six TotalSeq™-B barcoded antibodies (BioLegend) targeting surface markers: streptavidin-PE (Sca-1), CD117, CD48, CD150, CD135, and CD201 (Supp Table 3). Antibody staining was performed using 1 µL of each antibody in 50 µL of PBS containing 0.04% BSA, for 30 minutes on ice, protected from light. Following staining, cells were washed with cold PBS containing 0.04% BSA, filtered through a 40 µm cell strainer and assessed for viability (>90%) using Trypan Blue exclusion. After that, cells were resuspended at 1,200 cells/μL in PBS + 0.04% BSA.
Single-cell RNA Seq libraries were prepared using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index) (10x Genomics, PN-1000268), following the manufacturer’s protocol (User Guide CG000317 Rev D) with minor modifications. Cell partitioning and barcoding were performed using the Chromium Next GEM Chip G Single Cell Kit (PN- 1000127) and Chromium Dual Index Kit TT Set A (PN-1000215). GEM generation and reverse transcription (GEM-RT), followed by post-GEM cleanup, were conducted according to standard procedures. Purified cDNA was amplified for 11–13 cycles based on input cell number and quality, and then cleaned using SPRIselect beads (Beckman Coulter, Cat. No. B23318). Amplified cDNA was assessed using the Agilent Bioanalyzer High Sensitivity DNA Kit (Agilent, Cat. No. 5067-4626) to determine concentration and size distribution. Final gene expression (GEX) libraries were constructed as per the 10x Genomics protocol, adjusting the number of amplification cycles according to cDNA input. The libraries were quantified using the KAPA Library Quantification Kit for Illumina platforms (Roche/KAPA Biosystems, Cat. No. KK4824) and sequenced on the Illumina NovaSeq X Plus system using the XP workflow on an S4 Flow Cell with a paired-end 28 × 10 × 10 × 150 bp sequencing strategy. A target median depth of 50,000 reads per cell was achieved. Single-cell transcriptome and protein profiling were performed using the Chromium Next GEM Single Cell 3′ Reagent Kits v3.1 (Dual Index) (PN-1000268) in conjunction with the Feature Barcode Kit for Cell Surface Protein (PN-1000262), following the manufacturer’s protocol (User Guide CG000317 Rev D) with slight optimizations to the staining and preparation steps. Cells were loaded onto the Chromium Controller using the Chromium Next GEM Chip G (PN-1000127), targeting recovery of approximately 10,000 cells per channel. Gel bead-in-emulsion (GEM) generation, barcoding, and reverse transcription were carried out using the recommended thermal cycling conditions: Lid temperature 53 °C, 53 °C for 45 min, and 85 °C for 5 min; hold at 4 °C. Post-RT GEMs were broken, and barcoded cDNA was purified using Dynabeads™ MyOne™ Silane (PN-2000048). Amplified cDNA containing both mRNA- and antibody-derived tags (ADTs) was generated via PCR using cycling conditions recommended by 10x Genomics and cleaned up using SPRIselect reagent (Beckman Coulter, Cat. No. B23318). Separate libraries were prepared for gene expression and Feature Barcode (protein) profiling: 1. Gene Expression Library: A portion of the cDNA was enzymatically fragmented, end-repaired, A-tailed, and ligated to adapters, followed by sample index PCR amplification using the Dual index Kit TT Set A (PN-1000215). 2. Feature Barcode Library: A separate cDNA aliquot was amplified using primers targeting the Feature Barcode constructs using Dual index Kit NT Set A (PN-1000242). Final libraries were quantified using a Qubit 4 Fluorometer and assessed for size distribution using the Agilent Bioanalyzer High Sensitivity DNA Kit (Cat. No. 5067-4626). Libraries were pooled in appropriate ratios and sequenced on the Illumina NovaSeq X Plus system using an S4 flow cell with the following read configuration: 28 bp (Read 1), 10 bp (i7 index), 10 bp (i5 index), and 90 bp (Read 2). A target median sequencing depth of ~50,000 reads per cell was used for gene expression and 5,000–10,000 reads per cell for antibody-derived tags.

