title: MEF2C_VP1_NSC_proxTAD_A8_B_HOM

description:
MEF2C_VP1_NSC_proxTAD_A8_B_HOM
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_proxTAD_A8_B_HOM


title: MEF2C_VP1_NSC_ProxTAD_A8_A_HOMDEL

status: Public on Jun 10 2022

type: SRA

city: Boston

first: Rachita

last: Yadav

state: MA

address: 185 Cambridge street

department: Neurology

country: USA

institute: MGH

description:
MEF2C_VP1_NSC_ProxTAD_A8_A_HOMDEL
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_ProxTAD_A8_A_HOMDEL

library_source: genomic

data_processing:
STAR alignemnt and htseq quantification
DESEq2 based differentrial expressed genes
mSIGBD based functional class enrichment
R package "umi4cPackage" to generate 4C peaks, followed by DESeq2 based analysis for differential 4C pattern within peak regions
Standard ENCODE ATACSeq  processing approach to call ATAC peaks
Assembly: GRCh37.75
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample
Supplementary files format and content: tab-delimited text files include differentially expressed genes values for each comparison
Supplementary files format and content: tab-delimited text files include GO annotation for MEF2C and Proximal Boundary deletions
Supplementary files format and content: tab-delimited text files include differential MEf2C exon statistics
Supplementary files format and content: tab-delimited text files include differentially 4C statistics
Supplementary files format and content: tab-delimited ATAC peaks in narrowPeak format
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

molecule: genomic DNA

organism: Homo sapiens

extract_protocol:
TRIzol Reagent
TruSeq® Stranded mRNA Library Kit

tag: cell line

tag: cell type

value: Neural stem cells

tag: genotype

tag: treatment


title: MEF2C_VP1_NSC_proxTAD_H5_A_WT

description:
MEF2C_VP1_NSC_proxTAD_H5_A_WT
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_proxTAD_H5_A_WT


title: MEF2C_VP1_iN_MEF2C_HOM_X_B_VP1

description:
MEF2C_VP1_iN_MEF2C_HOM_X_B_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_MEF2C_HOM_X_B_VP1

value: Induced Neurons


title: 8-NSC_ProxLoop_HOM_GG_MEF2C_VP1

description:
8-NSC_ProxLoop_HOM_GG_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
8-NSC_ProxLoop_HOM_GG_MEF2C_VP1


title: 5-NSC_ProxLoop_HOM_AAB_MEF2C_VP1

description:
5-NSC_ProxLoop_HOM_AAB_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
5-NSC_ProxLoop_HOM_AAB_MEF2C_VP1


title: 1-NSC_proxLoop_HOM_GG_MEF2C_VP1

description:
1-NSC_proxLoop_HOM_GG_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
1-NSC_proxLoop_HOM_GG_MEF2C_VP1


title: MEF2C_VP1_iN_MEF2C_HOM_X_A

description:
MEF2C_VP1_iN_MEF2C_HOM_X_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_iN_MEF2C_HOM_X_A


title: 7-NSC_ProxLoop_HOM_AAA_MEF2C_VP1

description:
7-NSC_ProxLoop_HOM_AAA_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
7-NSC_ProxLoop_HOM_AAA_MEF2C_VP1


title: MEF2C_VP1_NSC_MEF2C_HOM_X_A_VP1

description:
MEF2C_VP1_NSC_MEF2C_HOM_X_A_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_MEF2C_HOM_X_A_VP1


title: MEF2C_VP1_NSC_Insul_A1_HET

description:
MEF2C_VP1_NSC_Insul_A1_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_Insul_A1_HET


title: MEF2C_VP1_NSC_MEF2C_HOM_H_A_VP1

description:
MEF2C_VP1_NSC_MEF2C_HOM_H_A_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_MEF2C_HOM_H_A_VP1


title: MEF2C_VP1_NSC_Insul_A3_WT

description:
MEF2C_VP1_NSC_Insul_A3_WT
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_Insul_A3_WT


title: MEF2C_VP1_NSC_insul_WT_F11

description:
MEF2C_VP1_NSC_insul_WT_F11
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_insul_WT_F11


title: MEF2C_VP1_NSC_distLOOP_WT_B1

description:
MEF2C_VP1_NSC_distLOOP_WT_B1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_distLOOP_WT_B1


title: MEF2C_VP1_NSC_Dist_Loop_A10_HET

description:
MEF2C_VP1_NSC_Dist_Loop_A10_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_Dist_Loop_A10_HET


title: 43_LRG_WT_D_c

description:
D_c, iN, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
43_LRG_WT_D_c

library_source: transcriptomic

molecule: polyA RNA

value: WT

value: Cell line


title: 39_LRG_WT_D_a

description:
D_a, iN, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
39_LRG_WT_D_a


title: MEF2C_VP1_NSC_FACS_B_5M

description:
MEF2C_VP1_NSC_FACS_B_5M
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_FACS_B_5M


title: MEF2C_VP1_NSC_distLOOP_WT_A3

description:
MEF2C_VP1_NSC_distLOOP_WT_A3
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_distLOOP_WT_A3


title: 41_LRG_WT_D_b

description:
D_b, iN, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
41_LRG_WT_D_b


title: 38_LRG_HET_B_b

description:
B_b, iN, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
38_LRG_HET_B_b

value: Heterozygous DEL


title: 37_LRG_HET_B_a

description:
B_a, iN, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
37_LRG_HET_B_a


title: 16-NSC_ProxLoop_HOM_AAC_MEF2C_VP1

description:
16-NSC_ProxLoop_HOM_AAC_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
16-NSC_ProxLoop_HOM_AAC_MEF2C_VP1


title: D_B_1_D_WT_NSC_FACS

description:
D_B_1_D, NSC, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
D_B_1_D_WT_NSC_FACS


title: 33_LRG_WT_A_c

description:
A_c, iN, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
33_LRG_WT_A_c


title: C9_C_1_C9_HET_NSC_FACS

description:
C9_C_1_C9, NSC, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
C9_C_1_C9_HET_NSC_FACS


title: 26_LRG_HET_C9_b

description:
C9_b, iN, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
26_LRG_HET_C9_b


title: C9_D_1_C9_HET_NSC_FACS

description:
C9_D_1_C9, NSC, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
C9_D_1_C9_HET_NSC_FACS


title: C9_B_1_C9_HET_NSC_FACS

description:
C9_B_1_C9, NSC, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
C9_B_1_C9_HET_NSC_FACS


title: C9_A_1_C9_HET_NSC_FACS

description:
C9_A_1_C9, NSC, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
C9_A_1_C9_HET_NSC_FACS


title: 24_LRG_HET_C9_a

description:
C9_a, iN, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
24_LRG_HET_C9_a


title: 12-NSC_LRG_HET_C9A_MEF2C_VP2

description:
12-NSC_LRG_HET_C9A_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
12-NSC_LRG_HET_C9A_MEF2C_VP2


title: J_1_J_WT_NSC_FACS

description:
J_1_J, NSC, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
J_1_J_WT_NSC_FACS


title: D_A_1_D_WT_NSC_FACS

description:
D_A_1_D, NSC, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
D_A_1_D_WT_NSC_FACS


title: C_1_C_WT_NSC_FACS

description:
C_1_C, NSC, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
C_1_C_WT_NSC_FACS


title: 31_LRG_WT_A_b

description:
A_b, iN, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
31_LRG_WT_A_b


title: DistalLoop_G2_4_G2_G2_WT

description:
C12, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_G2_4_G2_G2_WT


title: A_1_A_WT_NSC_FACS

description:
A_1_A, NSC, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A_1_A_WT_NSC_FACS


title: 28_LRG_HET_C9_c

description:
C9_c, iN, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
28_LRG_HET_C9_c


title: MEF2C_VP1_NSC_naive_B_5M

description:
MEF2C_VP1_NSC_naive_B_5M
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_naive_B_5M


title: DistalLoop_G2_1_G2_G2_WT

description:
B6, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_G2_1_G2_G2_WT


title: E_1_E_WT_NSC_FACS

description:
E_1_E, NSC, DistalCluster, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
E_1_E_WT_NSC_FACS


title: DistalLoop_G1_4_G1_G1_WT

description:
G2, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_G1_4_G1_G1_WT


title: DistalLoop_G1_3_G1_G1_WT

description:
G1, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_G1_3_G1_G1_WT


title: DistalLoop_G1_1_G1_G1_WT

description:
C10, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_G1_1_G1_G1_WT


title: 21-NSC_LRG_HET_C9D_MEF2C_VP2

description:
21-NSC_LRG_HET_C9D_MEF2C_VP2
UMI 4C
paired-end
Illumina NovaSeq 6000
21-NSC_LRG_HET_C9D_MEF2C_VP2


title: DistalLoop_D10_1_D10_D10_HET

description:
A3, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_D10_1_D10_D10_HET


