title: 65plex_Patient U120

description:
U120
51 year old PAH Male

value: Caucasian


title: 65plex_Patient U121

status: Public on Jan 20 2025

type: protein

city: Palo Alto

first: Lorinda

last: Chung

address: 1000 Welch Road

country: USA

institute: Stanford University

description:
U121
73 year old High risk Female

hyb_protocol: Samples were diluted 1:100 in assay buffer and run in duplicate. Diluted samples were incubated with magnetic beads for 1 hour. Beads were washed twice and incubated with detection antibody for 30 mins, followed by two washes and incubation with with Streptavidin-PE for 30 mins. Beads were washed twice, resuspended in reading buffer.

scan_protocol: A Luminex FlexMAP 3D instrument was used to measure fluorescence (in MFI) from each  barcoded bead.

data_processing: Sample replicate MFI values were averaged for each antigen. The average barebead MFI was then subtracted from the average MFI of each sample and antigen. Samples were normalized by background correction and removed if correlation between technical replicates was <0.8.

molecule: protein

organism: Homo sapiens

source_name: serum from patients at high risk of PAH

label_protocol: Immune Monitoring 65-plex

extract_protocol: Blood samples from patients  were collected in red top tubes from the Pulmonary Hypertension Assessment and Recognition of Outcomes in Scleroderma (PHAROS) study, a US-based, multi-center registry of SSc patients  .   The blood was then processed into serum which was then run on our arrays.

tag: tissue

value: serum

tag: age in year

tag: Sex

value: Female

tag: group

value: High risk

tag: race

tag: ssc subtype

value: Limited

tag: antibody

value: anticentromer


title: 65plex_Patient U119

description:
U119
69 year old High risk Female


title: 65plex_Patient U117

description:
U117
64 year old PAH Male

source_name: serum from patient with PAH

value: Male

value: PAH

value: Diffuse

value: Scl 70


title: 65plex_Patient U116

description:
U116
57 year old PAH Female


title: 65plex_Patient U115

description:
U115
67 year old High risk Female

value: isolated nucleolar pattern


title: 65plex_Patient U118

description:
U118
68 year old High risk Female


title: 65plex_Patient U113

description:
U113
73 year old PAH Male

value: polymerase III


title: 65plex_Patient U112

description:
U112
56 year old High risk Female

value: Mixed or other


title: 65plex_Patient U109

description:
U109
70 year old High risk Female


title: 65plex_Patient U107

description:
U107
74 year old High risk Female


title: 65plex_Patient U106

description:
U106
78 year old PAH Female


title: 65plex_Patient U114

description:
U114
49 year old PAH Female


title: 65plex_Patient U111

description:
U111
58 year old PAH Female


title: 65plex_Patient U104

description:
U104
73 year old PAH Female


title: 65plex_Patient U108

description:
U108
80 year old High risk Female


title: 65plex_Patient U103

description:
U103
37 year old High risk Female

value: Other Ethnic Origin


title: 65plex_Patient U101

description:
U101
50 year old High risk Female

value: Unclassified

value: negative


title: 65plex_Patient U098

description:
U098
59 year old High risk Female

value: Hispanic


title: 65plex_Patient U110

description:
U110
76 year old High risk Female

value: Caucasian


title: 65plex_Patient U100

description:
U100
69 year old High risk Female

value: serum


title: 65plex_Patient U105

description:
U105
61 year old PAH Male


title: 65plex_Patient U095

description:
U095
68 year old PAH Female

value: Female


title: 65plex_Patient U102

description:
U102
54 year old High risk Female

value: High risk


title: 65plex_Patient U096

description:
U096
57 year old High risk Female

value: Native American (i.e. American Indian)

value: Limited


title: 65plex_Patient U090

description:
U090
40 year old PAH Male

value: Male


title: 65plex_Patient U093

description:
U093
38 year old High risk Female


title: 65plex_Patient U099

description:
U099
62 year old High risk Female


title: 65plex_Patient U091

description:
U091
44 year old PAH Male

value: PAH

value: anticentromer


title: 65plex_Patient U097

description:
U097
62 year old High risk Female


title: 65plex_Patient U089

description:
U089
45 year old High risk Female

value: Scl 70


title: 65plex_Patient U092

description:
U092
33 year old High risk Female


title: 65plex_Patient U088

description:
U088
42 year old High risk Female


title: 65plex_Patient U087

description:
U087
62 year old High risk Female


title: 65plex_Patient U086

description:
U086
58 year old High risk Female


title: 65plex_Patient U085

description:
U085
58 year old High risk Female


title: 65plex_Patient U084

description:
U084
54 year old High risk Female


title: 65plex_Patient U083

description:
U083
53 year old High risk Female


title: 65plex_Patient U080

description:
U080
77 year old High risk Female


title: 65plex_Patient U081

description:
U081
66 year old High risk Female


title: 65plex_Patient U082

description:
U082
47 year old High risk Female


title: 65plex_Patient U079

description:
U079
74 year old High risk Female


title: 65plex_Patient U094

description:
U094
63 year old PAH Female


title: 65plex_Patient U078

description:
U078
71 year old High risk Female


title: 65plex_Patient U074

description:
U074
48 year old High risk Male

value: Diffuse


title: 65plex_Patient U073

description:
U073
41 year old High risk Male


title: 65plex_Patient U075

description:
U075
53 year old PAH Female


title: 65plex_Patient U070

description:
U070
59 year old PAH Female


title: 65plex_Patient U068

description:
U068
65 year old PAH Female


title: 65plex_Patient U072

description:
U072
62 year old PAH Female


title: 65plex_Patient U071

description:
U071
60 year old PAH Female


title: 65plex_Patient U064

description:
U064
58 year old PAH Male


title: 65plex_Patient U066

description:
U066
55 year old High risk Male


title: 65plex_Patient U063

description:
U063
39 year old PAH Female

value: Black


title: 65plex_Patient U065

description:
U065
51 year old PAH Female


title: 65plex_Patient U062

description:
U062
58 year old PAH Female


title: 65plex_Patient U059

description:
U059
63 year old PAH Female


title: 65plex_Patient U060

description:
U060
37 year old PAH Female


title: 65plex_Patient U067

description:
U067
60 year old High risk Male


title: 65plex_Patient U061

description:
U061
40 year old PAH Male


title: 65plex_Patient U058

description:
U058
35 year old PAH Female


title: 65plex_Patient U055

description:
U055
73 year old PAH Female


title: 65plex_Patient U077

description:
U077
70 year old High risk Female


title: 65plex_Patient U056

description:
U056
65 year old High risk Female


title: 65plex_Patient U051

description:
U051
71 year old High risk Male

value: isolated nucleolar pattern


title: 65plex_Patient U049

description:
U049
81 year old PAH Male

value: Mixed or other


title: 65plex_Patient U050

description:
U050
79 year old PAH Female


title: 65plex_Patient U076

description:
U076
62 year old PAH Female


title: 65plex_Patient U054

description:
U054
72 year old High risk Female


title: 65plex_Patient U048

description:
U048
74 year old PAH Female


title: 65plex_Patient U047

description:
U047
50 year old High risk Female


title: 65plex_Patient U069

description:
U069
64 year old PAH Male


title: 65plex_Patient U045

description:
U045
50 year old PAH Male


title: 65plex_Patient U046

description:
U046
55 year old PAH Male


title: 65plex_Patient U052

description:
U052
56 year old PAH Male


title: 65plex_Patient U057

description:
U057
54 year old PAH Female


title: 65plex_Patient U043

description:
U043
67 year old PAH Female

value: polymerase III


title: 65plex_Patient U040

description:
U040
62 year old PAH Female


title: 65plex_Patient U041

description:
U041
55 year old PAH Male

value: Unclassified


title: 65plex_Patient U042

description:
U042
57 year old PAH Male


title: 65plex_Patient U038

description:
U038
52 year old PAH Female


title: 65plex_Patient U039

description:
U039
59 year old PAH Male


title: 65plex_Patient U036

description:
U036
63 year old High risk Female


title: 65plex_Patient U035

description:
U035
54 year old High risk Female


title: 65plex_Patient U033

description:
U033
77 year old High risk Female


title: 65plex_Patient U034

description:
U034
52 year old High risk Female


title: 65plex_Patient U032

description:
U032
61 year old PAH Female


title: 65plex_Patient U031

description:
U031
54 year old PAH Female


title: 65plex_Patient U053


title: 65plex_Patient U029

description:
U029
57 year old PAH Female


title: 65plex_Patient U028

description:
U028
50 year old PAH Female


title: 65plex_Patient U027

description:
U027
62 year old PAH Female

value: negative


title: 65plex_Patient U026

description:
U026
29 year old PAH Female


title: 65plex_Patient U023

description:
U023
46 year old PAH Female


title: 65plex_Patient U044

description:
U044
67 year old PAH Female

value: Caucasian


title: 65plex_Patient U024

description:
U024
66 year old High risk Female

value: serum


title: 65plex_Patient U021

description:
U021
68 year old Healthy Female

source_name: serum from healthy control

value: Female

value: Healthy


title: 65plex_Patient U020

description:
U020
71 year old Healthy Female


title: 65plex_Patient U019

description:
U019
69 year old Healthy Female


title: 65plex_Patient U022

description:
U022
69 year old Healthy Female


title: 65plex_Patient U017

description:
U017
55 year old Healthy Female


title: 65plex_Patient U018

description:
U018
77 year old Healthy Female


title: 65plex_Patient U037

description:
U037
61 year old PAH Female


title: 65plex_Patient U016

description:
U016
53 year old Healthy Female


title: 65plex_Patient U015

description:
U015
55 year old Healthy Female


title: 65plex_Patient U014

description:
U014
53 year old Healthy Female


title: 65plex_Patient U013

description:
U013
58 year old Healthy Female


title: 65plex_Patient U011

description:
U011
66 year old Healthy Female


title: 65plex_Patient U012

description:
U012
68 year old Healthy Female


title: 65plex_Patient U010

description:
U010
68 year old Healthy Male


title: 65plex_Patient U009

description:
U009
53 year old Healthy Male


title: 65plex_Patient U030

description:
U030
64 year old PAH Male


title: 65plex_Patient U007

description:
U007
59 year old Healthy Female


title: 65plex_Patient U006

description:
U006
52 year old Healthy Male


title: 65plex_Patient U005

description:
U005
52 year old Healthy Female


title: 65plex_Patient U004

description:
U004
48 year old Healthy Female


title: mod[07570]:[L8] replicate3

type: SRA

city: Charleston

first: Vamsi

last: Gangaraju

address: 173 Ashley Ave

institute: Medical University of South Carolina

description: Library name: Sample 9

library_source: transcriptomic

data_processing:
Reads were analyzed by piPipes (PMCID: PMC4325541) RNA-seq workflow using default options. As part of the piPipes workflow, reads were mapped to the transposon consensus sequences and RefSeq genes using Bowtie and then quantified by eXpress.
Assembly: dm3
Supplementary files format and content: eXpress output in tab delimited text file