treatment_protocol: No treatment

value: Baseline mice

value: C-Kit+ Sca1+ Lineage- Bone Marrow sorted Cells

tag: genotype

tag: Sex

value: Female


title: HEK293T cell, HEK4, G2T, loop2-10-18-7-M, PE2, rep2

description:
5979
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-22-16-7-M, PE2, rep2

description:
5985
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_multi-omics_seq_GEX_baseline-Control_Jarid2_KO_Male_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_GEX_baseline-Jarid2_KO_Male
10X_Genomics

value: Male


title: Single_Cell_multi-omics_seq_ADT_baseline-Control_Jarid2_KO_Female_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_ADT_baseline-Jarid2_KO_Female
10X_Genomics

library_source: other

molecule: protein


title: m005 cells, GSK620_2

description:
Library name: Sample 56
raw_counts_3.txt
m005_GSK620_2


title: Single_Cell_multi-omics_seq_GEX_baseline-Control_Jarid2_KO_Female_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_GEX_baseline-Jarid2_KO_Female
10X_Genomics


title: HEK293T cell, HEK4, G2T, loop2-10-14-7-M, PE2, rep2

description:
5977
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-21-7-M, PE2, rep2

description:
5980
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_multi-omics_seq_ADT_baseline-Control_Ezh2_KO_Male_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_ADT_baseline-Ezh2_KO_Male
10X_Genomics


title: Single_Cell_multi-omics_seq_ADT_baseline-Control_Jarid2_KO_Male_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_ADT_baseline-Jarid2_KO_Male
10X_Genomics


title: HEK293T cell, HEK4, G2T, loop2-10-16-5-M, PE2, rep2

description:
5992
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK4, G2T, loop2-10-16-7-M, PE2, rep2

description:
5978
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_multi-omics_seq_GEX_baseline-Control_Ezh2_KO_Male_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_GEX_baseline-Ezh2_KO_Male
10X_Genomics


title: Single_Cell_multi-omics_seq_GEX_baseline-Control_Female_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_GEX_baseline-Control_Female
10X_Genomics

value: Control


title: Single_Cell_multi-omics_seq_ADT_baseline-Control_Ezh2_KO_Female_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_ADT_baseline-Ezh2_KO_Female
10X_Genomics


title: HEK293T cell, HEK4, G2T, loop2-10-12-7-M, PE2, rep2

description:
5976
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_multi-omics_seq_ADT_baseline-Control_Male_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_ADT_baseline-Control_Male
10X_Genomics


title: HEK293T cell, EMX1, G5T, loop2-25-18-5-M, PE2, rep2

description:
5974
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-24-5-M, PE2, rep3

description:
5972
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-24-7-M, PE2, rep3

description:
5973
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_RNA_seq_500K_WBM_1TX-Ezh2_KO_2_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_RNA_seq_500K_WBM_1TX-Ezh2_KO_2
10X_Genomics