title: DistalLoop_D10_3_D10_D10_HET

description:
A4, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_D10_3_D10_D10_HET


title: DistalLoop_C6_4_C6_C6_HET

description:
C6_A, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C6_4_C6_C6_HET


title: DistalLoop_C12_1_C12_C12_HET

description:
A7, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C12_1_C12_C12_HET


title: DistalLoop_C6_B_3_C6_B_C6_B_HET

description:
D10, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C6_B_3_C6_B_C6_B_HET


title: DistalLoop_C6_A_3_C6_A_C6_A_HET

description:
C6_B, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C6_A_3_C6_A_C6_A_HET


title: DistalLoop_C10_3_C10_C10_WT

description:
G1, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C10_3_C10_C10_WT


title: DistalLoop_C12_4_C12_C12_HET

description:
B6, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C12_4_C12_C12_HET


title: DistalLoop_C10_4_C10_C10_WT

description:
G2, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C10_4_C10_C10_WT


title: DistalLoop_G2_3_G2_G2_WT

description:
C6, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_G2_3_G2_G2_WT


title: DistalLoop_C10_1_C10_C10_WT

description:
C10, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_C10_1_C10_C10_WT


title: B_1_B_HET_NSC_FACS

description:
B_1_B, NSC, DistalCluster, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
B_1_B_HET_NSC_FACS


title: DistalLoop_B6_4_B6_B6_HET

description:
B1, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_B6_4_B6_B6_HET


title: DistalLoop_B1_3_B1_B1_WT

description:
B6, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_B1_3_B1_B1_WT


title: DistalLoop_B6_1_B6_B6_HET

description:
C12, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_B6_1_B6_B6_HET


title: DistalLoop_B6_3_B6_B6_HET

description:
D10, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_B6_3_B6_B6_HET


title: DistalLoop_A4_4_A4_A4_WT

description:
G1, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_A4_4_A4_A4_WT


title: DistalLoop_B1_1_B1_B1_WT

description:
A10, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_B1_1_B1_B1_WT


title: DistalLoop_A7_3_A7_A7_HET

description:
G2, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_A7_3_A7_A7_HET


title: DistalLoop_A3_4_A3_A3_WT

description:
C10, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_A3_4_A3_A3_WT


title: DistalLoop_A3_1_A3_A3_WT

description:
B1, iN, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_A3_1_A3_A3_WT


title: MEF2C_VP2_iN_proxLOOP_HET_BB_A

description:
MEF2C_VP2_iN_proxLOOP_HET_BB_A
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_iN_proxLOOP_HET_BB_A


title: Distal_Loop_G2_WT_NSC_1_R1.fastq.gz

description:
G2, NSC, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_G2_WT_NSC_1


title: Distal_Loop_G1_WT_NSC_1_R1.fastq.gz

description:
G1, NSC, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_G1_WT_NSC_1


title: DistalLoop_A10_1_A10_A10_HET

description:
A3, iN, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
DistalLoop_A10_1_A10_A10_HET


title: Distal_Loop_D10_HET_NSC_1_R1.fastq.gz

description:
D10, NSC, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_D10_HET_NSC_1


title: MEF2C_VP2_NSC_Dist_Loop_A10_HET

description:
MEF2C_VP2_NSC_Dist_Loop_A10_HET
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP2_NSC_Dist_Loop_A10_HET


title: Distal_Loop_C10_WT_NSC_1_R1.fastq.gz

description:
C10, NSC, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_C10_WT_NSC_1


title: Distal_Loop_A7_HET_NSC_1_R1.fastq.gz

description:
A7, NSC, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_A7_HET_NSC_1


title: Distal_Loop_B6_HET_NSC_1_R1.fastq.gz

description:
B6, NSC, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_B6_HET_NSC_1


title: Distal_Loop_C12_HET_NSC_1_R1.fastq.gz

description:
C12, NSC, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_C12_HET_NSC_1


title: Distal_Loop_A4_WT_NSC_1_R1.fastq.gz

description:
A4, NSC, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_A4_WT_NSC_1


title: Distal_Loop_A3_WT_NSC_1_R1.fastq.gz

description:
A3, NSC, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_A3_WT_NSC_1


title: Distal_Loop_B1_WT_NSC_1_R1.fastq.gz

description:
B1, NSC, DistalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_B1_WT_NSC_1


title: ProximalLoop_HH_C_HET

description:
HHC , iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_HH_C_HET


title: Distal_Loop_A10_HET_NSC_1_R1.fastq.gz

description:
A10, NSC, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_A10_HET_NSC_1


title: ProximalLoop_HH_A_A_HET

description:
HHA_A, iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_HH_A_A_HET


title: ProximalLoop_HH_B_HET

description:
HHB, iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_HH_B_HET


title: ProximalLoop_GG_B_HOMDEL

description:
GGB, iN, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_GG_B_HOMDEL

value: Homozygous DEL


title: ProximalLoop_H3_B_WT

description:
H3_B, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_H3_B_WT


title: ProximalLoop_GG_C_HOMDEL

description:
GGC , iN, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_GG_C_HOMDEL


title: ProximalLoop_H2_WT

description:
H2, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_H2_WT


title: ProximalLoop_GG_A_HOMDEL

description:
GGA, iN, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_GG_A_HOMDEL


title: ProximalLoop_HH_A_B_HET

description:
HHA_B, iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_HH_A_B_HET


title: ProximalLoop_H3_A_WT

description:
H3_A, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_H3_A_WT


title: ProximalLoop_C7_A_WT

description:
C7_A, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_C7_A_WT


title: ProximalLoop_C7_B_WT

description:
C7_B, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_C7_B_WT


title: ProximalLoop_C5_A_WT

description:
C5_A, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_C5_A_WT


title: ProximalLoop_C5_C_WT

description:
C5_C, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_C5_C_WT


title: ProximalLoop_C6_WT

description:
C6, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_C6_WT


title: ProximalLoop_C5_B_WT

description:
C5_B, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_C5_B_WT


title: ProximalLoop_BB_C_HET

description:
BBC , iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_BB_C_HET


title: ProximalLoop_BB_B_C_HET

description:
BBB_C, iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_BB_B_C_HET


title: Distal_Loop_C6_HET_NSC_1_R1.fastq.gz

description:
C6, NSC, DistalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Distal_Loop_C6_HET_NSC_1


title: ProximalLoop_BB_B_B_HET

description:
BBB_B, iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_BB_B_B_HET


title: ProximalLoop_AA_C_HOMDEL

description:
AAC, iN, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_AA_C_HOMDEL


title: ProximalLoop_H4_WT

description:
H4, iN, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_H4_WT


title: Prox_Loop_HH_C_HET_NSC_R1.fastq.gz

description:
HHC, NSC, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_HH_C_HET_NSC


title: ProximalLoop_AA_A_HOMDEL

description:
AAA, iN, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_AA_A_HOMDEL


title: ProximalLoop_AA_B_HOMDEL

description:
AAB, iN, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_AA_B_HOMDEL


title: Prox_Loop_GG_C_HOMDEL_NSC_R1.fastq.gz

description:
GGC, NSC, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_GG_C_HOMDEL_NSC


title: Prox_Loop_GG_A_HOMDEL_NSC_R1.fastq.gz

description:
GGA, NSC, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_GG_A_HOMDEL_NSC


title: Prox_Loop_HH_B_HET_NSC_R1.fastq.gz

description:
HHB, NSC, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_HH_B_HET_NSC


title: Prox_Loop_C7_B_WT_NSC_R1.fastq.gz

description:
D7, NSC, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_C7_B_WT_NSC


title: Prox_Loop_GG_B_HOMDEL_NSC_R1.fastq.gz

description:
GGB, NSC, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_GG_B_HOMDEL_NSC


title: Prox_Loop_C6_B_WT_NSC_R1.fastq.gz

description:
D6, NSC, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_C6_B_WT_NSC


title: Prox_Loop_C5_B_WT_NSC_R1.fastq.gz

description:
D5, NSC, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_C5_B_WT_NSC


title: Prox_Loop_C7_A_WT_NSC_R1.fastq.gz

description:
C7, NSC, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_C7_A_WT_NSC


title: Prox_Loop_BB_C_HET_NSC_R1.fastq.gz

description:
BBC, NSC, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_BB_C_HET_NSC


title: Prox_Loop_BB_B_HET_NSC_R1.fastq.gz

description:
BBB, NSC, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_BB_B_HET_NSC


title: Prox_Loop_AA_B_HOMDEL_NSC_R1.fastq.gz

description:
AAB, NSC, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_AA_B_HOMDEL_NSC


title: Prox_Loop_AA_C_HOMDEL_NSC_R1.fastq.gz

description:
AAC, NSC, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_AA_C_HOMDEL_NSC


title: F3_BA_iN

description:
C2_CB, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
F3_BA_iN