molecule: polyA RNA

organism: Drosophila melanogaster

source_name: Ovary

extract_protocol:
Total RNA was isolated from ovaries or heads using Trizol (ThermoFisher Scientific) following manufacturer's protocol.
Libraries were prepared by Novogene using the NEBNext Ultra RNA Library Prep Kit for Illumina

value: Ovary

tag: sample group


title: 65plex_Patient U003

description:
U003
52 year old Healthy Male


title: 65plex_Patient U025

description:
U025
49 year old PAH Female

value: Hispanic

value: Limited


title: Control+IAA 256c+3hr Rep2.2

city: Munich

first: Eva

last: Hoermanseder

state: Bavaria

address: Feodor-Lynen-Str. 21

department: Institute of Epigenetics and Stem Cells

country: Germany

institute: Helmholtz Center Munich

description:
Library name: 89
tpms_rep_2.csv

data_processing:
Paired sequencing reads were processed using Kallisto (v0.48) for pseudoalignment and quantification of transcript abundance. Transcript and annotation files were downloaded from Xenbase (v10.1) for Xenopus laevis (transcripts and annotation). After quantification, transcript-level abundances were imported using 'tximport' and converted to a 'SummarizedExperiment' object in R (v4.3.2).  Datasets of two independent batches were subjected to differential expression analysis on each of their three respective replicates performed with DESeq2 (v1.42.1).
Assembly: Xenopus laevis (v10.1)
Supplementary files format and content: Normalized counts (transcripts per million) for each biological replicate

molecule: total RNA

organism: Xenopus laevis

source_name: Whole embryos 7.5hpf

extract_protocol:
Independent experiments were performed on two different frogs, serving as two biological replicates. Within each biological replicate, three sets of three embryos each were collected per time point, corresponding to three replicates within each independent experiment. Embryos were collected as described at hourly intervals after the pre-ZGA stage (i.e. 4.5hpf/256-cell stage): at 5.5hpf, 6.5hpf and 7.5hpf. Total RNA was isolated using the RNeasy kit (Qiagen, #74106) according to the manufacturer’s instructions. Ribosomal RNA was depleted using custom-made oligomer mixes for Xenopus laevis rRNA as described in the manuscript.
Sequencing libraries were generated using the NEBNext Ultra II Directional RNA Library Preparation Kit for Illumina (NEB, #E7760) as per the manufacturer’s instructions using 12-13 PCR amplification cycles.

treatment_protocol: For the “treated” condition, embryos were co-injected at the 1-cell stage with 11ng Kdm5bwt, 345pg H3.3K4M and 5ng TIR1 mRNA. “Control” condition embryos were co-injected at the 1-cell stage with 4ng Kdm5bci, 345pg H3.3wt and 5ng TIR1 mRNA. For “+IAA” depletion treatment, embryos were grown until the pre-ZGA stage (4.5hpf/256-cell stage) and transferred to an auxin solution (500μM auxin in 0.1 × MMR) to develop further. “-IAA” depletion treatment embryos were grown in 0.1x MMR throughout development.

value: Whole embryos 7.5hpf

tag: cell type

value: Whole embryos

tag: genotype

value: WT

tag: treatment

value: Kdm5bci + H3.3wt + TIR1

tag: batch


title: Control+IAA 256c+3hr Rep2.1

description:
Library name: 88
tpms_rep_2.csv


title: mod[07570]:+ replicate3

description: Library name: Sample 3


title: DNAme_256c_IN_Rep1

description: Library name: 1

library_source: genomic

data_processing:
Sequencing reads were aligned to the Xenopus laevis genome (v10.1) with bowtie (v4.2). The alignment process excluded discordant and mixed reads, with paired-end reads mapped to the reference genome. Aligned reads were converted to BAM format and filtered to retain only properly paired alignments. HOMER (v4.11) was used for peak identification against corresponding input controls. Broad peaks were called using histone-style parameters, while narrow peaks were called with default settings. Identified peaks were converted to BED format for downstream analysis.
Assembly: Xenopus laevis (v10.1)
Supplementary files format and content: Coverage files (.bigwig)
Supplementary files format and content: Broad peak calling files (.bed)

molecule: genomic DNA

source_name: Whole embryos pre-ZGA (4.5hpf/256-cell)

extract_protocol:
250 pre-ZGA (4.5 hpf/256-cell) stage embryos were collected per replicate and nuclear isolation followed by genomic DNA extraction was performed as described in the manuscript.Methylated DNA was captured based on its affinity to the MethylCap (H6-GST-MBD fusion) protein according to the manufacturer's instructions (Diagenode; #C02020012). Methylated DNA and input DNA was purified and sequenced.
Sequencing libraries were generated using the NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, #E7645S) as per the manufacturer’s instructions using 6-8 PCR amplification cycles.

value: Whole embryos pre-ZGA (4.5hpf/256-cell)