library_source: transcriptomic single cell

data_processing:
For Single Cell RNA Seq experiment: FastQ files were demultiplexed, aligned to the mouse reference genome (mm10), and processed using Cell Ranger v3.1.0. After generation of the gene-barcode matrix, low-quality cells were filtered out based on quality control metrics: cells with >10% mitochondrial gene expression (indicative of stress or apoptosis) and cells in the top 5% of total UMI or feature counts (to exclude potential multiplets or doublets) were excluded from downstream analysis. Further analysis was performed using Seurat v3.0 in R and Partek Flow® software. Dimensionality reduction was conducted via principal component analysis (PCA), and clusters were visualized using both t-distributed stochastic neighbor embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP). Marker genes for each cluster were identified using a Wilcoxon rank-sum test, with significance set at p < 0.01 and absolute log2 fold change >1.5. Clusters were annotated based on known hematopoietic stem and progenitor cell (HSPC) gene markers. Differential gene expression analysis within clusters was performed to compare cells from control, Jarid2Δ/Δ, and Ezh2Δ/Δ mice. Enriched pathways were identified using the Gene Set Enrichment Analysis (GSEA) software package.
For Single Cell CITE Seq experiment: FastQ files were demultiplexed and processed using Cell Ranger v3.1.0. Gene expression and antibody capture reads were analyzed simultaneously using the cellranger count pipeline with a custom reference genome built from the mm10 genome assembly and the appropriate Feature Barcode reference file. Cells with >10% mitochondrial transcript content and those within the top 5% of UMI counts (potential doublets) were excluded from downstream analysis. Further analysis of the single-cell CITE-seq data was performed using Seurat v3.0 (R package) and Partek Flow® software. Dimensionality reduction was first conducted using principal component analysis (PCA) on the integrated gene expression and antibody-derived tag (ADT) matrices. Clustering was performed using graph-based algorithms and visualized via t-SNE and UMAP. Cluster-specific gene and protein surface markers were identified using the Wilcoxon rank-sum test, with a significance threshold of p < 0.01 and an absolute log2 fold change >2. Cluster annotation was guided by the expression patterns of well-established hematopoietic stem and progenitor cell (HSPC) transcriptomic and surface protein markers. Differential gene expression analysis within clusters was performed to compare cells from control, Jarid2Δ/Δ, and Ezh2Δ/Δ mice. Enriched pathways were identified using the Gene Set Enrichment Analysis (GSEA) software package. Antibodies used: TotalSeq B0952 PE Streptavidin Cat: 405287, TotalSeq B0203 anti-mouse CD150 (SLAM) Cat: 115951, TotalSeq B0012 anti-mouse CD117 (c-Kit), totalSeq B0429 anti-mouse CD48 Cat: 103457, TotalSeq B0439 anti-mouse CD201 (EPCR), TotalSeq B0098 anti-mouse CD135 Cat: 135319.
Assembly: Mus Musculus 10 (mm10)
Supplementary files format and content: The processed data files submitted to GEO include outputs generated by the Cell Ranger count pipeline for both single-cell RNA-seq and CITE-seq data. These files consist of the filtered gene and protein expression matrices in Matrix Market format (matrix.mtx), along with corresponding cell barcodes (barcodes.tsv) and feature annotations (features.tsv) that include both gene expression and antibody-derived tags. Additionally, the combined expression matrix is provided in HDF5 format (filtered_feature_bc_matrix.h5). These processed files were used for downstream analyses in Seurat, including normalization, dimensionality reduction (PCA, UMAP), clustering, and cell type annotation based on both gene and surface protein markers. Pseudobulk differential expression analysis was performed by aggregating UMI counts across cell populations, followed by statistical testing, and gene set enrichment analysis (GSEA) was conducted using clusterProfiler. Similar analyses were performed in Partek Flow, which was also used for quality control, clustering, marker detection, and pathway enrichment.

source_name: Primary Transplanted mice

value: Primary Transplanted mice


title: HEK293T cell, RUNX1, C1A, epegRNA+loop2-27-33-7-M, PE2, rep3

description:
5934
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-39-7-M, PE2, rep3

description:
5970
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_RNA_seq_500K_WBM_1TX-Ezh2_KO_1_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_RNA_seq_500K_WBM_1TX-Ezh2_KO_1
10X_Genomics


title: HEK293T cell, RUNX1, C1A, loop2-27-33-7-M, PE2, rep3

description:
5933
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_RNA_seq_500K_WBM_1TX-Control_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_RNA_seq_500K_WBM_1TX-Control
10X_Genomics


title: Single_Cell_multi-omics_seq_ADT_baseline-Control_Female_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_ADT_baseline-Control_Female
10X_Genomics


title: HEK293T cell, DNMT1, C2A, loop2-23-31-7-M, PE2, rep3

description:
5928
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_T532M_poly_2

city: Aurora

first: Nicole

middle: D

last: Moss

address: 1775 Aurora Ct

institute: University of Colorado

description:
Library name: cHetF_T532M_poly_2
50bp reads from polysome fraction
T532M_DESeq2.csv

data_processing:
Quality checked using FastQC (v0.11.7) and aligned to the mouse genome (Grm38) using STAR Aligner (2.7.11a). Raw gene counts were determined using featureCounts (subread/2.0.3). Differential expression of protein coding genes with a minimum read of 10 in one or more of the fractions were compared within each mouse line (T532M or LoF) using DESeq2 (1.34.0).
Assembly: Grm38
Supplementary files format and content: DDX3X_polysome_counts.txt contains the raw read counts as generated by featureCounts (subread/2.0.3).
Supplementary files format and content: Differential expression within the LoF and T532M lines presented in the LoF_DESeq2.csv and T532M_DESeq2.csv. Statistics denote differential expression between control and mutant in the input, monosome:input, and polysome:input.