title: Prox_Loop_C5_A_WT_NSC_R1.fastq.gz

description:
C5, NSC, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_C5_A_WT_NSC


title: ProximalLoop_BB_B_A_HET

description:
BBB_A, iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_BB_B_A_HET


title: Prox_Loop_BB_A_HET_NSC_R1.fastq.gz

description:
BBA, NSC, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_BB_A_HET_NSC


title: F3_AB_iN

description:
C2_CA, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
F3_AB_iN


title: F3_AA_iN

description:
C2_BA, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
F3_AA_iN


title: ProximalLoop_BB_A_HET

description:
BBA, iN, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
ProximalLoop_BB_A_HET


title: Prox_Loop_HH_A_HET_NSC_R1.fastq.gz

description:
HHA, NSC, ProximalBoundary, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_HH_A_HET_NSC


title: C2_CB_iN

description:
A8_AC, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_CB_iN


title: C2_CA_iN

description:
A8_CB, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_CA_iN


title: D3_iN

description:
C2_AB, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
D3_iN


title: D1_AB_iN

description:
C2_AA, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
D1_AB_iN


title: D1_AA_iN

description:
A8_BC, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
D1_AA_iN


title: Prox_Loop_C6_A_WT_NSC_R1.fastq.gz

description:
C6, NSC, ProximalBoundary, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_C6_A_WT_NSC


title: C2_BC_iN

description:
A8_CA, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_BC_iN


title: C2_BA_iN

description:
A8_BB, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_BA_iN


title: C2_AA_iN

description:
A8_AB, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_AA_iN


title: C2_AB_iN

description:
A8_BA, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_AB_iN


title: B9_B_iN

description:
D3, iN, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
B9_B_iN


title: A8_CB_iN

description:
B9_B, iN, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_CB_iN


title: A8_BB_iN

description:
D1_AB, iN, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_BB_iN


title: A8_AC_iN

description:
F3_BB, iN, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_AC_iN


title: B9_C_iN

description:
A8_AA, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
B9_C_iN


title: B9_A_iN

description:
B9_C, iN, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
B9_A_iN


title: A4_B_iN

description:
F3_AA, iN, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A4_B_iN


title: Prox_Loop_AA_A_HOMDEL_NSC_R1.fastq.gz

description:
AAA, NSC, ProximalBoundary, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
Prox_Loop_AA_A_HOMDEL_NSC


title: H5_B_NSC

description:
A8_C, NSC, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
H5_B_NSC


title: H5_A_NSC

description:
C2_C, NSC, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
H5_A_NSC


title: A8_BC_iN

description:
A4_B, iN, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_BC_iN


title: F3_BB_iN

description:
C2_BC, iN, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
F3_BB_iN


title: A8_CA_iN

description:
B9_A, iN, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_CA_iN


title: A8_AA_iN

description:
F3_AB, iN, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_AA_iN


title: F3_B_NSC

description:
C2_B, NSC, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
F3_B_NSC


title: F3_A_NSC

description:
C2_A, NSC, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
F3_A_NSC


title: D1_B_NSC

description:
E6, NSC, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
D1_B_NSC


title: MEF2C_VP1_NSC_MEF2C_HOM_H_B_VP1

description:
MEF2C_VP1_NSC_MEF2C_HOM_H_B_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
MEF2C_VP1_NSC_MEF2C_HOM_H_B_VP1


title: 2-NSC_proxLoop_HOM_AA_MEF2C_VP1

description:
2-NSC_proxLoop_HOM_AA_MEF2C_VP1
UMI 4C
paired-end
Illumina NovaSeq 6000
2-NSC_proxLoop_HOM_AA_MEF2C_VP1


title: A8_BA_iN

description:
D1_AA, iN, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_BA_iN


title: C2_B_NSC

description:
B9_A, NSC, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_B_NSC


title: C2_A_NSC

description:
A4_B, NSC, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_A_NSC


title: B9_B_NSC

description:
A4_A, NSC, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
B9_B_NSC


title: D1_A_NSC

description:
D3, NSC, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
D1_A_NSC


title: E6_NSC

description:
A8_B, NSC, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
E6_NSC


title: C2_C_NSC

description:
B9_B, NSC, AdjacentTAD, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
C2_C_NSC


title: B9_A_NSC

description:
H5_B, NSC, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
B9_A_NSC


title: A8_AB_iN

description:
F3_BA, iN, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_AB_iN


title: A8_B_NSC

description:
F3_B, NSC, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_B_NSC


title: A4_B_NSC

description:
D1_B, NSC, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A4_B_NSC


title: A8_A_NSC

description:
F3_A, NSC, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_A_NSC


title: A4_A_NSC

description:
D1_A, NSC, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A4_A_NSC


title: D3_NSC

description:
A8_A, NSC, AdjacentTAD, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
D3_NSC


title: H2_BC_iN

description:
C3_A, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H2_BC_iN


title: H2_BB_iN

description:
H2_BD, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H2_BB_iN


title: H2_BD_iN

description:
C3_B, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H2_BD_iN


title: F11_C_iN

description:
A1_B, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F11_C_iN


title: F6_A_iN

description:
A1_D, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F6_A_iN


title: F5_iN

description:
A1_C, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F5_iN


title: F6_B_iN

description:
H2_AA, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F6_B_iN


title: H2_BA_iN

description:
H2_BC, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H2_BA_iN


title: H2_AB_iN

description:
H2_BB, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H2_AB_iN


title: H2_AA_iN

description:
H2_BA, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H2_AA_iN


title: F9_iN

description:
H2_AB, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F9_iN


title: A8_C_NSC

description:
H5_A, NSC, AdjacentTAD, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A8_C_NSC


title: D11_iN

description:
D11, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
D11_iN


title: C3_B_iN

description:
F5, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
C3_B_iN


title: F11_B_iN

description:
A1_A, iN, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F11_B_iN


title: H1_NSC

description:
C3, NSC, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H1_NSC


title: H2_NSC

description:
C6, NSC, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H2_NSC


title: F9_NSC

description:
H1, NSC, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F9_NSC


title: F11_NSC

description:
G11, NSC, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F11_NSC


title: D11_NSC

description:
A1, NSC, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
D11_NSC


title: A1_B_iN

description:
F11_B, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A1_B_iN


title: A1_D_iN

description:
F6_A, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A1_D_iN


title: A1_C_iN

description:
F11_C, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A1_C_iN


title: C6_NSC

description:
F9, NSC, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
C6_NSC


title: C3_A_iN

description:
F6_B, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
C3_A_iN


title: C3_NSC

description:
D11_B, NSC, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
C3_NSC


title: A1_NSC

description:
A3, NSC, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A1_NSC


title: A1_A_iN

description:
F11_A, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A1_A_iN


title: H5_MEF2C_HET_Kc

description:
HET_Kc, iN, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
H5_MEF2C_HET_Kc


title: H4_MEF2C_HD_Xa

description:
HD_Xa, iN, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
H4_MEF2C_HD_Xa


title: G3_MEF2C_HET_Kb

description:
HET_Kb, iN, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
G3_MEF2C_HET_Kb


title: F5_MEF2C_WT_Jb

description:
WT_Jb, iN, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
F5_MEF2C_WT_Jb


title: G6_MEF2C_HD_Hb

description:
HD_Hb, iN, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
G6_MEF2C_HD_Hb


title: G11_NSC

description:
H2, NSC, Separator, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
G11_NSC


title: F3_MEF2C_HET_Ra

description:
HET_Ra, iN, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
F3_MEF2C_HET_Ra


title: D11_B_NSC

description:
F11, NSC, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
D11_B_NSC


title: F11_A_iN

description:
F9, iN, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
F11_A_iN


title: A3_NSC

description:
D11, NSC, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A3_NSC


title: A3_B_NSC

description:
A3_B, NSC, Separator, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
A3_B_NSC


title: NSC_6_HOMDEL

description:
N, NSC, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_6_HOMDEL


title: E4_MEF2C_HD_Ha

description:
HD_Ha, iN, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
E4_MEF2C_HD_Ha


title: NSC_5_HET

description:
J_A, NSC, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_5_HET


title: E6_MEF2C_HD_Hc

description:
HD_Hc, iN, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
E6_MEF2C_HD_Hc


title: E3_MEF2C_HET_Rb

description:
HET_Rb, iN, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
E3_MEF2C_HET_Rb


title: NSC_5_HOMDEL

description:
J_B, NSC, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_5_HOMDEL


title: D6_MEF2C_HET_Rc

description:
HET_Rc, iN, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
D6_MEF2C_HET_Rc


title: NSC_4_HOMDEL

description:
X_B, NSC, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_4_HOMDEL


title: NSC_3_WT

description:
H_C, NSC, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_3_WT


title: C5_MEF2C_WT_Ja

description:
WT_Ja, iN, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
C5_MEF2C_WT_Ja


title: C3_MEF2C_WT_Ma

description:
WT_Ma, iN, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
C3_MEF2C_WT_Ma