value: Input


title: mod[07570]:+ replicate1

description: Library name: Sample 1


title: mod[L8]:+ replicate2

description: Library name: Sample 5


title: mod[L8]:+ replicate3

description: Library name: Sample 6


title: Control+IAA 256c+3hr Rep2.3

description:
Library name: 90
tpms_rep_2.csv


title: mod[07570]:[L8] replicate1

description: Library name: Sample 7


title: DNAme_256c_IN_Rep2

description: Library name: 2


title: mod[L8]:+ replicate1

description: Library name: Sample 4


title: Treated+IAA 256c+3hr Rep2.3

description:
Library name: 87
tpms_rep_2.csv

value: Kdm5bwt + H3.3K4M + TIR1


title: Wt-IAA 256c+3hr Rep2.2

description:
Library name: 83
tpms_rep_2.csv


title: Wt-IAA 256c+3hr Rep2.1

description:
Library name: 82
tpms_rep_2.csv


title: DNAme_256c_IP_Rep2

description: Library name: 4

value: H6-GST-MBD IP


title: DNAme_256c_IP_Rep1

description: Library name: 3


title: Treated+IAA 256c+3hr Rep2.1

description:
Library name: 85
tpms_rep_2.csv


title: Treated+IAA 256c+3hr Rep2.2

description:
Library name: 86
tpms_rep_2.csv


title: Wt-IAA 256c+3hr Rep2.3

description:
Library name: 84
tpms_rep_2.csv


title: Treated-IAA 256c+3hr Rep2.2

description:
Library name: 77
tpms_rep_2.csv


title: mod[07570]:+ replicate2

description: Library name: Sample 2


title: Control-IAA 256c+3hr Rep2.3

description:
Library name: 81
tpms_rep_2.csv


title: Control+IAA 256c+2hr Rep2.3

description:
Library name: 75
tpms_rep_2.csv

source_name: Whole embryos 6.5hpf

value: Whole embryos 6.5hpf


title: Control-IAA 256c+3hr Rep2.2

description:
Library name: 80
tpms_rep_2.csv


title: mod[07570]:[L8] replicate2

description: Library name: Sample 8


title: Treated-IAA 256c+3hr Rep2.1

description:
Library name: 76
tpms_rep_2.csv


title: Control+IAA 256c+2hr Rep2.2

description:
Library name: 74
tpms_rep_2.csv


title: Control-IAA 256c+3hr Rep2.1

description:
Library name: 79
tpms_rep_2.csv


title: 65plex_Patient U008

description:
U008
47 year old Healthy Male

value: Male


title: Treated+IAA 256c+2hr Rep2.3

description:
Library name: 72
tpms_rep_2.csv


title: Treated+IAA 256c+2hr Rep2.1

description:
Library name: 70
tpms_rep_2.csv


title: Treated+IAA 256c+2hr Rep2.2

description:
Library name: 71
tpms_rep_2.csv


title: Control-IAA 256c+2hr Rep2.2

description:
Library name: 65
tpms_rep_2.csv


title: Treated-IAA 256c+3hr Rep2.3

description:
Library name: 78
tpms_rep_2.csv


title: Wt-IAA 256c+2hr Rep2.3

description:
Library name: 69
tpms_rep_2.csv


title: Wt-IAA 256c+2hr Rep2.1

description:
Library name: 67
tpms_rep_2.csv


title: Wt-IAA 256c+2hr Rep2.2

description:
Library name: 68
tpms_rep_2.csv


title: Control+IAA 256c+2hr Rep2.1

description:
Library name: 73
tpms_rep_2.csv


title: Control-IAA 256c+2hr Rep2.3

description:
Library name: 66
tpms_rep_2.csv


title: Treated-IAA 256c+2hr Rep2.1

description:
Library name: 61
tpms_rep_2.csv


title: Treated-IAA 256c+2hr Rep2.2

description:
Library name: 62
tpms_rep_2.csv


title: Control-IAA 256c+2hr Rep2.1

description:
Library name: 64
tpms_rep_2.csv


title: Control+IAA 256c+1hr Rep2.1

description:
Library name: 58
tpms_rep_2.csv

source_name: Whole embryos 5.5hpf

value: Whole embryos 5.5hpf


title: Treated-IAA 256c+2hr Rep2.3

description:
Library name: 63
tpms_rep_2.csv


title: Treated+IAA 256c+1hr Rep2.2

description:
Library name: 56
tpms_rep_2.csv


title: Wt-IAA 256c+1hr Rep2.3

description:
Library name: 54
tpms_rep_2.csv


title: Wt-IAA 256c+1hr Rep2.2

description:
Library name: 53
tpms_rep_2.csv


title: Wt-IAA 256c+1hr Rep2.1

description:
Library name: 52
tpms_rep_2.csv


title: Control-IAA 256c+1hr Rep2.2

description:
Library name: 50
tpms_rep_2.csv


title: Control-IAA 256c+1hr Rep2.3

description:
Library name: 51
tpms_rep_2.csv


title: Treated-IAA 256c+1hr Rep2.1

description:
Library name: 46
tpms_rep_2.csv


title: Control+IAA 256c+3hr Rep1.3

description:
Library name: 45
tpms_rep_1.csv


title: Control-IAA 256c+1hr Rep2.1

description:
Library name: 49
tpms_rep_2.csv


title: Control+IAA 256c+1hr Rep2.3

description:
Library name: 60
tpms_rep_2.csv


title: Control+IAA 256c+1hr Rep2.2

description:
Library name: 59
tpms_rep_2.csv


title: Control+IAA 256c+3hr Rep1.1

description:
Library name: 43
tpms_rep_1.csv


title: Treated-IAA 256c+1hr Rep2.3

description:
Library name: 48
tpms_rep_2.csv


title: Treated+IAA 256c+3hr Rep1.3

description:
Library name: 42
tpms_rep_1.csv


title: Treated+IAA 256c+1hr Rep2.1

description:
Library name: 55
tpms_rep_2.csv


title: Treated-IAA 256c+1hr Rep2.2

description:
Library name: 47
tpms_rep_2.csv


title: Treated+IAA 256c+1hr Rep2.3

description:
Library name: 57
tpms_rep_2.csv


title: Treated+IAA 256c+3hr Rep1.1

description:
Library name: 40
tpms_rep_1.csv


title: Treated+IAA 256c+3hr Rep1.2

description:
Library name: 41
tpms_rep_1.csv


title: Wt-IAA 256c+3hr Rep1.1

description:
Library name: 37
tpms_rep_1.csv


title: Wt-IAA 256c+3hr Rep1.2

description:
Library name: 38
tpms_rep_1.csv


title: Wt-IAA 256c+3hr Rep1.3

description:
Library name: 39
tpms_rep_1.csv


title: Control-IAA 256c+3hr Rep1.2

description:
Library name: 35
tpms_rep_1.csv


title: Treated-IAA 256c+3hr Rep1.2

description:
Library name: 32
tpms_rep_1.csv


title: Control-IAA 256c+3hr Rep1.3

description:
Library name: 36
tpms_rep_1.csv


title: Treated+IAA 256c+2hr Rep1.3

description:
Library name: 27
tpms_rep_1.csv


title: Control+IAA 256c+2hr Rep1.3

description:
Library name: 30
tpms_rep_1.csv


title: Treated-IAA 256c+3hr Rep1.3

description:
Library name: 33
tpms_rep_1.csv


title: Treated-IAA 256c+3hr Rep1.1

description:
Library name: 31
tpms_rep_1.csv


title: Treated+IAA 256c+2hr Rep1.2

description:
Library name: 26
tpms_rep_1.csv


title: Treated+IAA 256c+2hr Rep1.1

description:
Library name: 25
tpms_rep_1.csv


title: Wt-IAA 256c+2hr Rep1.3

description:
Library name: 24
tpms_rep_1.csv


title: Wt-IAA 256c+2hr Rep1.2

description:
Library name: 23
tpms_rep_1.csv


title: Control+IAA 256c+3hr Rep1.2

description:
Library name: 44
tpms_rep_1.csv


title: Wt-IAA 256c+2hr Rep1.1

description:
Library name: 22
tpms_rep_1.csv


title: Control-IAA 256c+2hr Rep1.3

description:
Library name: 21
tpms_rep_1.csv


title: Control-IAA 256c+3hr Rep1.1

description:
Library name: 34
tpms_rep_1.csv


title: Control+IAA 256c+2hr Rep1.1

description:
Library name: 28
tpms_rep_1.csv


title: Control-IAA 256c+2hr Rep1.1

description:
Library name: 19
tpms_rep_1.csv


title: Treated-IAA 256c+2hr Rep1.2

description:
Library name: 17
tpms_rep_1.csv


title: Control-IAA 256c+2hr Rep1.2

description:
Library name: 20
tpms_rep_1.csv


title: Control+IAA 256c+1hr Rep1.2

description:
Library name: 14
tpms_rep_1.csv


title: Control+IAA 256c+1hr Rep1.3

description:
Library name: 15
tpms_rep_1.csv


title: Treated+IAA 256c+1hr Rep1.2

description:
Library name: 11
tpms_rep_1.csv


title: Treated+IAA 256c+1hr Rep1.3

description:
Library name: 12
tpms_rep_1.csv


title: Treated-IAA 256c+2hr Rep1.3

description:
Library name: 18
tpms_rep_1.csv


title: Treated+IAA 256c+1hr Rep1.1

description:
Library name: 10
tpms_rep_1.csv


title: Treated-IAA 256c+2hr Rep1.1

description:
Library name: 16
tpms_rep_1.csv


title: Control-IAA 256c+1hr Rep1.3

description:
Library name: 6
tpms_rep_1.csv


title: Wt-IAA 256c+1hr Rep1.1

description:
Library name: 7
tpms_rep_1.csv


title: Control+IAA 256c+1hr Rep1.1

description:
Library name: 13
tpms_rep_1.csv


title: Wt-IAA 256c+1hr Rep1.2

description:
Library name: 8
tpms_rep_1.csv


title: 4C_DRB_Rep3

city: Wuhan

first: Li-quan

last: Zhou

state: Hubei

address: 13 Hangkong road

department: Tongji Medical College

country: China

institute: Huazhong University of Science and Technology

description: Library name: 4C_DRB_Rep3

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Assembly: mm10
Supplementary files format and content: Tab-delimited txt file includes FPKM values for each samples

organism: Mus musculus

source_name: embryo

extract_protocol:
early embryos were collected in tubes with lysis component and ribonuclease inhibitor.
we carried out the amplification by the Smart-Seq2 method. An Oligo-dT primer was introduced to the reverse transcription reaction for first-strand cDNA synthesis, followed by PCR amplification to enrich the cDNA and magbeads purification step to clean up the production. Then the cDNA production was checked by Qubit 3.0 Flurometer and Agilent 2100 Bioanalyzer to ensure the expected production with length around 1~2KB. Then the cDNA was sheared randomly by ultrasonic waves for Illumina library preparation protocol including DNA fragmentation, end repair, 3’ ends A-tailing, adapter ligation, PCR amplification and library validation. After library preparation, PerkinElmer LabChip GX Touch and Step OnePlus Real-Time PCR System were introduced for library quality inspection. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.

value: embryo

value: DRB


title: 4C_DRB_Rep1

description: Library name: 4C_DRB_Rep1


title: Wt-IAA 256c+1hr Rep1.3

description:
Library name: 9
tpms_rep_1.csv


title: Control-IAA 256c+1hr Rep1.2

description:
Library name: 5
tpms_rep_1.csv


title: Control+IAA 256c+2hr Rep1.2

description:
Library name: 29
tpms_rep_1.csv


title: 4C_DRB_Rep2

description: Library name: 4C_DRB_Rep2


title: Treated-IAA 256c+1hr Rep1.3

description:
Library name: 3
tpms_rep_1.csv


title: Treated-IAA 256c+1hr Rep1.2

description:
Library name: 2
tpms_rep_1.csv


title: 4C_Con_Rep3

description: Library name: 4C_Con_Rep3

value: Con


title: Control-IAA 256c+1hr Rep1.1

description:
Library name: 4
tpms_rep_1.csv


title: 4C_Con_Rep2

description: Library name: 4C_Con_Rep2


title: Treated-IAA 256c+1hr Rep1.1

description:
Library name: 1
tpms_rep_1.csv


title: 4C_Con_Rep1

description: Library name: 4C_Con_Rep1


title: NI Ctrl 256c+3hr Rep II.3

description:
Library name: 72
tpms_rep_II.csv

treatment_protocol: 1-cell stage embryos were injected with 9.2nl of 1mM morpholino solution and developed in 0.5x MMR solution for 2 hours before moving to 0.1x MMR. Embryos were grown at 18°C until the desired stage.


title: Ctrl MO 256c+3hr Rep II.3

description:
Library name: 71
tpms_rep_II.csv

value: Ctrl MO


title: MII_12m2

data_processing:
Raw reads were processed with Cutadapt v1.16. Trimmed reads were mapped to mouse genome using STAR with default settings.
Raw counts for genes and transposable elements were calcualted by TEcount v2.2.3.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: MII oocytes

extract_protocol:
For low-Input RNA Sequencing of mouse oocytes and early embryos, we collected samples and transferred them into RNase-free microtubes with lysis buffer for following RNA-seq libraries preparation. For transcriptome analysis of mouse embryonic stem cells, we extracted total RNA by the TRIzol reagent, followed by polyA RNA capture with Oligo-dT beads for following standard RNA-seq library preparation.
Low-Input RNA Sequencing was carried out by the Smart-Seq2 method. For transcriptome analysis of mouse embryonic stem cells, standard RNA-seq library was prepared using TruSeq RNA Sample Preparation Kit from Illumina.