source_name: cortex

extract_protocol:
RNA was extracted from pooled fractions and input samples using the Zymo Direct-zol RNA Miniprep kit (Zymo Research, R2050).
RNA-Seq library prep with KAPA HyperPrep

treatment_protocol: Embryonic cortices were microdissected, flash-frozen in liquid nitrogen, and stored at -80C until use. Cortices from two embryos of like genotype were pooled per sample. Cortices were thawed on ice, lysed in 400uL polysome buffer using a hand-blender, then triturated 10x with a 10-gauge needle. Triton X-100 was added to 1%, then lysates were clarified by spinning at 20krcf for 10 mins at 4C. 50uL of clarified lysate was removed as input, to which 150uL of TRIzol LS was added before storage at -80C. Clarified lysates were loaded onto 15-50% sucrose gradients prepared in polysome buffer and ultracentrifuged in an SW41 Ti rotor at 35krcf for 2 hours at 4C. Gradients were fractionated into 12 ~1mL fractions using a BioComp Piston Gradient Fractionator instrument with a TRIAX flow cell to measure absorbance at 260nm.

tag: Stage

value: cortex

value: female

value: Emx1-Cre/+;Ddx3x-T532M lox/+

tag: fraction

value: polysome fraction


title: cHetF_T532M_poly_3

description:
Library name: cHetF_T532M_poly_3
50bp reads from polysome fraction
T532M_DESeq2.csv


title: HEK293T cell, HEK3, G2C, epegRNA+loop2-22-31-7-M, PE2, rep2

description:
5925
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_T532M_poly_3

description:
Library name: CtrlF_T532M_poly_3
50bp reads from polysome fraction
T532M_DESeq2.csv


title: HEK293T cell, FANCF, A7C, epegRNA+loop2-29-32-7-M, PE2, rep3

description:
5917
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_T532M_poly_1

description:
Library name: cHetF_T532M_poly_1
50bp reads from polysome fraction
T532M_DESeq2.csv


title: HEK293T cell, RNF2, A4C, epegRNA+loop2-26-33-7-M, PE2, rep3

description:
5921
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, HEK3, G2C, loop2-22-31-7-M, PE2, rep3

description:
5924
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, RNF2, A4C, loop2-26-33-7-M, PE2, rep3

description:
5920
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_T532M_poly_2

description:
Library name: CtrlF_T532M_poly_2
50bp reads from polysome fraction
T532M_DESeq2.csv


title: cHetF_T532M_mono_3

description:
Library name: cHetF_T532M_mono_3
50bp reads from monosome fraction
T532M_DESeq2.csv

value: monosome fraction


title: HEK293T cell, VEGFA, A3C, epegRNA(3xPBS-RTT), PE2, rep3

description:
5911
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Single_Cell_RNA_seq_500K_WBM_1TX-Jarid2_KO_1_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_RNA_seq_500K_WBM_1TX-Jarid2_KO_1
10X_Genomics


title: CtrlF_T532M_poly_1

description:
Library name: CtrlF_T532M_poly_1
50bp reads from polysome fraction
T532M_DESeq2.csv


title: Single_Cell_multi-omics_seq_GEX_baseline-Control_Male_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_multi-omics_seq_GEX_baseline-Control_Male
10X_Genomics


title: cHetF_T532M_mono_2

description:
Library name: cHetF_T532M_mono_2
50bp reads from monosome fraction
T532M_DESeq2.csv


title: HEK293T cell, FANCF, A7C, loop2-29-32-7-M, PE2, rep3

description:
5916
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_T532M_mono_3

description:
Library name: CtrlF_T532M_mono_3
50bp reads from monosome fraction
T532M_DESeq2.csv


title: Single_Cell_RNA_seq_500K_WBM_1TX-Jarid2_KO_2_KSL_Cells

description:
Library name: 10X_Genomics_Single_Cell_RNA_seq_500K_WBM_1TX-Jarid2_KO_2
10X_Genomics


title: HEK293T cell, VEGFA, A3C, tetraloop-34-31-7-M, PE2, rep2

description:
5906
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_T532M_mono_2

description:
Library name: CtrlF_T532M_mono_2
50bp reads from monosome fraction
T532M_DESeq2.csv


title: HEK293T cell, VEGFA, A3C, epegRNA+loop2-34-31-7-M, PE2, rep3

description:
5910
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-33-1-M, PE2, rep3

description:
5903
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_T532M_mono_1

description:
Library name: CtrlF_T532M_mono_1
50bp reads from monosome fraction
T532M_DESeq2.csv


title: cHetF_T532M_input_3

description:
Library name: cHetF_T532M_input_3
50bp reads from input fraction
T532M_DESeq2.csv

value: input fraction


title: cHetF_T532M_input_2

description:
Library name: cHetF_T532M_input_2
50bp reads from input fraction
T532M_DESeq2.csv


title: HEK293T cell, VEGFA, A3C, tetraloop-34-25-7-M, PE2, rep2

description:
5905
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, VEGFA, A3C, tetraloop-34-37-7-M, PE2, rep2