title: B7_MEF2C_HD_Xb

description:
HD_Xb, iN, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
B7_MEF2C_HD_Xb


title: B5_MEF2C_WT_Mb

description:
WT_Mb, iN, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
B5_MEF2C_WT_Mb


title: NSC_2_HET

description:
R_A, NSC, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_2_HET


title: B3_MEF2C_WT_N

description:
WT_N, iN, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
B3_MEF2C_WT_N


title: A7_MEF2C_HD_Xc

description:
HD_Xc, iN, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
A7_MEF2C_HD_Xc


title: A6_MEF2C_HET_Ka

description:
HET_Ka, iN, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
A6_MEF2C_HET_Ka


title: NSC_6_WT

description:
Q, NSC, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_6_WT


title: NSC_1_HOMDEL

description:
K_B, NSC, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_1_HOMDEL


title: NSC_6_HET

description:
M_B, NSC, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_6_HET


title: NSC_5_WT

description:
M_A, NSC, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_5_WT


title: NSC_4_HET

description:
X_A, NSC, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_4_HET


title: NSC_3_HET

description:
H_A, NSC, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_3_HET


title: NSC_2_WT

description:
R_C, NSC, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_2_WT


title: NSC_3_HOMDEL

description:
H_B, NSC, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_3_HOMDEL


title: NSC_4_WT

description:
X_C, NSC, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_4_WT


title: NSC_1_WT

description:
K_C, NSC, MEF2CDEL, WT
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_1_WT


title: NSC_2_HOMDEL

description:
R_B, NSC, MEF2CDEL, HOM
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_2_HOMDEL


title: PZ-sortChIC-k562-k4me1-3

status: Public on Jun 08 2022

city: Utrecht

first: Jake

last: Yeung

address: Uppsalalaan 8

country: Netherlands

institute: Hubrecht Institute

data_processing:
fastq files were mapped using BWA-0.7.16a (r1181) to ENSEMBL Build 95
Count tables are 50 kb regions genome-wide across individual cells, counted from bam files
Assembly: mm10
Supplementary files format and content: Count tables are 50 kb regions genome-wide across individual cells, counted from bam files. Metadata contains UMAP coordinates and cell type labels. Metadata LSK contains FACS-information for Sca1, cKit, and Lineage for a subset of cells.

extract_protocol:
Cells were resuspended in 500ul wash buffer (47.5ml H2O RNAse free, 1ml 1M HEPES pH 7.5, 1.5ml 5M NaCl, 3.6ul pure spermidine solution). Aliquot in a 0.5ml protein low-binding tubes (1 per antibody to be used). Following steps are performed on ice.
Cells were pelleted at 600g for 3min and resuspended in 400 ul Wash Buffer 1 (wash buffer with extra 0.05% saponin (Sigma Aldrich), protease inhibitor cocktail (Sigma Aldrich), 4 ul/ml 0.5M EDTA) containing the primary antibody (1:100 dilution for H3K4me1, H3K9me3 and H3K27me3 and 1:200 dilution for H3K4me3, Saponin has to be prepared fresh every time as a 10% solution in PBS). Cells were incubated overnight at 4oC on a roller, before they were washed once with 500 ul Wash Buffer 2 (wash buffer with extra 0.05% saponin, protease inhibitor).
Afterwards cells were resuspended in 500 ul Wash Buffer 2 containing PaMN (3ng/ml) and incubated for 1h at 4C on a roller.
Finally, cells were washed an additional 2 times with 500 ul Wash Buffer 2 before passing it through a 70um cell strainer (Corning, 431751) and sorting them on a JAZZ FACS machine into 384 well plates containing 50nl Wash buffer 3 (Wash buffer containing 0,05% saponin) and 5ul sterile filtered mineral oil (Sigma Aldrich) per well. Small volumes were distributed using a Nanodrop II system (Innovadyme). 50nl of Wash Buffer 3, containing 4uM CaCl2, were added per cell to induce Protein A-MN mediated chromatin digestion that was performed for 30min on ice. Afterwards the reaction was stopped by adding 100nl of a stop solution containing 40mM EGTA (chelates Ca2+ and stops MN), 1.5% NP40 and 10ul 2mg/ml proteinase k (Ambion). Chromatin is subsequently released and PaMN permanently destroyed by proteinase k digestion at 65C for 6h followed by 80C for 20min to heat inactivate proteinase k. Afterwards plates can be stored at -20C until further processing.
DNA fragments are further blunt ended using Klenow large fragment (NEB) and T4 PNK (NEB) in the presence of dNTPs. Afterwards nonintegrated dNTPs are removed using schrimp alkaline phosphatase (NEB) to increase A-tail efficiency. Subsequently blunt fragments are A-Tailed using AmpliTaq™ 360 DNA Polymerase (Thermofisher) in the presence of fresh dATP and T4 PNK (NEB). Next fragments are ligated to T-tail adaptors containing 3 bp UMIs and an 8bp cell barcode (final concentration 9nM from IDT) for 16h at 16C using T4-ligase (NEB). Adaptors were added with a Mosquito HTS (ttp labtech). Ligation products were pooled by centrifugation and cleaned using Ampure XP beads at a bead to sample ratio of 0.8 (Beckman Coulter). The cleaned DNA is then linear amplified by invitro transcription with components of MessageAmp II (Invitrogen) for 16h at 37C. The produced RNA is purified 1-3 times depending on Adaptor dimer contamination using RNA Clean XP beads (Beckman Coulter) at 0.8 beads to sample ratio, followed by RNA fragmentation for 2.5 min at 94C. After another bead cleanup, 20% of the RNA is reverse transcribed with Superscript II (NEB) and PCR amplified to add the Illumina smallRNA barcodes and handles with NEBNext Ultra II Q5 Master Mix. PCR cycles depended on the abundance of the histone modification assayed and the number of RNA cleanup cycles after IVT needed (8-10 for H3K9me3 and H3K27me3 10-12 for H3K4me1 and 12-15 for H3K4me3).


title: PZ-sortChIC-k562-k4me3-2


title: PZ-sortChIC-k562-k4me1-1


title: PZ-sortChIC-k562-k9me3-1


title: PZ-sortChIC-k562-k9me3-3


title: PZ-sortChIC-k562-k4me3-1


title: PZ-sortChIC-k562-k27me3-2


title: PZ-sortChIC-k562-k27me3-1


title: NSC_1_HET

description:
K_A, NSC, MEF2CDEL, HET
PolyA RNA
paired-end
Illumina NovaSeq 6000
NSC_1_HET