tag: cell line

value: no

value: MII oocytes

tag: age of female


title: MII_12m1


title: Cxxc1 MO 256c+3hr Rep II.3

description:
Library name: 70
tpms_rep_II.csv

value: Whole embryos 7.5hpf

value: Cxxc1 MO


title: MII_8w1

value: WT


title: Kmt2b MO 256c+3hr Rep II.3

description:
Library name: 69
tpms_rep_II.csv

value: Whole embryos

value: Kmt2b MO


title: IVF_WT_4C_2

source_name: 4-cell embryo

value: 4-cell embryo

value: DMSO


title: MII_8w2


title: Cxxc1 MO 256c+3hr Rep II.2

description:
Library name: 66
tpms_rep_II.csv


title: IVF_WT_4C_1


title: Kmt2b MO 256c+3hr Rep II.2

description:
Library name: 65
tpms_rep_II.csv


title: IVF_CHX_4C_2

value: Cycloheximide


title: Cxxc1 MO 256c+3hr Rep II.1

description:
Library name: 62
tpms_rep_II.csv


title: IVF_CHX_4C_1


title: IVF_APH_4C_2

value: Aphidicolin


title: IVF_MG132_4C_1


title: Kmt2b MO 256c+3hr Rep II.1

description:
Library name: 61
tpms_rep_II.csv


title: IVF_APH_4C_1


title: NI Ctrl 256c+3hr Rep II.1

description:
Library name: 64
tpms_rep_II.csv


title: NI Ctrl 256c+3hr Rep I.3

description:
Library name: 60
tpms_rep_I.csv


title: Ctrl MO 256c+3hr Rep I.3

description:
Library name: 59
tpms_rep_I.csv


title: IVFWT2cell1

source_name: 2-cell embryo

value: 2-cell embryo


title: Cxxc1 MO 256c+3hr Rep I.3

description:
Library name: 58
tpms_rep_I.csv


title: IVFMG132_2


title: NI Ctrl 256c+3hr Rep II.2

description:
Library name: 68
tpms_rep_II.csv


title: Kmt2b MO 256c+3hr Rep I.3

description:
Library name: 57
tpms_rep_I.csv


title: Ctrl MO 256c+3hr Rep II.2

description:
Library name: 67
tpms_rep_II.csv


title: Ctrl MO 256c+3hr Rep I.2

description:
Library name: 55
tpms_rep_I.csv


title: IVF_MG132_4C_2


title: IVFCHX2


title: NI Ctrl 256c+3hr Rep I.2

description:
Library name: 56
tpms_rep_I.csv


title: Ctrl MO 256c+3hr Rep II.1

description:
Library name: 63
tpms_rep_II.csv


title: Kmt2b MO 256c+3hr Rep I.2

description:
Library name: 53
tpms_rep_I.csv


title: IVFAPH2


title: Cxxc1 MO 256c+3hr Rep I.2

description:
Library name: 54
tpms_rep_I.csv


title: IVFMG132_1


title: IVFAPH1


title: IVF12M2cell1


title: IVFWT2cell2


title: NI Ctrl 256c+2hr Rep II.3

description:
Library name: 48
tpms_rep_II.csv

value: Whole embryos 6.5hpf


title: AB22_WT_Long_1

source_name: embryonic stem cell AB2.2

value: embryonic stem cell AB2.2

value: embryonic stem cell


title: AB22_MG132_Long_2


title: Kmt2b MO 256c+3hr Rep I.1

description:
Library name: 49
tpms_rep_I.csv


title: Ctrl MO 256c+2hr Rep II.3

description:
Library name: 47
tpms_rep_II.csv


title: Cxxc1 MO 256c+3hr Rep I.1

description:
Library name: 50
tpms_rep_I.csv


title: IVFCHX1


title: Kmt2b MO 256c+2hr Rep II.3

description:
Library name: 45
tpms_rep_II.csv


title: NI Ctrl 256c+2hr Rep II.2

description:
Library name: 44
tpms_rep_II.csv


title: Ctrl MO 256c+3hr Rep I.1

description:
Library name: 51
tpms_rep_I.csv


title: AB22_MG132_Long_1


title: Cxxc1 MO 256c+2hr Rep II.2

description:
Library name: 42
tpms_rep_II.csv


title: P14_Oo_WT_1

source_name: P14 growing oocyte

value: P14 growing oocyte

value: H3.3WT transgenic


title: NI Ctrl 256c+3hr Rep I.1

description:
Library name: 52
tpms_rep_I.csv


title: P14_Oo_WT_2

value: no


title: Kmt2b MO 256c+2hr Rep II.2

description:
Library name: 41
tpms_rep_II.csv


title: AB22_CHX_Long_1


title: P14_Oo_K4M_1

value: H3.3K4M transgenic


title: P14_Oo_K4M_2


title: AB22_CHX_Long_2


title: 4C_IVF_MG132_PolII_Ps_2

data_processing:
Raw reads were processed with Trim Galore to remove adaptor sequences and poor quality bases.
Trimmed reads were then aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters.
Picard was used to remove PCR duplicates.
Peaks were called using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: The UCSC Genome Browser utility, bedGraphToBigWig, was used to transform the bedgraph ﬁles to bigwig ﬁles
Supplementary files format and content: bigwig file for each sample

extract_protocol:
Generally, we collected superovulated eggs, performed in vitro fertilization, cultured fertilized eggs in KSOM for preimplantation development until reaching specific developmental stages, with indicated drugs added to culture medium at specific time points. Growing and fully-grown oocytes were also collected from mouse ovaries. These oocytes and early embryos were used for following ChIP-seq library preparation after removal of zona pellucida.
ChIP-seq libraries were prepared using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, China) according to the manufacturer’s protocol. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.