description:
5907
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-27-1-M, PE2, rep1

description:
5902
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_T532M_input_1

description:
Library name: cHetF_T532M_input_1
50bp reads from input fraction
T532M_DESeq2.csv


title: cHetF_T532M_mono_1

description:
Library name: cHetF_T532M_mono_1
50bp reads from monosome fraction
T532M_DESeq2.csv


title: CtrlF_T532M_input_3

description:
Library name: CtrlF_T532M_input_3
50bp reads from input fraction
T532M_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-25-24-1-M, PE2, rep3

description:
5901
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-22-1-M, PE2, rep3

description:
5900
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_T532M_input_2

description:
Library name: CtrlF_T532M_input_2
50bp reads from input fraction
T532M_DESeq2.csv


title: CtrlF_T532M_input_1

description:
Library name: CtrlF_T532M_input_1
50bp reads from input fraction
T532M_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-25-20-1-M, PE2, rep2

description:
5899
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-18-1-M, PE2, rep3

description:
5898
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_LoF_poly_3

description:
Library name: cHetF_LoF_poly_3
50bp reads from polysome fraction
LoF_DESeq2.csv

value: Emx1-Cre/+;Ddx3x lox/+


title: HEK293T cell, EMX1, G5T, loop2-13-39-1-M, PE2, rep1

description:
5897
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1

value: base editing by prime editing


title: cHetF_LoF_poly_2

description:
Library name: cHetF_LoF_poly_2
50bp reads from polysome fraction
LoF_DESeq2.csv


title: HEK293T cell, VEGFA, A3C, tetraloop-34-43-7-M, PE2, rep2

description:
5908
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-33-1-M, PE2, rep3

description:
5896
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-27-1-M, PE2, rep1

description:
5895
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_LoF_poly_3

description:
Library name: CtrlF_LoF_poly_3
50bp reads from polysome fraction
LoF_DESeq2.csv

value: Ddx3x lox/+


title: HEK293T cell, EMX1, G5T, loop2-13-24-1-M, PE2, rep1

description:
5894
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_LoF_mono_3

description:
Library name: cHetF_LoF_mono_3
50bp reads from monosome fraction
LoF_DESeq2.csv


title: CtrlF_LoF_poly_1

description:
Library name: CtrlF_LoF_poly_1
50bp reads from polysome fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-13-20-1-M, PE2, rep3

description:
5892
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-22-1-M, PE2, rep1

description:
5893
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_LoF_mono_2

description:
Library name: cHetF_LoF_mono_2
50bp reads from monosome fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-13-18-1-M, PE2, rep1

description:
5891
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_LoF_mono_1

description:
Library name: cHetF_LoF_mono_1
50bp reads from monosome fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-25-39-3-M, PE2, rep2

description:
5890
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-33-3-M, PE2, rep1

description:
5889
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-20-3-M, PE2, rep3

description:
5886
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-18-3-M, PE2, rep2

description:
5885
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-27-3-M, PE2, rep3

description:
5888
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_LoF_mono_2

description:
Library name: CtrlF_LoF_mono_2
50bp reads from monosome fraction
LoF_DESeq2.csv


title: cHetF_LoF_input_3

description:
Library name: cHetF_LoF_input_3
50bp reads from input fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-13-39-3-M, PE2, rep1

description:
5884
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_LoF_input_2

description:
Library name: cHetF_LoF_input_2
50bp reads from input fraction
LoF_DESeq2.csv


title: CtrlF_LoF_input_3

description:
Library name: CtrlF_LoF_input_3
50bp reads from input fraction
LoF_DESeq2.csv


title: cHetF_LoF_input_1

description:
Library name: cHetF_LoF_input_1
50bp reads from input fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-13-27-3-M, PE2, rep1

description:
5882
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: cHetF_LoF_poly_1

description:
Library name: cHetF_LoF_poly_1
50bp reads from polysome fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-13-22-3-M, PE2, rep3

description:
5880
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_LoF_input_2

description:
Library name: CtrlF_LoF_input_2
50bp reads from input fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-13-24-3-M, PE2, rep1

description:
5881
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-20-3-M, PE2, rep3

description:
5879
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_LoF_input_1

description:
Library name: CtrlF_LoF_input_1
50bp reads from input fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-25-39-5-M, PE2, rep2

description:
5878
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: PanNET 2 MobiDrop