title: PZ-sortChIC-k562-k4me1-2


title: BM-k4me3-SL4-2

description: genomicDNA_cut_from_MNase-ProteinA_with_staining_of_k4me3

organism: Mus musculus

source_name: Bone Marrow

tag: strain

tag: tissue

value: Bone Marrow

tag: age


title: PZ-sortChIC-k562-k4me3-3


title: BM-k27me3-SL5-1

description: genomicDNA_cut_from_MNase-ProteinA_with_staining_of_k27me3


title: BM-k4me1-SL1-1

description: genomicDNA_cut_from_MNase-ProteinA_with_staining_of_k4me1


title: BM-k27me3-SL1-2


title: BM-k9me3-SL5-2

description: genomicDNA_cut_from_MNase-ProteinA_with_staining_of_k9me3


title: BM-k9me3-SL5-9


title: BM-k4me1-SL2-1


title: PZ-sortChIC-k562-k9me3-2


title: BM-k4me3-SL5-6


title: BM-k4me1-SL5-8


title: PZ-sortChIC-k562-k27me3-3


title: BM-k4me1-SL5-10


title: BM-k9me3-SL5-4


title: BM-k27me3-SL5-7


title: BM-k4me1-SL4-1


title: BM-k4me1-SL5-3


title: BM-k4me3-SL1-2


title: BM-k4me3-SL4-4


title: BM-k4me1-SL5-5


title: BM-k27me3-SL4-1


title: BM-k9me3-SL5-10


title: BM-k9me3-SL5-8


title: BM-k9me3-SL5-3


title: BM-k4me3-SL4-3


title: BM-k4me1-SL5-4


title: BM-k4me1-SL3-2


title: BM-k9me3-SL4-1


title: BM-k4me1-SL5-2


title: BM-k9me3-SL2-1


title: BM-k4me3-SL4-5


title: BM-k9me3-SL1-1


title: BM-k27me3-SL5-6


title: BM-k4me3-SL3-1


title: BM-k4me1-SL5-9


title: BM-k4me3-SL5-7


title: BM-k4me3-SL5-2


title: BM-k27me3-SL3-2


title: BM-k4me1-SL4-5


title: BM-k4me1-SL5-7


title: BM-k9me3-SL4-2


title: BM-k4me3-SL5-9


title: BM-k4me3-SL5-10


title: BM-k4me3-SL2-2


title: BM-k27me3-SL2-2


title: BM-k4me3-SL5-1


title: BM-k27me3-SL2-1


title: BM-k4me1-SL3-1


title: BM-k9me3-SL1-2


title: BM-k27me3-SL4-5


title: BM-k27me3-SL5-3


title: BM-k9me3-SL4-4


title: BM-k27me3-SL4-3


title: BM-k27me3-SL5-8


title: BM-k4me3-SL3-2


title: BM-k27me3-SL3-1


title: BM-k27me3-SL5-5


title: BM-k4me1-SL4-3


title: BM-k9me3-SL5-5


title: BM-k4me1-SL5-1


title: BM-k4me3-SL5-4


title: BM-k4me1-SL5-6


title: BM-k4me3-SL5-8


title: BM-k4me1-SL2-2


title: BM-k27me3-SL1-1


title: BM-k9me3-SL5-1


title: BM-k27me3-SL5-9


title: BM-k27me3-SL4-4


title: BM-k9me3-SL4-3


title: BM-k9me3-SL5-6


title: BM-k4me3-SL4-1


title: BM-k27me3-SL5-2


title: BM-k4me1-SL4-4


title: BM-k9me3-SL4-5


title: BM-k4me1-SL4-2


title: BM-k27me3-SL5-10


title: BM-k27me3-SL4-2


title: BM-k4me3-SL1-1


title: BM-k27me3-SL5-4


title: BM-k9me3-SL5-7


title: BM-k9me3-SL2-2


title: BM-k4me3-SL5-5


title: Retic_ac4C_80S

city: Bethesda

first: David

last: Sturgill

state: MARYLAND

address: Building 41, Rm B622

department: NCI

institute: NIH

data_processing:
Raw reads were pre-processed to remove low quality bases and adapter sequences using cutadapt
For Ribo-Seq: After trimming, reads were stringently filtered for the presence of ribosomal RNA using a two-step process.  First, we performed local alignments to the ribosomal repeating subunit (gb|U13369.1) in very sensitive mode using bowtie2 (v.2.3.5.1)). Second, we mapped remaining reads using Hisat2 (v2.2.1.0), explicitly allowing for mismatches at the first nucleotide position. Trimmed and filtered reads were then aligned to a reference composed of canonical transcript sequence from the UCSC genome browser in the hg19 assembly, using bowtie2 (v.2.3.5.1)
RedaC:T-seq reads were aligned to the human genome (hg19) and the human transcriptome (longest isoform from UCSC) using STAR (v 2.5.4.a) in local alignment mode, keeping uniquely aligned reads and allowing five mismatches per read. Separate alignments to 18S rRNA, 28S rRNA and tRNA sequences were performed to specifically analyze reads originating from these features. Variant calls were performed in pooled biological replicates using Samtools mpileup including a minimum base quality -Q 20, the BAQ (Base Alignment Quality) and -C50 parameters activated and supplying a -f indexed reference fasta file. mpileup results were then tabulated using the mpileup2readcounts script.
For Polysome sequencing: reads were aligned to the human genome (hg19 assembly) containing the Luciferase Spike-in sequence using Hisat2 (v2.2.1.0). Gene counts within each fraction were obtained using StringTie2, normalized to the spike-in probe and converted to Transcripts per million (TPM)
For rabbit reticulocyte sequencing, reference transcripts for oryCun2 were retrieved from the UCSC genome browser for index construction using Kallisto (v0.48).  Transcript abundances in units of TPM were calculated against this reference with kallisto quant.
Assembly: hg19
Supplementary files format and content: HR_riboseq.txt contains P-sites called from Harringtonine-treated Ribo-seq
Supplementary files format and content: RedaCTseq_ac4C_sites.txt contains data for ac4C sites called from RedaCT-Seq
Supplementary files format and content: Counts text files contain raw gene abundance values from Stringtie2

molecule: total RNA

organism: Oryctolagus cuniculus

source_name: Rabbit reticulocyte lysate

extract_protocol:
Total RNA was isolated from resuspended ribosome pellets with TRIzol Reagent and subjected to RT-qPCR analysis and deep-sequencing
Ribodepleted RNA isolated from purified initiation complexes was also sequenced in a MiSeq instrument in paired-end mode at 75 bp read lengths.

treatment_protocol: To capture 80S translation initiation complexes, 140 ml of rabbit reticulocyte lysates was preincubated with 20 ng/ml Harringtonine for 10 min at 30°C, followed by addition of 800 ng mRNA (pre-heated at 65°C for 2 min) in a total volume of 200 ml.


title: 19659X20

city: Salt Lake City

first: Eric

last: Snyder

state: UT

address: 2000 Circle of Hope Drive

department: Pathology

institute: University of Utah, Huntsman Cancer Institute

description:
Bulk RNA sequencing
19659R_counts.txt

data_processing:
The human GRCm38 FASTA and GTF files were downloaded from Ensembl release 102.
The reference database was created using STAR version 2.7.6a with splice junctions optimized for 125 base pair reads.
Reads were trimmed of adapters and aligned to the reference database using STAR in two pass mode to output a BAM file sorted by coordinates.
Mapped reads were assigned to annotated genes in the GTF file using featureCounts version 1.5.1
Non-coding features, histones, and ribosomal RNAs were removed and differentially expressed genes were identified using a 5% false discovery rate with DESeq2.
Assembly: GRCm38
Supplementary files format and content: FeatureCounts output files combined into a single tab-delimited matrix

growth_protocol: Organoids were established by digesting individual murine LUAD tumors. Cells are suspended in Matrigel and are cultured in L-WRN conditioned media

extract_protocol:
PureLink RNA Mini Kit
NEBNext Ultra II Directional RNA Library Prep

treatment_protocol: Organoids were treated with vehicle or 2 um 4-OHT for 72 hours. Cells were crosslinked 21 days post-tamoxifen treatment.

value: Mixed 129/B6

tag: disease state

value: Lung adenocarcinoma

value: 4-hydroxytamoxifen (2 um)

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, and Foxa1flox


title: Retic_C_80S


title: 19659X19

description:
Bulk RNA sequencing
19659R_counts.txt

value: Vehicle (Ethanol)


title: 19659X17

description:
Bulk RNA sequencing
19659R_counts.txt


title: 19659X18

description:
Bulk RNA sequencing
19659R_counts.txt


title: BM-k4me3-SL5-3


title: 19659X16

description:
Bulk RNA sequencing
19659R_counts.txt


title: 19659X14

description:
Bulk RNA sequencing
19659R_counts.txt


title: BM-k4me1-SL1-2


title: 19659X15

description:
Bulk RNA sequencing
19659R_counts.txt


title: BM-k9me3-SL3-1


title: 19659X11

description:
Bulk RNA sequencing
19659R_counts.txt


title: 19659X10

description:
Bulk RNA sequencing
19659R_counts.txt


title: 19659X12

description:
Bulk RNA sequencing
19659R_counts.txt


title: 19659X7

description:
Bulk RNA sequencing
19659R_counts.txt

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, and Foxa2flox


title: 19659X6

description:
Bulk RNA sequencing
19659R_counts.txt


title: 19659X9

description:
Bulk RNA sequencing
19659R_counts.txt


title: 17992X7

description:
Bulk RNA sequencing
19659R_counts.txt


title: 17699X10

description:
Bulk RNA sequencing
19659R_counts.txt


title: BM-k4me3-SL2-1


title: 19659X8

description:
Bulk RNA sequencing
19659R_counts.txt


title: 17992X8

description:
Bulk RNA sequencing
19659R_counts.txt


title: 17699X9

description:
Bulk RNA sequencing
19659R_counts.txt


title: 19659X5

description:
Bulk RNA sequencing
19659R_counts.txt


title: 11-17_IP

description:
19455X5
fragmented genomic DNA

data_processing:
Fastq reads were aligned to the standard mouse chromosomes (build mm10) with Novocraft novoalign (v4.03.01) using their default Novaseq tuned settings. Standard Illumina adapter sequences were provided to novoalign for masking. Alignments were run through samtools fixmate (v1.12).
Alignments were put through the MultiRepMacsChIPSeq pipeline (v17, https://github.com/HuntsmanCancerInstitute/MultiRepMacsChIPSeq). Exclusion intervals were generated  de novo by calling peaks on combined, unfiltered Input sample alignments. Alignments on the mitochondrial chromosome and overlapping these exclusion intervals were subsequently discarded from analysis. Only properly paired alignments were used. Optical duplicates with a threshold of 2500 pixels were discarded. Coordinate duplicate alignments were randomly subsampled to a uniform 5% rate. Peaks were independently called for each sample using Macs2 on filtered alignments using a q-value threshold of 0.01, minimum peak length of 200 bp, and minimum peak gap of 100 bp.
Fragment coverage tracks were generated using MultiRepMacsChIPSeq pipeline based on properly-paired, filtered alignments. Multi-mapping alignments were scored as a fraction based on the reported number of hits in the genome (alignment tag NH). Tracks were depth-normalized to 1 million fragments.
Assembly: UCSC mm10
Supplementary files format and content: BigWig files representing depth-normalized, fragment coverage of ChIP samples

source_name: 1027B Organoids

extract_protocol:
Lysates were sonicated and Antibody:chromatin complexes were immunoprecipitated using Chromatrap ChIPseq kits. IP and input DNA purified with Zymo ChIP DNA Clean and Concentrator columns
NEBNext Ultra II DNA Library Prep Kit

treatment_protocol: Organoids were treated with vehicle or 2 um 4-OHT for 72 hours. Cells were crosslinked 14-20 days post-tamoxifen treatment.