tag: chip-antibody

value: Phospho-POLR2A CTD-S2


title: NI Ctrl 256c+2hr Rep II.1

description:
Library name: 40
tpms_rep_II.csv


title: 4C_IVF_MG132_PolII_Ps_1


title: AB22_WT_Long_2


title: IVF12M2cell2


title: 4C_IVF_CHX_PolII_Ps_2


title: Kmt2b MO 256c+2hr Rep II.1

description:
Library name: 37
tpms_rep_II.csv


title: NI Ctrl 256c+2hr Rep I.3

description:
Library name: 36
tpms_rep_I.csv


title: Ctrl MO 256c+2hr Rep I.3

description:
Library name: 35
tpms_rep_I.csv

value: Ctrl MO


title: Ctrl MO 256c+2hr Rep II.2

description:
Library name: 43
tpms_rep_II.csv

value: WT


title: Ctrl MO 256c+2hr Rep II.1

description:
Library name: 39
tpms_rep_II.csv

value: Whole embryos


title: 4C_IVF_APH_PolII_Ps_2


title: 4C_IVF_CHX_PolII_Ps_1


title: Cxxc1 MO 256c+2hr Rep II.3

description:
Library name: 46
tpms_rep_II.csv

value: Cxxc1 MO


title: 4C_IVF_APH_PolII_Ps_1

value: 4-cell embryo


title: Cxxc1 MO 256c+2hr Rep I.3

description:
Library name: 34
tpms_rep_I.csv


title: Aged_2C_IVF_PolII_Ps_2


title: MG132_IVF_PolII_Ps_1


title: Kmt2b MO 256c+2hr Rep I.3

description:
Library name: 33
tpms_rep_I.csv

value: Kmt2b MO


title: MG132_IVF_PolII_Ps_2


title: Kmt2b MO 256c+2hr Rep I.2

description:
Library name: 29
tpms_rep_I.csv


title: Ctrl MO 256c+2hr Rep I.2

description:
Library name: 31
tpms_rep_I.csv


title: Cxxc1 MO 256c+2hr Rep I.2

description:
Library name: 30
tpms_rep_I.csv


title: Aged_2C_IVF_PolII_Ps_1


title: MG132_IVF_PolII_2


title: Ctrl MO 256c+2hr Rep I.1

description:
Library name: 27
tpms_rep_I.csv


title: NI Ctrl 256c+2hr Rep I.1

description:
Library name: 28
tpms_rep_I.csv


title: MG132_IVF_PolII_1


title: CHX_IVF_PolII_Ps_2

value: Cycloheximide


title: Cxxc1 MO 256c+2hr Rep II.1

description:
Library name: 38
tpms_rep_II.csv


title: Cxxc1 MO 256c+2hr Rep I.1

description:
Library name: 26
tpms_rep_I.csv


title: MG132_IVF_H3K4me3_2


title: Kmt2b MO 256c+2hr Rep I.1

description:
Library name: 25
tpms_rep_I.csv


title: MG132_IVF_H3K4me3_1


title: CHX_IVF_PolII_Ps_1


title: NI Ctrl 256c+1hr Rep II.3

description:
Library name: 24
tpms_rep_II.csv

value: Whole embryos 5.5hpf


title: NI Ctrl 256c+2hr Rep I.2

description:
Library name: 32
tpms_rep_I.csv


title: CHX_IVF_PolII_2

value: 2-cell embryo


title: Ctrl MO 256c+1hr Rep II.3

description:
Library name: 23
tpms_rep_II.csv


title: Cxxc1 MO 256c+1hr Rep II.3

description:
Library name: 22
tpms_rep_II.csv


title: CHX_IVF_PolII_1


title: Kmt2b MO 256c+1hr Rep II.3

description:
Library name: 21
tpms_rep_II.csv


title: APH_IVF_PolII_Ps_2

value: Aphidicolin


title: CHX_IVF_H3K4me3_1


title: Ctrl MO 256c+1hr Rep II.2

description:
Library name: 19
tpms_rep_II.csv


title: CHX_IVF_H3K4me3_2


title: NI Ctrl 256c+1hr Rep II.2

description:
Library name: 20
tpms_rep_II.csv


title: APH_IVF_PolII_Ps_1


title: Cxxc1 MO 256c+1hr Rep II.2

description:
Library name: 18
tpms_rep_II.csv


title: Kmt2b MO 256c+1hr Rep II.2

description:
Library name: 17
tpms_rep_II.csv


title: Ctrl MO 256c+1hr Rep II.1

description:
Library name: 15
tpms_rep_II.csv


title: Cxxc1 MO 256c+1hr Rep II.1

description:
Library name: 14
tpms_rep_II.csv


title: APH_IVF_H3K4me3_2


title: 2C_IVF_PolII_2


title: APH_IVF_PolII_2


title: Ctrl MO 256c+1hr Rep I.3

description:
Library name: 11
tpms_rep_I.csv


title: NI Ctrl 256c+1hr Rep II.1

description:
Library name: 16
tpms_rep_II.csv


title: 2C_IVF_H33_1


title: APH_IVF_PolII_1


title: Cxxc1 MO 256c+1hr Rep I.3

description:
Library name: 10
tpms_rep_I.csv


title: APH_IVF_H3K4me3_1


title: NI Ctrl 256c+1hr Rep I.3

description:
Library name: 12
tpms_rep_I.csv


title: APH_IVF_H3K4me3_3


title: Kmt2b MO 256c+1hr Rep II.1

description:
Library name: 13
tpms_rep_II.csv


title: 2C_IVF_H3K27me3_2


title: 2C_IVF_PolII_1


title: Kmt2b MO 256c+1hr Rep I.3

description:
Library name: 9
tpms_rep_I.csv


title: NI Ctrl 256c+1hr Rep I.2

description:
Library name: 8
tpms_rep_I.csv


title: Ctrl MO 256c+1hr Rep I.2

description:
Library name: 7
tpms_rep_I.csv


title: 2C_IVF_H3K4me3_1


title: Cxxc1 MO 256c+1hr Rep I.2

description:
Library name: 6
tpms_rep_I.csv


title: 2C_IVF_H3K27ac_1


title: 2C_IVF_H2AX_1


title: Kmt2b MO 256c+1hr Rep I.2

description:
Library name: 5
tpms_rep_I.csv


title: WT_P14_PolII_Ps_2


title: WT_P14_PolII_Ps_1


title: Ctrl MO 256c+1hr Rep I.1

description:
Library name: 3
tpms_rep_I.csv


title: WT_P14_IgG_1

value: IgG


title: WT_P14_H3K27ac_2


title: WT_P14_H3K27ac_1


title: Cxxc1 MO 256c+1hr Rep I.1

description:
Library name: 2
tpms_rep_I.csv


title: K4M_P14_PolII_Ps_2


title: Kmt2b MO 256c+1hr Rep I.1

description:
Library name: 1
tpms_rep_I.csv


title: brain_BL6_HFD_Tregs_33_37

first: Carolin

last: Daniel

address: Heidemannstr. 1

department: Diabetes Center

institute: Helmholtz Munich

description:
sequencing data from FACS-sorted T cell
24L012483

data_processing:
Paired FASTQ files were processed using the nf-core/rnaseq pipeline (version 3.16)  with default parameters and gene counts were quantified with Salmon
Single End FASTQ Files were mapped with BWA-mem with default configuration and reads were quantified using HTSeq count
Assembly: mm10
Supplementary files format and content: tab-separated Salmon gene quantification file;  tab-separated HTseq output file

source_name: brain

growth_protocol: Mice were fed ad libitum the indicated diet or genetically obese.

extract_protocol:
T cells were FACS-sorted for purity on a BD Aria III, Takara SMARTER
Nextera or Takara Smarter as indicated in the methods section of the manuscript.

treatment_protocol: Brains and hypothalami were homogenized manually, followed by density centrifugation over Percoll. T cells were FACS-sorted for purity on a BD Aria III.

value: brain

value: Tregs

value: HFD


title: brain_BalbC_HFD_Tregs_15_21

description:
sequencing data from FACS-sorted T cell
24L012482

value: BalbC


title: brain_BalbC_SD_Tregs_42_46

description:
sequencing data from FACS-sorted T cell
24L012484

value: SD


title: K4M_P14_PolII_Ps_1

value: P14 growing oocyte

value: H3.3K4M transgenic

value: Phospho-POLR2A CTD-S2

value: no


title: Dam-only-256c-Rep1

description:
Library name: 1
Chromatin Accessibility profiling using Targeted DamID (CATaDa) sequencing

data_processing:
Analysis of fastq-files from CATaDa experiments was performed with the damidseq pipeline script (Marshall & Brand, 2015). Preprocessed fastq-files were mapped to the Xl.v10.1 genome assembly using bowtie2, and mapped reads were binned into fragments delineated by 5’-GATC-3’ motifs. Files were converted to the bigwig file format with bedGrapgToBigWig (v4) for visualization with the Integrative Genomics Viewer (IGV) (v2.13.0). MACS (v3.0.1) (Y. Zhang et al., 2008) was used to call broad peaks on the mapped read (.bam) files generated by the damidseq_pipeline.
Assembly: Xenopus laevis (v10.1)
Supplementary files format and content: Coverage files (.bigwig)
Supplementary files format and content: Broad peak calling files (.bed)

source_name: Whole embryos 4.5hpf

extract_protocol:
Genomic DNA was extracted from embryos using nuclear isolation followed by use of the Monarch Genomic DNA Purification Kit (#T3010S), as described in the manuscript. All samples were processed for CATaDa as described previously (Marshall et al., 2016).
CATaDa fragments were prepared for Illumina sequencing according to a modified TruSeq protocol (Marshall et al., 2016).

treatment_protocol: Chromatin accessibility of pre-ZGA embryos was profiled using CATaDa (Chromatin Accessibility profiling using Targeted DamID) as described previously (Aughey et al., 2018). Embryos were injected at the 1-cell stage with 2.3ng pRN3P_AID-Dam-only construct (a kind gift by Maria-Elena Torres-Padilla; Addgene plasmid # 136065) (Borsos et al., 2019). 500x injected or non-injected control pre-ZGA (256-cell stage i.e. 4.5 hpf) embryos were collected per replicate.

value: Whole embryos 4.5hpf

value: Whole embryos

value: WT

value: Dam mRNA-injected


title: brain_BalbC_SD_Tregs_37_41

description:
sequencing data from FACS-sorted T cell
24L012479


title: loxP7 design, pool transfection, PCR sequencing, medium gate, replicate 2

city: Hinxton

first: Pierre

last: Murat

address: Wellcome Trust Genome Campus

country: United Kingdom

institute: Wellcome Sanger Institute

description:
Library name: loxPsym.7.pool.PCR.medium.rep.2
OTX2_loxP7_medium.vcf

data_processing:
The Dorado basecaller with the dna_r9.4.1_e8_sup@v3.6 model was used for base calling without modifications, as well as for calling mCpG-modified bases. For m6A-modified base calling, the Guppy basecaller with the res_dna_r941_min_modbases-all-context_v001.cfg model was employed. The reads were aligned to the hg38 reference genome using either Dorado (for Cas9 sequencing) or bwa mem (for long-range PCR amplicon sequencing). BAM files were sorted and filtered using samtools, and further filtered for a region surrounding the OTX2 gene (chr14:56839500-56908200). Structural variants were called using SAVANA with relaxed QC settings (--buffer 100, --depth 1) or a custom structural variants caller. Read names associated with the filtered variants were extracted.
Assembly: hg38
Supplementary files format and content: .read.groups.txt, read assignements to genotypes
Supplementary files format and content: .breakpoints.vcf, vcf files reporting breakpoints
Supplementary files format and content: sv_breakpoints_read_support.tsv, read groups associated with breakpoints
Supplementary files format and content: .tsv, Fiber-seq analysis result

growth_protocol: HAP1 ∆MLH1 cells expressing a doxycycline-inducible prime editor were cultured in IMDM (Invitrogen) with 10% FBS (Invitrogen) and glutamine and penicillin-streptomycin  (Invitrogen) at 37 °C and 5% CO2

extract_protocol:
Between 2 and 4 million cells were collected by centrifugation, and high molecular weight (HMW) genomic DNA was extracted using the Monarch High Molecular Weight DNA Extraction Kit (New England BioLabs) with agitation speeds set to 1,500 rpm or 2,000 rpm. A modified version of the Monarch protocol was used to simultaneously assess DNA accessibility when required. In this modified protocol, 129 µl of nuclei prep buffer was combined with 10 µl of recombinant Cutsmart, 1 µl of 32 mM S-adenosylmethionine (final concentration 160 µM), 10 µl of 5000 Units/ml EcoGII methyltransferase (50 Units; New England BioLabs), and 5 µl of 20 mg/ml RNase A (200 µg; New England BioLabs). Approximately 2–3 million cells were resuspended in this reaction buffer and incubated at 37°C for 30 minutes. The reaction was then heated to 65°C for 5 minutes to inactivate the enzymes. Subsequently, 150 µl of nuclei prep buffer containing 10 µl of proteinase K was added to the nuclei preparation, and HMW DNA was extracted following the standard Monarch High Molecular Weight DNA Kit protocol. For samples containing six loxPsym sites obtained from screens, an additional step was included to eliminate low-molecular-weight DNA. This was achieved using the Short Fragment Eliminator Kit (Oxford Nanopore Technologies), following the manufacturer’s instructions.
Cas9-targeted sequencing: Cas9 enrichment was carried out using the Cas9 sequencing kit protocol with minor modifications (CAS9106 Protocol v109, Oxford Nanopore Technologies). Briefly, 5 µg of high molecular weight (HMW) DNA was dephosphorylated. tracrRNA and crRNA were annealed and complexed with HifiCas9 V3 (Integrated DNA Technologies) to form RNPs. The dephosphorylated DNA was incubated with Cas9 RNPs for 30 minutes at 37°C. Sequencing adapters were then ligated to the cleaved DNA, with the ligation step extended to 1 hour at room temperature. The libraries were purified using Ampure XP beads (Agilent), washed with Long Fragment Buffer, and eluted in an elution buffer for 16 hours. Sequencing was performed using the MinION Mk1B platform with R9.4.1 flow cells (FLO-MIN106). Long-range PCR: PCR amplification was performed using the LongAmp Hot Start Taq 2X Master Mix (New England BioLabs), using 250 ng of genomic DNA as input and 1 µM of forward and reverse primers, under the following cycling conditions: initial denaturation at 94°C for 30 seconds, followed by 30 cycles of 94°C for 30 seconds, 59°C for 1 minute, and 65°C for 25 minutes, with a final extension at 65°C for 10 minutes. PCR products were purified using AMPure XP Beads (Beckman Coulter) at a bead-to-sample ratio of 0.66X and eluted with the elution buffer from the Monarch HMW DNA Extraction Kit for Cells & Blood. Genomic DNA from cell samples sorted into different gates was amplified using primers with custom index extensions for multiplexing. The resulting amplicons were sequenced on the MinION Mk1B platform using R10.4.1 flow cells (FLO-MIN114).