city: Moscow

first: Alesya

last: Maluchenko

address: Kulakova str. 20

country: Russia

institute: Moscow Center for Advanced Studies

description:
Library name: PanNET2_MobiDrop
SurfSeq 5000

data_processing:
In each tissue type, fastq files were subsetted to have an equal number of reads in data from each sample using seqtk. ScRNA-seq reads from 10x Genomics samples were mapped to human GRCh38 (GENCODE v32/Ensembl98) or mouse mm10 (GENCODE vM23/Ensembl98) reference genome using 10x Genomics Cell Ranger v9.0.1 software with default parameters. ScRNA-seq reads from SeekOne samples were mapped to human GRCh38 reference genome downloaded from seeksoultools v1.2.2 documentation site or mouse mm10 (GENCODE vM23/Ensembl98) reference genome built by Cell Ranger. Mapping was conducted using seeksoultools v1.2.2 with chemistry DDV2 and including introns. ScRNA-seq reads from MobiDrop samples were mapped to human GRCh38 (GENCODE v32/Ensembl98) or mouse mm10 (GENCODE vM23/Ensembl98) reference genome created by mobivision mkindex. Mapping was conducted using MobiVision v3.2 software. Count matrices were filtered using the R package pagoda2 v1.0.12. with minimal UMI count per cell was 1,000, maximal UMI count was 50,000, minimal number of genes per cell was 500 and minimal cells per gene number was 3. Doublets were identified using Scrublet v0.2.3. Decontamination was performed using DecontX from celda package v1.16.1. The following analysis was performed using the Seurat library. Seurat objects of PBMC samples were filtered with maximum percent of mitochondrial genes per cell set to 15%, maximum percent of hemoglobin genes per cell set to 2%, scrublet score lower than 0.2, number of total RNA count for each cell lower than 12,000, number of RNA features between 1,000 and 6,000. Cluster contaminated with neutrophil genes was removed. For murine adrenal samples and pancreatic neuroendocrine tumor samples cells having percent of mitochondrial genes more than 25%, percent of ribosomal genes more than 40%, scrublet score greater than 0.2, number of total RNA count greater than 50,000 and less than 500, number of RNA features lower than 250 were filtered out.
Assembly: GRCh38 (GENCODE v32/Ensembl98), mm10 (GENCODE vM23/Ensembl98)
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tumor

extract_protocol:
A patient's whole blood sample was diluted in PBS at a ratio of 1:1. Ficoll solution was added to a clean 15 ml falcon. The diluted blood sample was carefully layered on the Ficoll layer, preventing their mixing. Then, the sample was centrifuged with the following parameters: 450 g, 30 minutes, without brake. After that, the mononuclear cell ring was carefully collected from the Ficoll surface with a dispenser, and transferred to a clean 15 ml tube. The sample volume was brought to 10 ml using PBS. The sample was centrifuged at the parameters: 300 g for 10 minutes, after which the supernatant was removed. These steps were performed twice. Cryopreservation of the isolated cells was carried out according to the manufacturer's protocol. The samples were defrosted, washed, samples from 4 patients were pooled with 1 million cells from each patient for further loading onto the chip. Murine adrenal glands were excised and placed in PBS 1X with 10% fetal bovine serum (FBS) on ice. Under a binocular microscope, adipose tissue was removed with two tweezers/scalpel, and adrenal glands were mechanically homogenized with a scalpel on ice. Next, the adrenal gland homogenates were placed in a dissociating solution (HBSS buffer, Ca2+ 1.26 mM, collagenase IV 20 mg/mL, DNAse I 0.7 mg/ul, 0.5% BSA, RNase inhibitor) followed by 30-minute incubation at 37°C in a shaker-incubator (100 RPM). During the incubation, the suspension was pipetted every 10 minutes. Following the incubation, it was carefully pipetted, and 800 μl of PBS 1X with 10% FBS were added. The suspension was centrifuged 450 rcf for 6 min at +4◦C, then the supernatant was decanted, and the pellet was resuspended in 700 μl PBS 1X with 10% bovine serum and passed through a 70 μm filter. Then it was centrifuged 450 rcf 6 min at +4◦C, the supernatant was collected, the pellet was resuspended in 450 μl 1x PBS-0.05% BSA. The cell suspensions were gently mixed with cooled methanol in a ratio of 1:10 and placed for long-term storage at −80°C. For further work, the samples were defrosted on ice and rehydrated using a citrate buffer. Human pancreatic neuroendocrine tumor tissue was dissociated for single cell RNA sequencing using the Multi Tissue Dissociation Kit 2 by Miltenyi Biotec (cat. no. 130-110-203). Briefly, the tissue was placed in a petri dish on ice and cut into small pieces of 2–4 mm. The pieces were infused with the RPMI/enzyme mix (Miltenyi Biotec), transferred to a gentleMACS C tube containing RPMI/enzyme mix, attached to the sleeve of the single cell suspension dissociator (DSC-400) and run using the standard “H_Tumor_heater_1” program. After the termination of the program, the cells were centrifuged at 650 x g for 6 min at +4°C, resuspended in PBS 1X with 0.04 % bovine serum, passed through a 70 µm strainer and centrifugation was repeated. The supernatant was collected, the pellet was resuspended in 1 ml 1x PBS-0.04% BSA. Next, the cell suspension was fixed in cooled methanol. The cell suspension obtained in the previous step was mixed with methanol in a ratio of 1:10 and placed for long-term storage at −80°C. For further work, the samples were defrosted on ice and rehydrated using a citrate buffer.
The Chromium Next GEM Single Cell 5′ v2 Kit, Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (10× Genomics, Pleasanton, CA, USA) and the Chromium Single Cell Controller Instrument were used to generate 10× single-cell libraries according to the manufacturer’s instructions. The SeekOne DD Single Cell 3’ Transcriptome-seq Kit v1.1 and the SeekOne Digital Droplet System Instrument were used to generate single-cell libraries according to the manufacturer’s instructions. The MobiCube Single-Cell 3’ RNA-seq Kit v2.0, MobiCube Single-Cell 5’ V(D)J Kit v1.0 and the MobiNovaSP-100 Instrument were used to generate single-cell libraries according to the manufacturer’s instructions.