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox

tag: chip antibody

value: FoxA2 CST D56D6


title: 11-17_Input

description:
19455X6
fragmented genomic DNA

value: no antibody


title: 11-22_IP

description:
19455X7
fragmented genomic DNA


title: 6-26_IP

description:
19455X3
fragmented genomic DNA


title: 6-26_Input

description:
19455X4
fragmented genomic DNA


title: 6-21_IP

description:
19455X1
fragmented genomic DNA


title: 19659X13

description:
Bulk RNA sequencing
19659R_counts.txt


title: Kidney carcinoma cells - 786-0, PDL1-IFNg, rep3

status: Public on Jun 05 2022

city: Rockville

first: Alexis

middle: L

last: Norris

state: MD

address: 7500 Standish Place

institute: US FDA

description: Sample 24

data_processing:
Base calling with bcl2fastq2 version 2.19.0
Sequencing reads were trimmed using trimmomatic (version 0.36.6; parameters: SLIDINGWINDOW:4:20 MINLEN:50)
Aligned to GRCh38/hg38 using HISAT2 (version 2.1.0; parameters: --n-ceil L,0.0,0.15 --mp 6,2 --no-softclip --np 1 --rdg 5,3 --rfg 5,3 --sp 2,1 --score-min L,0.0, -0.2 --pen-cansplice 0 --pen-noncansplice 12 --pen-canintronlen G,-8.0,1.0 --pen-noncanintronlen G,-8.0,1.0 --min-intronlen 20 --max-intronlen 500000)
Gene counts were estimated using featureCounts (version 1.6.3; parameters: -s 1 -t 'exon' -g 'gene_id' -J -Q 12 --minOverlap 1 --fracOverlap 0 --fracOverlapFeature 0) with GENCODE gene annotation (version 33; Ensembl version 99)
Assembly: hg38
Supplementary files format and content: FASTQ files have adapters trimmed but were not trimmed for quality using trimmomatic.
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

growth_protocol: The ccRCC cell lines 786-O and A498 were purchased from ATCC. They were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM) growth media containing 25mM glucose and glutamine supplemented with 10% heat-inactivated fetal bovine serum and 1% penicillin-streptomycin at 37⁰C in a humidified atmosphere of 5% CO2. Stable 786-O and A498 cell lines expressing Renilla luciferase were generated by transducing cells with LP462-025 lentiviral particles (Genecopia). Briefly, 786-O and A498 cells were transduced with lentiviral particles at a MOI (multiplicity of infection) of 5 in complete media with polybrene at a concentration of 5 μg/mL. Transduced cells were selected with media containing puromycin at a concentration of 4 μg/mL. Renilla Luciferase activity in cells was measured according to the manufacturer protocol.

extract_protocol:
Total RNA from three groups (Cnsi, Cnsi-IFNγ, and PD-L1si IFNγ) for both A498 and 786-O cell lines, was extracted using RNeasy Mini Kit (Qiagen, Germany) according to the manufacturer’s protocol. Quality of the RNA samples was checked using the Agilent Bioanalyzer RNA Nano Chip (Santa Clara, CA) to determine RNA Integrity Number (RIN) ≥ 8.
RNA samples were processed following the Illumina (San Diego, CA) TruSeq Stranded messenger RNA Sample Preparation Kit performed at FDA Core Facility (36). Briefly, poly (A) tailed RNA was purified from 100-200 ng of total RNA, fragmented, and reverse-transcribed into cDNAs. Double strand cDNAs were adenylated at the 3’ ends and individually indexed, followed by limited-cycle (15) amplification.

treatment_protocol: On-Target plus SMARTpool small interfering RNAs (siRNAs) against PD-L1 was purchased from Dharmacon. All siRNA transfections were conducted at a final concentration of 20 nM using Lipofectamine RNAiMAX (Invitrogen) following the manufacturer instructions. Non-targeting pool siRNA was used as a control (Cnsi). Transient silencing experiments had four groups, Cnsi (control scrambled siRNA, untreated), Cnsi IFNγ (IFNγ treated), PD-L1si (PD-L1 siRNA) and PD-L1si IFNγ (PD-L1 siRNA and IFNγ treatment). A498 and 786-O cells were transfected with control (scrambled siRNA) or PD-L1 siRNA, at the end of 24 hours of transfection, select groups were treated with IFNγ (50 ng/mL) for another 24 hours.

value: clear cell renal cell carcinoma (ccRCC)

value: Kidney carcinoma cells

tag: sirna

value: PD-L1 siRNA

value: PD-L1 knockout

value: Interferon gamma


title: SOXC_Prx1Cre_E11.5

city: Philadelphia

first: Véronique

last: Lefebvre

state: Pennsylvania

address: 3615 Civic Center Boulevard, ARC 912

department: Division of Orthopaedic Surgery

institute: The Children's Hospital of Philadelphia Research Institute

data_processing:
Alignment, demultiplexing, barcode assignment and UMI quantification Cell Ranger (10X Genomics)
Clustering and gene expression analysis Seurat v3
Pseudotime analysis Monocle 3
RNA velocity velocyto.py and velocyto.R
Assembly: mm10
Supplementary files format and content: Cell Ranger output files as Matrix (.mtx) and .tsv formats, and gene expression analysis from Seurat as Excel Spreadsheet (.xlsx)

source_name: Cranium

extract_protocol:
Cranial tissues were digested in LiberaseTM to obtain single cell suspensions
Chromium Single Cell 3’ v2 Reagent Kit (10X Genomics) for E15.5 samples, and Chromium Single Cell 3’ v3 Reagent Kit (10X Genomics) for all the other samples. Libraries were sequenced using a NovaSeq sequencer.

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl Prx1Cre

value: Cranial mesenchyme


title: SOXC_WT_E12.5

value: Sox4fl/fl Sox11fl/fl Sox12fl/fl


title: Kidney carcinoma cells - 786-0, PDL1-IFNg, rep2

description: Sample 23


title: SOXC_WT_E11.5


title: Kidney carcinoma cells - 786-0, PDL1-IFNg, rep1

description: Sample 22


title: Kidney carcinoma cells - 786-0, Control-IFNg, rep3

description: Sample 18

value: Control scrambled siRNA

value: control


title: Kidney carcinoma cells - 786-0, PDL1, rep3

description: Sample 21

source_name: Kidney carcinoma cells - 786-0, PDL1


title: Kidney carcinoma cells - 786-0, Control-IFNg, rep1

description: Sample 16


title: 11-22_Input

description:
19455X8
fragmented genomic DNA

value: Mixed 129/B6

value: Lung adenocarcinoma


title: Kidney carcinoma cells - 786-0, Control-IFNg, rep2

description: Sample 17


title: Kidney carcinoma cells - 786-0, Control, rep3

description: Sample 15

source_name: Kidney carcinoma cells - 786-0, Control


title: Kidney carcinoma cells - 786-0, PDL1, rep1

description: Sample 19


title: Kidney carcinoma cells - 786-0, Control, rep1

description: Sample 13


title: Kidney carcinoma cells - 786-0, Control, rep2

description: Sample 14


title: ATAC_WT_1

status: Public on Jun 03 2022

city: paris

first: Pablo

last: Navarro

address: 25 rue du Docteur Roux

country: France

institute: Institut Pasteur

description: Drosophila chromatin spiked in

data_processing:
ChIP-seq: reads were aligned using Bowtie2 local alignments --very-sensitive option. No bamq filter was used to allow multimappers.  ATAC-seq: Paired end reads were trimmed by alignment for reverse complementary regions surrounded by relevant adapters. Reads were aligned using Bowtie2 with options “-k 10 -I 0 -X 1000 --no-discordant --no-mixed”. Pairs were filtered for mapping quality 255 and mean edit-distance <= 4
ChIP-seq: regions of enrichment were identified following an established approach (Nicetto et al. Science 2019)  ATAC-seq: peaks were identified with MACS2
Assembly: mm10
Supplementary files format and content: H3K9me3_regions.txt contains spike and input normalised enrichment values
Supplementary files format and content: ATAC_peaks.txt contains spike normalised enrichment values