value: deletion


title: 2C_IVF_H3K27me3_1

value: 2-cell embryo


title: K4M_P14_IgG_1


title: brain_BL6_SD_Tregs_01_05

description:
sequencing data from FACS-sorted T cell
24L012480


title: K4M_P14_H3K27ac_2


title: K4M_P14_H3K27ac_1


title: NI Ctrl 256c+1hr Rep I.1

description:
Library name: 4
tpms_rep_I.csv

value: Whole embryos 5.5hpf


title: loxP7 design, pool transfection, PCR sequencing, dim gate, replicate 1

description:
Library name: loxPsym.7.pool.PCR.dim.rep.1
OTX2_loxP7_dim.vcf


title: Mla_IVF_RNaseA_PolII_Ps_2

source_name: Morula

value: Morula

value: RNase A


title: loxP7 design, pool transfection, PCR sequencing, dim gate, replicate 2

description:
Library name: loxPsym.7.pool.PCR.dim.rep.2
OTX2_loxP7_dim.vcf


title: brain_BL6_SD_Tregs_67_71

description:
sequencing data from FACS-sorted T cell
24L012476

value: brain

value: Tregs


title: loxP7 design, pool transfection, PCR sequencing, dark gate, replicate 2

description:
Library name: loxPsym.7.pool.PCR.dark.rep.2
OTX2_loxP7_dark.vcf


title: Mla_IVF_RNaseA_PolII_Ps_1


title: loxP7 design, pool transfection, PCR sequencing, dark gate, replicate 1

description:
Library name: loxPsym.7.pool.PCR.dark.rep.1
OTX2_loxP7_dark.vcf


title: brain_BalbC_HFD_Tregs_47_25

description:
sequencing data from FACS-sorted T cell
24L012475

value: BalbC

value: HFD


title: loxP7 design, pool transfection, PCR sequencing, bright gate, replicate 2

description:
Library name: loxPsym.7.pool.PCR.bright.rep.2
OTX2_loxP7_bright.vcf


title: brain_BL6_HFD_Tregs_21_25

description:
sequencing data from FACS-sorted T cell
24L012474


title: loxP3 design, clonal, PCR sequencing, medium gate, replicate 2

description:
Library name: loxPsym.3.clonal.PCR.medium.rep.2
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: Dam-only-256c-Rep2

description:
Library name: 2
Chromatin Accessibility profiling using Targeted DamID (CATaDa) sequencing


title: loxP3 design, clonal, PCR sequencing, dim gate, replicate 2

description:
Library name: loxPsym.3.clonal.PCR.dim.rep.2
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: 2C_IVF_DRB_PolII_Ps_2

value: DRB


title: loxP3 design, clonal, PCR sequencing, dim gate, replicate 1

description:
Library name: loxPsym.3.clonal.PCR.dim.rep.1
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: 2C_IVF_DRB_PolII_Ps_1


title: loxP3 design, clonal, PCR sequencing, dark gate, replicate 2

description:
Library name: loxPsym.3.clonal.PCR.dark.rep.2
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: loxP7 design, pool transfection, PCR sequencing, medium gate, replicate 1

description:
Library name: loxPsym.7.pool.PCR.medium.rep.1
OTX2_loxP7_medium.vcf


title: brain_BalbC_HFD_Tregs_16_20

description:
sequencing data from FACS-sorted T cell
24L012473


title: loxP3 design, clonal, PCR sequencing, medium gate, replicate 1

description:
Library name: loxPsym.3.clonal.PCR.medium.rep.1
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: brain_BL6_SD_Tregs_62_66

description:
sequencing data from FACS-sorted T cell
24L012471

value: SD


title: loxP3 design, clonal, PCR sequencing, dark gate, replicate 1

description:
Library name: loxPsym.3.clonal.PCR.dark.rep.1
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: P14_Oo_PolII_Ps_2

data_processing:
Raw reads were processed with Trim Galore to remove adaptor sequences and poor quality bases.
Trimmed reads were then aligned to the mouse reference genome (mm10) using Bowtie2 with default parameters.
Picard was used to remove PCR duplicates.
Peaks were called using MACS2 with default parameters.
Assembly: mm10
Supplementary files format and content: The UCSC Genome Browser utility, bedGraphToBigWig, was used to transform the bedgraph ﬁles to bigwig ﬁles
Supplementary files format and content: bigwig file for each sample
Library strategy: CUT&Tag

extract_protocol:
Generally, we collected superovulated eggs for in vitro fertilization, isolated fertilized eggs and cultured in KSOM for preimplantation development until reaching different developmental stages. Growing and fully-grown oocytes were also collected from ovaries. These oocytes and early embryos were used for following ChIP-seq library preparation after removal of zona pellucida.
ChIP-seq libraries were prepared using a Hyperactive In-Situ ChIP Library Prep Kit for Illumina (pG-Tn5) (Vazyme, China) according to the manufacturer’s protocol. Qualified libraries were then loaded on Illumina Hiseq platform for PE150 sequencing.

value: embryo


title: 2C_IVF_DRB_PolII_2


title: loxP7 design, pool transfection, PCR sequencing, bright gate, replicate 1

description:
Library name: loxPsym.7.pool.PCR.bright.rep.1
OTX2_loxP7_bright.vcf


title: loxP3 design, clonal, PCR sequencing, bright gate, replicate 1

description:
Library name: loxPsym.3.clonal.PCR.bright.rep.1
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: brain_BL6_SD_Tregs_11_15

description:
sequencing data from FACS-sorted T cell
24L012478


title: brain_BalbC_HFD_Tregs_26_31

description:
sequencing data from FACS-sorted T cell
24L012470


title: loxP6 design, pool transfection, Cas9 sequencing, medium gate, replicate 2

description: Library name: loxPsym.6.pool.Cas9.medium.rep.2


title: brain_BL6_HFD_Tregs_38_42

description:
sequencing data from FACS-sorted T cell
24L012469


title: loxP6 design, pool transfection, Cas9 sequencing, dim gate, replicate 2

description: Library name: loxPsym.6.pool.Cas9.dim.rep.2


title: Mla_IVF_PolII_Ps_2


title: loxP6 design, pool transfection, Cas9 sequencing, medium gate, replicate 1

description: Library name: loxPsym.6.pool.Cas9.medium.rep.1


title: loxP6 design, pool transfection, Cas9 sequencing, bright gate, replicate 2

description: Library name: loxPsym.6.pool.Cas9.bright.rep.2


title: loxP6 design, pool transfection, Cas9 sequencing, dim gate, replicate 1

description: Library name: loxPsym.6.pool.Cas9.dim.rep.1


title: 2C_IVF_DRB_PolII_1


title: hypo_BalbC_SD_act_06_10

description:
sequencing data from FACS-sorted T cell
24L012468

source_name: hypothalamus

value: hypothalamus

value: act


title: loxP3 design, clonal, PCR sequencing, bright gate, replicate 2

description:
Library name: loxPsym.3.clonal.PCR.bright.rep.2
OTX2_LCR_scramble_all_reads.sv_breakpoints.vcf
OTX2_LCR_scramble_all_reads.sv_breakpoints_read_support.tsv


title: brain_BL6_HFD_Tregs_77_80

description:
sequencing data from FACS-sorted T cell
24L012472


title: loxP6 design, clonal, Cas9 sequencing, dim gate, replicate 2

description:
Library name: loxPsym.6.clonal.Cas9.dim.rep.2
Fiberseq_enhancer_scramble.tsv


title: hypo_BalbC_SD_act_37_41

description:
sequencing data from FACS-sorted T cell
24L012463


title: hypo_BalbC_SD_act_32_36

description:
sequencing data from FACS-sorted T cell
24L012464


title: loxP6 design, pool transfection, Cas9 sequencing, dark gate, replicate 1

description: Library name: loxPsym.6.pool.Cas9.dark.rep.1


title: hypo_BalbC_SD_act_42_46

description:
sequencing data from FACS-sorted T cell
24L012465


title: loxP6 design, pool transfection, Cas9 sequencing, dark gate, replicate 2

description: Library name: loxPsym.6.pool.Cas9.dark.rep.2


title: P14_Oo_PolII_Ps_1


title: Mla_IVF_IgG_1


title: L2C_IVF_PolII_Ps_2


title: loxP6 design, clonal, Cas9 sequencing, medium gate, replicate 1

description:
Library name: loxPsym.6.clonal.Cas9.medium.rep.1
Fiberseq_enhancer_scramble.tsv


title: loxP6 design, clonal, Cas9 sequencing, dim gate, replicate 1

description:
Library name: loxPsym.6.clonal.Cas9.dim.rep.1
Fiberseq_enhancer_scramble.tsv


title: loxP6 design, clonal, Cas9 sequencing, dark gate, replicate 2

description:
Library name: loxPsym.6.clonal.Cas9.dark.rep.2
Fiberseq_enhancer_scramble.tsv


title: L2C_IVF_IgG_1


title: L2C_IVF_PolII_Ps_1


title: hypo_BalbC_HFD_act_15_21

description:
sequencing data from FACS-sorted T cell
24L012459


title: loxP6 design, clonal, Cas9 sequencing, bright gate, replicate 1

description:
Library name: loxPsym.6.clonal.Cas9.bright.rep.1
Fiberseq_enhancer_scramble.tsv


title: Mla_IVF_PolII_Ps_1


title: loxP6 design, pool transfection, Cas9 sequencing, bright gate, replicate 1

description: Library name: loxPsym.6.pool.Cas9.bright.rep.1


title: L1C_IVF_PolII_Ps_2


title: hypo_BalbC_HFD_act_11_14

description:
sequencing data from FACS-sorted T cell
24L012455


title: L1C_IVF_IgG_1


title: loxP3 design, clonal, Cas9 sequencing, medium gate, replicate 2

description: Library name: loxPsym.3.clonal.Cas9.medium.rep.2


title: hypo_BalbC_HFD_Tregs_11_14

description:
sequencing data from FACS-sorted T cell
24L012452


title: hypo_BalbC_HFD_act_26_31

description:
sequencing data from FACS-sorted T cell
24L012460


title: loxP3 design, clonal, Cas9 sequencing, dark gate, replicate 2

description: Library name: loxPsym.3.clonal.Cas9.dark.rep.2


title: loxP3 design, clonal, Cas9 sequencing, medium gate, replicate 1

description: Library name: loxPsym.3.clonal.Cas9.medium.rep.1


title: hypo_BalbC_HFD_act_16_20

description:
sequencing data from FACS-sorted T cell
24L012453


title: loxP3 design, clonal, Cas9 sequencing, dim gate, replicate 2

description: Library name: loxPsym.3.clonal.Cas9.dim.rep.2


title: loxP3 design, clonal, Cas9 sequencing, bright gate, replicate 1

description: Library name: loxPsym.3.clonal.Cas9.bright.rep.1


title: IVF_6h_PolII_Ps_2


title: loxP3 design, clonal, Cas9 sequencing, bright gate, replicate 2

description: Library name: loxPsym.3.clonal.Cas9.bright.rep.2


title: loxP6 design, clonal, Cas9 sequencing, dark gate, replicate 1

description:
Library name: loxPsym.6.clonal.Cas9.dark.rep.1
Fiberseq_enhancer_scramble.tsv