value: tumor

tag: age

value: 53 years old

value: male

tag: disease

value: non-functioning pancreatic neuroendocrine tumor


title: CtrlF_LoF_poly_2

description:
Library name: CtrlF_LoF_poly_2
50bp reads from polysome fraction
LoF_DESeq2.csv


title: CtrlF_LoF_mono_3

description:
Library name: CtrlF_LoF_mono_3
50bp reads from monosome fraction
LoF_DESeq2.csv


title: HEK293T cell, EMX1, G5T, loop2-25-27-5-M, PE2, rep3

description:
5876
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-33-5-M, PE2, rep1

description:
5877
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: PanNET 2, 10x

description:
Library name: PanNET2_10x
SurfSeq 5000


title: HEK293T cell, EMX1, G5T, loop2-25-24-5-M, PE2, rep1

description:
5875
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-39-5-M, PE2, rep1

description:
5872
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: tRNA_seq_8hpi_rep2

city: Wako

first: Shintaro

last: Iwasaki

state: Saitama

address: 2-1, Hirosawa

department: Center for Pioneering Research

country: Japan

institute: RIKEN

data_processing:
Basecalling with Illumina Casava 1.8 software
3' adapter trimming with Fastp;
Library sorting based on sample barcode sequence with custom script;
Random barcode triming with custom script;
Reads quality control with fastqc v0.12.1 and trimming with fastx-trimmer v0.0.14;
Alignment to non-coding RNA excluding tRNAs with Bowtie2;
Alignment to tRNAs with Bowtie2;
Read quantitation using custom scripts
Assembly: Amoeba genome assembly: https://zenodo.org/records/6800059; Amoeba mitochondrial genome: NC_001637.1; Virus genome: NC_014649.1
Supplementary files format and content: tRNA_counts_matrix.csv: Mapped counts on tRNA genes; First column is the tRNA name and the 2th to 9th columns are counts in each sample.

organism: Acanthamoeba castellanii

source_name: amoeba cell

growth_protocol: A. castellanii, strain Neff [American Type Culture Collection (ATCC), 30010] was cultured with 10 ml peptone-yeast-glucose (PYG) medium in a 10cm dish at 28°C.