source_name: mouse ES cell

growth_protocol: ES cells were grown in standard FCS+LIF conditions

extract_protocol:
Formaldehyde-fixed chromatin was exctrated and ChIP was performed using standard procedures using ab1220. ATAC-seq was also performed with standard procedures using Nextera kit (Illumina, Cat# FC-121-1030)
ChIP-seq: Precipitated DNA was resuspended in 37.5µl of water and mixed with 2µl of 10mM dNTPs, 5µl of NEB T4 ligase buffer, 2.5µl of NEB T4 polymerase (Cat# M0203L), 0.5µl of NEB Klenow polymerase (Cat# M0210L) and 2.5µl of NEB T4 PNK (Cat# M0201L). Samples were incubated 30min at 20oC. DNA was purified with 90µl of SPRI beads and 50µl isopropanol and eluted in 21µl of water. DNA was mixed with 2.5µl of NEB Buffer #2, 1µl of 5mM dATP, 1.5µl of NEB Klenow 3'-5' exo minus (Cat# M0212L), and incubated at 37oC for 30min. DNA was purified with SPRI beads as before, but using a volume of 45µl of beads and 25µl isopropanol. DNA was elute in 20µl of water and mixed with 2.5µl of NEB T4 ligase buffer, 1.25µl of a 0.2µM solution of annealed adapters (See below), and 2.5µl of NEB concentrated T4 ligase (Cat# M0202M) and incubated overnight at 16oC. DNA was purified with SPRI beads as before, but using a volume of 35µl of beads and no isopropanol, eluting in 20 µl of water. Sample were mixed with 1µl of a 1:10 dilution of Quant-iT Picogreen dye (Invitrogen, Cat# P11496), 25µl of KAPA HiFi HotStart 2× master Mix (Kapa Bioscience Cat# KK2502), 1µl of 10µM PCR 1.0 and 1µl of PCR 2.0 Illumina primers. The amplification mix was distributed in two wells of a LightCycler 384 plate (Roche, Cat# 4729749001) and on a LightCycler 480 II instrument (Roche, Cat# 05015243001) using the following program: 1’ at 98°C; N cycles: 10” at 98°C; 20” at 64°C; 45” at 72°C. The number of cycles N was determined on real time by monitoring the fluorescence such that the amplification was stopped during the exponential phase. Samples were removed from the plate and purified with SPRI beads using 70µl beads, no isopropanol, and eluting in water. Barcoded adaptor: 5’P-GATCGGAAGAGCACACGTCTGAACTCCAGTCAC-IIIIII-NNNNNNNN-ATCTCGTATGCCGTCTTCTGCTTG. 5’P indicates the presence of a 5’phosphate group. IIIIII represent the six base index nucleotides, and NNNNNNNN a stretch of 8 random nucleotides used for single molecule barcoding. Universal adapter: AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC*T. * indicates the presence of a phosphorothioate bond between the last C and T.  ATAC-seq: Amplification was carried out under the following conditions: Pre-amplification: 1 cycle: 5’ at 72°C; 30” at 98°C; 5 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C; Amplification: 1 cycle: 30” at 98°C; 11/12 cycles: 10” at 98°C; 30” at 63°C; 1’ at 72°C. After amplification libraries were purified with SPRI beads, using a sample to bead ratio of 1: 1.4.

value: mouse ES cell

value: WT (E14Tg2a)

value: parental control


title: ATAC_D8_2

description: Drosophila chromatin spiked in

value: Crispr/Cas9 deletion


title: ATAC_A8_1

description: Drosophila chromatin spiked in


title: Input_WT_1

description:
Drosophila chromatin spiked in
adapters have random molecular identifiers

value: none (input)


title: Input_WT_2


title: SOXC_Prx1Cre_E12.5


title: 6-21_Input

description:
19455X2
fragmented genomic DNA

value: Vehicle (Ethanol)

value: KrasFSF-G12D, p53frt, Rosa-FSF-CreERT2, Foxa1flox, and Foxa2flox

value: no antibody


title: ATAC_D8_1

description: Drosophila chromatin spiked in


title: Input_D8_2


title: Input_D8_1


title: H3K9me3_WT_1


title: H3K9me3_D8_1


title: H3K9me3_D8_2


title: Kidney carcinoma cells - 786-0, PDL1, rep2

description: Sample 20

value: clear cell renal cell carcinoma (ccRCC)

value: Kidney carcinoma cells

value: PD-L1 siRNA

value: PD-L1 knockout


title: Input_A8_1


title: Input_A8_2


title: H3K9me3_A8_2


title: ATAC_A8_2

description: Drosophila chromatin spiked in


title: H3K9me3_WT_2


title: Cultured H9 hPSCs in mTeSR1

city: Syracuse

first: Yi

last: Zheng

state: New York

address: 900 S Crouse Ave

department: Biomedical and Chemical Engineering

institute: Syracuse University

data_processing:
The .Rd files can be loaded into RStudio using "load ("file_name.Rd")", and analyzed using the Seurat R package (https://satijalab.org/seurat/).
Assembly: GRCh38.p13 and Pan_tro_3.0
Supplementary files format and content: .Rd files are the output of R Studio containing the data anlaysis ressults.

source_name: Cultured H9 hPSCs in mTeSR1

extract_protocol: 10x genomics

value: wildtype


title: Human microfluidic embryoids at 0h

source_name: microfluidic embryoids


title: Human microfluidic embryoids at 12h


title: H3K9me3_A8_1


title: m6A-CLIP SM-Input2

city: Planegg-Martinsried

first: Taku

last: Kureha

address: Grosshaderner Str. 9

department: Institute for Immunology

country: Germany

institute: Ludwig-Maximilians-Universität

data_processing:
Reads were de-multiplexed based on the experimental barcode and adapter sequences were removed from the read ends (Flexbar v3.5.0). UMIs were trimmed and added to the read names. Individual samples were mapped to the respective genome (assembly version GRCm38.p6 for all mouse samples) and its annotation (GENCODE release M25 for all mouse samples) using STAR (v2.7.6a). Reads were de-duplicated if they had identical UMIs. For both m6A-CLIP and Ythdf2-iCLIP significant crosslink sites at single-nucleotide resolution were called using PureCLIP (v1.3.1) with default parameters.
Genome_build: mm10
Supplementary_files_format_and_content: Bigwig files were generated usingbed GraphToBigWig.

source_name: wild-type_CD4+ cells

growth_protocol: CD4+ T cells were cultured in DMEM (Invitrogen) cell culture medium supplemented with 10% FCS (Gibco), 100U Pen-Strep (Thermo Fisher), 10 mM HEPES-Buffer (Invitrogen), 1% non-essential amino acids (NEAA; Invitrogen) and 50 µM b-mercaptoethanol (Invitrogen) at 37 ºC, 10% CO2

extract_protocol: Total RNA was isolated with TRIzol. For mRNA purification, two rounds of poly(A) selection were perfomed using Dynabeads mRNA purification kit (Ambion) according to the manufacturer’s instructions, which was followed by fragmentation using RNA fragmentation reagents (Invitrogen). To verify the size of fragmented mRNAs, the mRNA samples were analyzed with the Agilent RNA 6000 pico kit on an Agilent 2100 Bioanalyzer System. The fragmented mRNA samples were incubated with anti-m6A antibody (Synaptic Systems) and cross-linked twice with 150 mJ/cm2 UV light (254 nm) in a Stratalinker. After cross-linking, the solution was further incubated with protein A beads. After stringent washing, RNA 3’ ends were dephosphorylated with T4 PNK and subsequentlys the 3’ adaptor was ligated. The samples were radioactively end-labled and were subjected to NuPAGE gel electrophoresis and tranferred onto Nitrocellulose Membrane. The RNA was isolated from the membrane by treatment with proteinase K. After phonol/chloroform extraction and precipitation, the RNA was reversed transcribed and cDNA was purified with Dynabeads MyOne Silane (Invitrogen). The 5’ adaptor was ligated. First-strand cDNA was synthesized with 6 cycles and size-selected using ProNex Size-Selective Purification System (Promega). Libraries were PCR amplified for 8–13 cycles and sequencing was performed on a Illumina HiSeq1500 sequencer.

treatment_protocol: For activation and differentiation, T cells were stimulated with anti-CD3 (1 µg/mL; cl. 145-2C11, in house production), anti-CD28 (2.5 µg/mL; cl. 37.5N, in house production) under Th1 conditions, 10 μg/mL α-IL-4 (cl. 11B11, in house production) and 10 ng/mL IL-12 (BD Pharmingen) and cultured on six-well plates pre-coated with goat anti-hamster IgG (50 μg/mL, MP Biochemicals) for 40-48h. Following stimulation cells were resuspended in T cell medium supplemented with 200 IU/mL recombinant hIL-2 (Novartis) and expanded in an incubator with 10% CO2. Cells were harvested on day 4 after stimulation.