title: loxP3 design, clonal, Cas9 sequencing, dim gate, replicate 1

description: Library name: loxPsym.3.clonal.Cas9.dim.rep.1


title: L1C_IVF_PolII_Ps_1


title: loxP6 design, clonal, Cas9 sequencing, bright gate, replicate 2

description:
Library name: loxPsym.6.clonal.Cas9.bright.rep.2
Fiberseq_enhancer_scramble.tsv


title: loxP3 design, clonal, Cas9 sequencing, dark gate, replicate 1

description: Library name: loxPsym.3.clonal.Cas9.dark.rep.1


title: loxP6 design, clonal, Cas9 sequencing, medium gate, replicate 2

description:
Library name: loxPsym.6.clonal.Cas9.medium.rep.2
Fiberseq_enhancer_scramble.tsv


title: hypo_BL6_SD_Tregs_62_66

description:
sequencing data from FACS-sorted T cell
24L012451


title: hypo_BalbC_SD_Tregs_06_10

description:
sequencing data from FACS-sorted T cell
24L012450


title: IVF_6h_PolII_Ps_1


title: IVF_6h_IgG


title: Donor1, Day7, KI-treated

city: Chapel Hill

first: Mark

last: Woodcock

state: NC

address: 170 Manning Drive

institute: University of North Carolina at Chapel Hill

data_processing:
Alignment: STAR (v.2.7.6a)
Quantification: Salmon (v.1.4.0)
QA: FastQC (v0.11.9)
QA: Picard (v2.22.4) CollectRnaSeqMetrics
Assembly: Ensembl release 99, GRCh38
Supplementary files format and content: Salmon count data matrix

molecule: nuclear RNA

source_name: blood

growth_protocol: After transduction with CD19-directed CAR via retroviral vector, cells were expanded in media with recombinant IL-7 and IL-15.

extract_protocol:
RNA extracted with Qiagen AllPrep DNA/RNA kit and Qiagen Rneasy Plus for isolation.
Messenger RNA libraries were prepared (Illumina Stranded mRNA library kit, catalog #20040532) were prepared via manufacturers instructions and library quality checked with Qubit 4 Fluorometer and TapeStation 2200 with high sensitivity D1000 reagents.  Samples were sequenced on a NextSeq 2000 using paired-end 100-bp reads.

treatment_protocol: DMSO (0.75µM) or KIs (0.75µM) were added to the culture medium. the samples were collected at day1, day3 and day7 post adding DMSO or Inhibitors. A second dose was added at day3 for samples that collected at day7. The samples were washed, collected, lysed, and kept in -80 until all the samples were collected.

value: blood

value: Mononuclear cells

value: T cell

value: 0.75µM KIs


title: Donor3, Day7, KI-treated


title: Donor1, Day7, DMSO-treated

value: 0.75µM DMSO


title: Donor3, Day3, KI-treated


title: Donor3, Day1, DMSO-treated


title: Donor1, Day3, KI-treated


title: Donor3, Day1, KI-treated


title: hypo_BL6_HFD_Tregs_33_37

description:
sequencing data from FACS-sorted T cell
24L012446


title: Donor1,Day3, DMSO-treated


title: FGO_PolII_Ps_1


title: hypo_BL6_HFD_Tregs_72_76

description:
sequencing data from FACS-sorted T cell
24L012448


title: hypo_BL6_SD_Tregs_43_47

description:
sequencing data from FACS-sorted T cell
24L012445


title: hypo_BL6_HFD_Tregs_77_80

description:
sequencing data from FACS-sorted T cell
24L012444


title: Donor1, Day1, KI-treated


title: hypo_BL6_HFD_Tregs_06_10

description:
sequencing data from FACS-sorted T cell
24L012447


title: Hypothalamus, Foxp3 GFP BalbC, 16 wks regular diet, pooled n=9 females, CD4+ CD25+ Foxp3GFP+ Tregs

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001410

value: CD4+ CD25+ Foxp3+ Tregs

value: Foxp3 GFP

value: regular diet


title: hypo_BL6_SD_Tregs_11_15

description:
sequencing data from FACS-sorted T cell
24L012449


title: FGO_IgG


title: FGO_PolII_Ps_2


title: Donor3, Day3, DMSO-treated


title: Donor1, Day1, DMSO-treated


title: 8cell_Ps_2


title: Donor3, Day7, DMSO-treated


title: 8cell_Ps_1


title: Hypothalamus, Foxp3 GFP BalbC, 16 wks regular diet, pooled n=9 females, CD4+ CD44- naive T cells

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001409

value: CD4+ CD44- naive T cells


title: hypo_BL6_SD_Tregs_67_71

description:
sequencing data from FACS-sorted T cell
24L012443

value: Tregs


title: hypo_BalbC_HFD_Tregs_15_21

description:
sequencing data from FACS-sorted T cell
24L012442

value: BalbC


title: Hypothalamus, Foxp3 GFP BalbC, 16 wks HFHSD, pooled n=9 females, CD4+ CD25+ Foxp3GFP+ Tregs

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001408

value: diet-induced obesity


title: 4C_IVF_PolII_Ps_2


title: 8cell_IgG


title: Hypothalamus, Foxp3 GFP BalbC, 16 wks HFHSD, pooled n=9 females, CD4+ CD44- naive T cells

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001407


title: Hypothalamus, Bl6, pooled n=7 females, CD25hi Tregs

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001406

value: CD25hi Tregs

value: WT

value: controls


title: hypo_BalbC_HFD_Tregs_16_20

description:
sequencing data from FACS-sorted T cell
24L012440

value: hypothalamus

value: HFD


title: Hypothalamus, ob/ob, pooled n=7 females, CD25high Tregs

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001404

value: ob/ob

value: genetically obese


title: hypo_BalbC_HFD_Tregs_26_31

description:
sequencing data from FACS-sorted T cell
24L012441


title: mod[07570]_L8_Panx IP

description: Library name: mod[07570]_L8_Panx IP

data_processing:
The 3’-adapter 5’-AGATCGGAAGAGCACACGTCT-3’ was trimmed from the sequenced reads using Cutadapt version 1.15. Trimmed reads less than 18 nucleotides and reads without the adapter were discarded. Trimmed reads were then analyzed using the piPipes small RNA pipeline.
Assembly: dm3
Supplementary files format and content: A bed file with non-rRNA and non-miRNA dm3 genome mapping reads

extract_protocol:
Ovary lystaes from repsective genotypes were incubated with Panx antibody overnight. To extract small RNAs bound to Panx, the beads, after the washing step, were treated with TRIzol, and the total RNA was extracted and submitted for sequencing. Prior to library preparation and sequencing, the RNA sample was supplemented with 1 µl of 10 µM 2S Block oligo (5’- TAC AAC CCT CAA CCA TAT GTA GTC CAA GCA/3SpC3/-3’) to inhibit amplification of ribosomal RNA.
Libraries were prepared by Novogene using the NEBNext Small RNA Library Prep Set for Illumina

value: Ovary

tag: ip antibody

value: Panoramix


title: mod[07570]_L8_Piwi IP

description: Library name: mod[07570]_L8_Piwi IP

extract_protocol:
Ovary lystaes from repsective genotypes were incubated with Piwi antibody overnight. To extract small RNAs bound to Piwi, the beads, after the washing step, were treated with TRIzol, and the total RNA was extracted and submitted for sequencing. Prior to library preparation and sequencing, the RNA sample was supplemented with 1 µl of 10 µM 2S Block oligo (5’- TAC AAC CCT CAA CCA TAT GTA GTC CAA GCA/3SpC3/-3’) to inhibit amplification of ribosomal RNA.
Libraries were prepared by Novogene using the NEBNext Small RNA Library Prep Set for Illumina

value: Piwi


title: Hypothalamus, ob/ob, pooled n=7 females, CD4+ T cells

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001403

value: CD4+ T cells


title: mod[07570]_Piwi IP

description: Library name: mod[07570]_Piwi IP


title: hypo_BalbC_SD_Tregs_42_46

description:
sequencing data from FACS-sorted T cell
24L012439

value: SD


title: mod[07570]_L8_Input

description: Library name: mod[07570]_L8_Input


title: 2C_IVF_PolII_Ps_2

value: embryo


title: hypo_BalbC_SD_Tregs_32_36

description:
sequencing data from FACS-sorted T cell
24L012438


title: 2C_IVF_IgG_1


title: Mut-1_1026

city: Shanghai

first: Yu

last: Liang

address: Yueyang Road 320

department: SIBCB

institute: CEMCS, CAS

description: Testicular cells mixed with plasmid DNA

data_processing:
library strategy: END-seq
Read1 Reads were aligned to the mouse (GRCm38p2/mm10 plus plasmid) genome using Bowtie version 1.2.1.1 and three mismatches were allowed and the best strata for reads were kept with multiple alignments (-n 3 -k 1 -l 50). Functions “view” and “sort” of samtools (version 1.9) were used to convert and sort the mapping output to sorted bam file. Bam files were further converted to bed files using the bedtools (v.2.25.0) bamToBed command. The function “genomecov” from the bedtools(v.2.25.0) was used to normalized read density (reads per million, RPM).Break positions were identified utilizing 5' end of the reads.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: testis

extract_protocol:
Reactions for sequencing were carried out in a 35 μL volume of Cleavage Buffer (50 mM HEPES, pH 7.5, 30 mM KCl, 2 mM DTT and 1 mM MgCl2) with 5 nM plasmid substrate, 400 nM WT or Y138F protein were used.  Reactions were incubated for 60 minutes at 37°C.  Reactions were terminated with 0.5 μL 500 mM EDTA and 0.8 μL proteinase K (Roche, 20 mg/mL) and further incubated for 30 minutes at 55°C.  NaCl were then added to 150 mM.END-seq was performed as previously described, with modifications.In brief, 12.5 day mouse testicular cells were washed twice in ice-cold PBS and resuspended in ice-cold cell suspension buffer.  After being equilibrated at room temperature for 5 min, the resuspended testicular cells and cleavage reaction were mixed then embedded in 0.75% agarose (final concentration) and solidified at 4°C for 15 min. Subsequently, the embedded cells were lysed and digested with proteinase K (50°C for 1 h then 37°C for 7 h). After washing with TE buffer (Tris-EDTA, pH 8.0),  the plugs were then digested with RNase at 37°C for 1 h followed treatment of Exonuclease VII (NEB) at 37°C for 1 h and Exonuclease T (NEB) at 24°C for 45 min to blunt the DNA ends.
After blunting, A-tails were added to the free 3′-OH of blunted ends, then ligated with END-seq hairpin adaptor 1.  Subsequently, agarose plugs were melted and dialyzed, and the released DNA was sonicated to a shear DNA fragments at a length of about 170 bp.  Shear DNA fragments were collected and purified, then the DNA pellet was dissolved in 70 μl TE buffer.  Biotinylated adaptor 1-DNA fragment was further isolated using MyOne Streptavidin Beads.  The second end was repaired and A-tails added, then ligated with END-seq hairpin adaptor 2.  Both sides of hairpin were digested by using USER (NEB) and the resulting DNA fragments amplified by PCR.  The libraries were then sequenced using Illumina HiSeq 2000.