extract_protocol:
The cell pellets were resuspended with 600 µl lysis buffer (20mM Tris pH 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol, 1% Triton X-100, 100 µg/ml of cycloheximide, and 100 µg/ml chloramphenicol), treated with 5 μl of TURBO DNase (2 U/μl, ThermoFisher Scientific) on ice for 10 min, and then centrifuged at 20,000 × g, at 4°C for 10 min.
The tRNA fraction was collected by mirVana miRNA Isolation Kit (Thermo Fisher Scientific) and deacylated, preadenylated linker ligation, reverse transcription, cDNA circularization, and PCR amplification.
mim-tRNA-seq

treatment_protocol: Cells were infected with APMV at MOI of 10 and harvested at 2, 4 and 8 hours after infection. For mock infection, PYG medium was used. Samples were treated with 100μg/mL CHX for 1 minute and scraped down and pelleted at 300 × g at 4°C for 3 min, washed with 1 ml of PBS containing 100 µg of CHX and 100 µg of chloramphenicol, and then pelleted again 300 × g at 4°C for 2 min.

value: amoeba cell

tag: strain

value: Acanthamoeba castellanii strain Neff

value: Infected with Acanthamoeba polyphage mimivirus at MOI of 10

tag: time


title: tRNA_seq_8hpi_rep1


title: PanNET 1, MobiDrop

description:
Library name: PanNET1_MobiDrop
SurfSeq 5000

value: 37 years old


title: HEK293T cell, EMX1, G5T, loop2-25-22-5-M, PE2, rep3

description:
5874
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: CtrlF_LoF_mono_1

description:
Library name: CtrlF_LoF_mono_1
50bp reads from monosome fraction
LoF_DESeq2.csv

value: cortex


title: HEK293T cell, EMX1, G5T, loop2-13-33-5-M, PE2, rep3

description:
5871
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: tRNA_seq_4hpi_rep1


title: tRNA_seq_4hpi_rep2


title: HEK293T cell, EMX1, G5T, loop2-13-27-5-M, PE2, rep3

description:
5870
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: tRNA_seq_2hpi_rep2


title: tRNA_seq_mock_rep2

value: Mock infection

value: mock


title: HEK293T cell, EMX1, G5T, loop2-25-33-7-M, PE2, rep1

description:
5866
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-24-7-M, PE2, rep3

description:
5864
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-20-5-M, PE2, rep1

description:
5869
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Ribo_seq_8hpi_rep2

data_processing:
Basecalling with Illumina Casava 1.8 software
Base correction, filtering, 3' adapter trimming with Fastp
Alignment to rRNA and other non-coding RNA with STAR v2.7.0a
Alignment to genome with STAR v2.7.0a
Read quantitation using custom scripts
Assembly: Amoeba genome assembly: https://zenodo.org/records/6800059; Amoeba mitochondrial genome: NC_001637.1; Virus genome: NC_014649.1
Supplementary files format and content: csv file contains 9 columns. The first column is transcript name. The 2nd to 9th columns are read counts in each sample.
Library strategy: Ribo-seq

extract_protocol:
The cell pellets were resuspended with 600 µl lysis buffer (20mM Tris pH 7.5, 150mM NaCl, 5mM MgCl2, 1mM dithiothreitol, 1% Triton X-100, 100 µg/ml of cycloheximide, and 100 µg/ml chloramphenicol), treated with 5 μl of TURBO DNase (2 U/μl, ThermoFisher Scientific) on ice for 10 min, and then centrifuged at 20,000 × g, at 4°C for 10 min.
RNase I treatment, ribosome pelleting, size selection, preadenylated linker ligation, rRNA depeletion with Ribo-Zero Gold (Human/Mouse/Rat) kit (Illumina), reverse transcription, cDNA circularization, and PCR amplification.


title: tRNA_seq_2hpi_rep1


title: HEK293T cell, EMX1, G5T, loop2-13-18-5-M, PE2, rep3

description:
5868
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-25-22-7-M, PE2, rep3

description:
5863
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: tRNA_seq_mock_rep1


title: Ribo_seq_4hpi_rep1


title: Ribo_seq_8hpi_rep1


title: Ribo_seq_2hpi_rep2


title: HEK293T cell, EMX1, G5T, loop2-25-20-7-M, PE2, rep2

description:
5862
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Ribo_seq_2hpi_rep1


title: Ribo_seq_4hpi_rep2


title: HEK293T cell, EMX1, G5T, loop2-25-18-7-M, PE2, rep3

description:
5861
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Ribo_seq_mock_rep2


title: HEK293T cell, EMX1, G5T, loop2-13-33-7-M, PE2, rep3

description:
5860
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: HEK293T cell, EMX1, G5T, loop2-13-27-7-M, PE2, rep1

description:
5859
The G5T mutation was introduced into the EMX1 gene in HEK293T cells via PE2 with the loop2-25-22-7 , rep1


title: Ribo_seq_mock_rep1