value: CD4+ cells

tag: antibody


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-on-target

status: Public on Jun 01 2022

city: Beijing

first: Hua-nan

last: Zhao

state: Beijing

address: 5 Yiheyuan Road Haidian District

department: School of Life Sciences

country: China

institute: Peking University

description: Targeted deep sequencing

data_processing:
alignment: BWA
mpileup: samtools mpileup
bmat: parse-mpileup-V04.py
plot base mutation ratio using Python tool: plot-targetseq-bmat-V04.py
Assembly: hg38
Supplementary files format and content: Excel table, the off-target editing ratio list
Library strategy: Targeted deep sequencing

source_name: HEK293T cells

extract_protocol: Primers containing the paired Illumina adaptor sequences in the overhangs were designed based on regions flanking the targeting sites (Supplementary Table 2). A 10-nt barcode was also added into each primer pairs to reduce the detection limit from 0.1% to 0.005%10. 10-100 ng of genomic DNA was used for the first round of PCR amplification using NEBNext® Q5U® Hot Start HiFi PCR Master Mix (NEB, M0515L) for approximately 10 cycles. Q5U is capable of reading and amplifying templates containing uracil bases and hence ensures accurate measurement of off-target editing level. The PCR products were purified with 1× Agencourt AMPure XP beads and eluted in nuclease-free water. The second round of amplification was performed on the purified DNA samples with different index primers for about 15 cycles. The PCR products were purified with 0.8× Agencourt AMPure XP beads and eluted in nuclease-free water. The libraries were quantified using Qubit dsDNA HS Assay kit (Invitrogen) and Qubit 2.0 Fluorometer (INVITROGEN), and then pooled together for high-throughput sequencing by Illumina HiSeq X Ten or MGISEQ-2000.

value: HEK293T cells


title: m6A-CLIP SM-Input1


title: m6A-CLIP2

value: miclip antibody:rabbit anti-m6A antibody (Synaptic Systems, Cat. 202 003)


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-63

description: Targeted deep sequencing


title: m6A-CLIP3


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-519

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-48

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-436

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-484

description: Targeted deep sequencing


title: m6A-CLIP1


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-405

description: Targeted deep sequencing


title: Human microfluidic embryoids at 48h with IWP2


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-386

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-271

description: Targeted deep sequencing


title: ATAC_WT_2

description: Drosophila chromatin spiked in


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-70

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-66

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-33

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-489

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-75

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-154

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-44

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-59

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-63

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-220

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-489

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-484

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-454

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-436

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-271

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-386

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-519

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-66

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-154

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-48

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-44

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-59

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-63

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-48

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-70

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-33

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-519

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-489

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-454

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-386

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-436

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-75

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.IND-220

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep2_ND6-TAS.IND-454

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-220

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-271

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LTX12-rep1_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-154

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-484

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-59

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-33

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-66

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-48

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-489

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-519

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-70

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-454

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-63

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-484

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-44

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-386

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-154

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-220

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep2_ND6-TAS.DL-75

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-75

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-70

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-271

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-33

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-59

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-66

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-60

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-410

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-346

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-429

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-47

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-134

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.DR-8

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-Extend-75

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-Extend-64

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.DL-44

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.DR-43

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-Extend-28

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-371

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-429

description: Targeted deep sequencing


title: SupFig7_ND6-L1397N-LIPO2000-rep1_ND6-TAS.IND-436

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-47

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-60

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.DR-85

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-TAS.IND-257

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-371

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-410

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-257

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep2_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-134

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.DR-43

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-Extend-28

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.DR-85

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.DR-8

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-346

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-48

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-42

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-Extend-64

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-Extend-75

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-6

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-46

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-on-target

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-11

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-30

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-27

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-17

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-34

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.DR-22

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.DR-23

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.DR-19

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.DR-21

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.DR-26

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.DR-14

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-44

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-Extend-15

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-Extend-2

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-Extend-14

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-on-target

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-6

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.IND-31

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-48

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-TAS.DR-28

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-42

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-34

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-27

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-46

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-30

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-31

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.DR-23

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.DR-28

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.DR-21

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.DR-19

description: Targeted deep sequencing


title: SupFig7_ND5.1-L1397N-LIPO2000-rep1_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-11

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.DR-26

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-Extend-15

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-44

description: Targeted deep sequencing


title: SupFig2_Untreated-rep2_SupFig7_Untreated-rep2_ND4-on-target

description: Targeted deep sequencing

value: Untreated


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-Extend-4

description: Targeted deep sequencing


title: SupFig2_ND6-L1397N-LTX21-rep2_SupFig7_ND6-L1397N-LTX21-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig2_ND6-L1397N-LTX21-rep1_SupFig7_ND6-L1397N-LTX21-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep2_ND4-Extend-4

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.IND-17

description: Targeted deep sequencing


title: SupFig2_Untreated-rep2_ND1-on-target

description: Targeted deep sequencing


title: SupFig2_Untreated-rep2_ND5.3-on-target

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.DR-14

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-Extend-2

description: Targeted deep sequencing


title: SupFig2_ND5.3-L1397C-LTX21-rep2_ND5.3-on-target

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-TAS.DR-22

description: Targeted deep sequencing


title: SupFig2_ND4-L1397N-LTX21-rep1_SupFig7_ND4-L1397N-LTX21-rep1_ND4-on-target

description: Targeted deep sequencing


title: SupFig2_ND5.3-L1397C-LTX21-rep1_ND5.3-on-target

description: Targeted deep sequencing


title: SupFig2_Untreated-rep1_ND5.3-on-target

description: Targeted deep sequencing


title: SupFig2_Untreated-rep1_ND1-on-target

description: Targeted deep sequencing


title: SupFig7_ND4-L1397N-LIPO2000-rep1_ND4-Extend-14

description: Targeted deep sequencing


title: SupFig2_ND5.1-L1397N-LTX21-rep1_SupFig7_ND5.1-L1397N-LTX21-rep1_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig2_ND4-L1397N-LTX21-rep2_SupFig7_ND4-L1397N-LTX21-rep2_ND4-on-target

description: Targeted deep sequencing


title: SupFig2_ND5.1-L1397N-LTX21-rep2_SupFig7_ND5.1-L1397N-LTX21-rep2_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig2_ND4-L1397C-LTX21-rep2_ND4-on-target

description: Targeted deep sequencing


title: SupFig2_ND4-L1397C-LTX21-rep1_ND4-on-target

description: Targeted deep sequencing


title: SupFig2_Untreated-rep1_SupFig7_Untreated-rep1_ND4-on-target

description: Targeted deep sequencing


title: SupFig2_ND4-L1333N-LTX21-rep1_ND4-on-target

description: Targeted deep sequencing


title: SupFig2_ND1-L1397N-LTX21-rep2_ND1-on-target

description: Targeted deep sequencing


title: SupFig27_ND6-L1397N-LTX21-N1368A-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig27_ND6-L1397N-LTX21-N1367A-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig27_ND6-L1397N-LTX21-N1368A-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig2_ND1-L1397N-LTX21-rep1_ND1-on-target

description: Targeted deep sequencing


title: SupFig2_ND4-L1333N-LTX21-rep2_ND4-on-target

description: Targeted deep sequencing


title: SupFig27_ND6-L1397N-LTX21-G1309A-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig27_ND6-L1397N-LTX21-N1367A-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig27_ND6-L1397N-LTX21-G1309A-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep2_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep1_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep1_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep1_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep1_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1-rep2_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep1_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs1.5-rep1_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep1_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep2_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.IND-405

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep1_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.5-rep1_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.DL-19

description: Targeted deep sequencing


title: SupFig25_Untreated-rep2_SupFig2_Untreated-rep2_SupFig7_Untreated-rep2_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.DL-49

description: Targeted deep sequencing


title: SupFig25_Untreated-rep1_SupFig2_Untreated-rep1_SupFig7_Untreated-rep1_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.IND-215

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.IND-398

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.DL-71

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep1_ND6-TAS.IND-241

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig26_ND6-L1397N-LTX21-DddIA-1vs0.25-rep2_ND6-TAS.IND-297

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep1_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep2_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep2_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-TAS.IND-207

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-DddA-NES-rep2_ND5.1-TAS.IND-342

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-TAS.DL-14

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-DddA-NES-rep2_ND5.1-on-target

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-UGI-NES-rep1_ND5.1-Extend-18

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-DddA-NES-rep2_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-DddA-NES-rep2_ND5.1-TAS.IND-388

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-WT-rep2_ND5.1-Extend-6

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-TALE-NES-rep1_ND5.1-TAS.IND-230

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-DddA-NES-rep2_ND5.1-TAS.IND-184

description: Targeted deep sequencing


title: SupFig25_ND5.1-L1397N-LTX21-DddA-NES-rep2_ND5.1-TAS.IND-207

description: Targeted deep sequencing