value: testis

value: testicular cells

value: Y138F mutant protein


title: mod[07570]_H3K9me3 ChIP DNA

description: Library name: Sample 4

data_processing:
Reads were analyzed by piPipes (PMCID: PMC4325541) ChIP-seq workflow using default options. As part of the piPipes workflow, reads were mapped to the dm3 genome using Bowtie 2 and peaks were identifed by MACS2.
Assembly: dm3
Supplementary files format and content: MACS2 output in tab delimited text file format.

source_name: Ovary

extract_protocol:
Approximately 50 μl ovaries were crosslinked with 1% formaldehyde in PBS for 10 min at room temperature, quenched with 150 mM glycine for 5 min, and washed three times, 5 min each, in PBT. Lysis was performed in 500 µl of lysis buffer (10 mM Tris-HCl at pH 8, 100 mM NaCl, 1 mM EDTA, 0.1% sodium deoxycholate, 0.5% N lauroylsarcosine, 1 mM DTT and 1x Halt Protease Inhibitor from Thermo). Ovaries were homogenized on a 1 ml Wheaton homogenizer with 5 loose and 5 tight strokes and kept on ice for 30 min. Lysates were prepared as 100 μl aliquots and sonicated on a Bioruptor (Diagenode) for 10 cycles at high strength with 30 s ON and 45 s OFF pulses. The lysates were then pooled, and the volume was adjusted to 1 ml with lysis buffer, followed by centrifugation at 12,000 rpm for 10 min at 4°C. The supernatants containing the soluble chromatin were transferred to new tubes, and 100 μl was saved as input control. Immunoprecipitation was carried out by adding 2 μg of anti-H3K9me3 (Abcam, ab8898) to the respective supernatants and incubating overnight on a rotating wheel at 4°C. Protein A/G Magnetic Beads (ThermoFisher, #88802) were added to the supernatant-antibody mix, and the samples were incubated for an additional 3 hr at 4°C. The ChIP samples were washed five times: once with low-salt buffer (20 mM Tris-HCl at pH 8, 150 mM NaCl, 2 mM EDTA, 0.1% SDS, and 0.1% Triton-X 100), twice with high-salt buffer (20 mM Tris-HCl at pH 8, 500 mM NaCl, 2 mM EDTA, 0.1% SDS, and 0.1% Triton-X 100), once with LiCl buffer (10 mM Tris-HCl at pH 8, 1 mM EDTA, 1% NP40, 1% deoxycholate and 250 mM LiCl) and once with TE buffer (10 mM Tris-HCl at pH 8 and 1 mM EDTA). Then, the beads were resuspended in 100 μl of elution buffer (50 mM Tris-HCl at pH 8, 10 mM EDTA, 1% SDS, and 300 mM NaCl). The input samples were thawed, mixed with an equal volume of elution buffer, and processed in parallel with the ChIP samples. Crosslinking was reversed by incubating the beads and inputs overnight at 65°C. The samples were sequentially treated with 2 μl of RNAseA+T1 (Thermo, EN0551) for 30 min at 37°C, and 5 μl of Proteinase K (Thermo, EO0491) for 2 hr at 37°C, and the immunoprecipitated DNA was then extracted using a PCR purification kit (Qiagen). ChIP was repeated thrice with three independent biological replicates. One replicate was sequenced using the Illumina SE150 strategy, and all three biological replicates were used for qPCR.
Libraries were prepared by Novogene using the NEBNext Ultra II DNA Library Prep Kit for Illumina

tag: chip antibody

value: H3K9me3 (Abcam, ab8898)


title: hypo_BalbC_SD_Tregs_37_41

description:
sequencing data from FACS-sorted T cell
24L012437

tag: tissue

value: Tregs

value: BalbC


title: 4C_IVF_PolII_Ps_1


title: mod[07570]_[L8]_H3K9me3 ChIP DNA

description: Library name: Sample 2


title: 4C_IVF_IgG_1


title: mod[07570]_Input

description: Library name: mod[07570]_Input


title: mod[07570]_[L8]_Input

description: Library name: Sample 1


title: 2C_IVF_PolII_Ps_1


title: brain_BalbC_SD_act_42_46

description:
sequencing data from FACS-sorted T cell
24L012436

value: brain

value: act


title: Mut-2_1026

description: Testicular cells mixed with plasmid DNA

value: WT

value: Y139F mutant protein


title: mod[07570]]_Input

description: Library name: Sample 3


title: mod[07570]_Panx IP

description: Library name: mod[07570]_Panx IP


title: Hypothalamus, Bl6, pooled n=7 females, CD4+ T cells

description:
sequencing data from FACS-sorted T cells from hypothalamus
16s001405

value: hypothalamus

value: controls


title: brain_BalbC_SD_act_32_36

description:
sequencing data from FACS-sorted T cell
24L012431


title: mod[07570]_[L8]_with no ectopic outgrowths_replicate3

description: Library name: Sample 21

source_name: Head

value: Head


title: brain_BalbC_HFD_act_16_20

description:
sequencing data from FACS-sorted T cell
24L012433

value: HFD


title: mod[07570]_[L8]_with no ectopic outgrowths_replicate1

description: Library name: Sample 19


title: mod[07570]_[L8]_with no ectopic outgrowths_replicate2

description: Library name: Sample 20


title: WT-1_1026

description: Testicular cells mixed with plasmid DNA

value: SPO11 WT protein


title: WT-2_1026

description: Testicular cells mixed with plasmid DNA


title: brain_BalbC_HFD_act_15_21

description:
sequencing data from FACS-sorted T cell
24L012425


title: mod[07570]_[L8]_with ectopic outgrowths_replicate3

description: Library name: Sample 18

value: mod[07570]_[L8]_with ectopic outgrowths


title: mod[07570]_[L8]_with ectopic outgrowths_replicate2

description: Library name: Sample 17


title: TFBS screen, round 2, replicate C

description: Library name: OTX2_12TFBS_round2_repC.amplicon

data_processing:
After demultiplexing, paired-end reads were merged using PEAR. Reads containing both forward and reverse PCR primer sequences were identified using the amplicon function of SeqKit. Amplicon sequences were then analyzed to identify and quantify deletions using CRISPResso2.
Supplementary files format and content: .txt, read count for modifications detected within the amplicons.

growth_protocol: HAP1 ∆MLH1 cells expressing a doxycycline-inducible prime editor were cultured in IMDM (Invitrogen) with 10% FBS (Invitrogen) and glutamine and penicillin-streptomycin (Invitrogen) at 37 °C and 5% CO2

extract_protocol:
Between 2 and 4 million cells were collected by centrifugation, and high molecular weight (HMW) genomic DNA was extracted using the Monarch High Molecular Weight DNA Extraction Kit (New England BioLabs).
The R5-2 region of interest was amplified and prepared for Illumina sequencing with index adapters.

value: TFBS screen, round 2


title: mod[07570]_+ replicate3

description: Library name: Sample 15


title: mod[07570]_[L8]_with ectopic outgrowths_replicate1

description: Library name: Sample 16


title: TFBS screen, round 2, replicate B

description: Library name: OTX2_12TFBS_round2_repB.amplicon


title: brain_BalbC_HFD_act_47_25

description:
sequencing data from FACS-sorted T cell
24L012424


title: mod[07570]_+ replicate1

description: Library name: Sample 13


title: mod[07570]_[L8] replicate3

description: Library name: Sample 12


title: hypo_BL6_HFD_act_77_80

description:
sequencing data from FACS-sorted T cell
24L012467


title: TFBS screen, round 2, replicate A

description: Library name: OTX2_12TFBS_round2_repA.amplicon


title: RSA 3

city: Nanjing

first: Chao

last: Ding

state: Jiangsu

address: 138 Xianlin Avenue

institute: Nanjing University of Chinese Medicine

description:
Library name: Sample 6
RSA_VS_Control.xlsx

data_processing:
bcl2fastq software was used to analyze the original sequencing data
FastQC software was used for quality assessment
Raw data is filtered using cutadapt-1.7.1 and FASTX-Tool-0.0.14
miRNA was analyzed by bowtie-1.1.1 software
The differential expression of miRNA was analyzed by R package edgeR/limma package
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: xlsx files include FPKM values for each Sample

source_name: Placenta

growth_protocol: The female and male C57BL/6 mice were kept  in CP-4 cages (L×W×H: 290 mm×178 mm×160 mm). The mice density of each cage did not exceed 6. The mice eat and drink freely at a temperatures of 24 ± 2 ℃, a relative humidity of 40-60%, and a light-dark cycle for 12 h.

extract_protocol:
Total RNA was extracted by TRIzol and miRNA libraries were constructed
miRNA libraries for miRNA-seq were prepared using QIAseq miRNA Library Kit (Qiagen)

treatment_protocol: Pregnant mice were intraperitoneally injected with 10 µg β2-GPI or normal saline.

value: Placenta

value: abortion


title: RSA 1

description:
Library name: Sample 4
RSA_VS_Control.xlsx


title: mod[07570]_+ replicate2

description: Library name: Sample 14

extract_protocol:
Total RNA was isolated from ovaries or heads using Trizol (ThermoFisher Scientific) following manufacturer's protocol.
Libraries were prepared by Novogene using the NEBNext Ultra RNA Library Prep Kit for Illumina


title: hypo_BL6_SD_act_67_66

description:
sequencing data from FACS-sorted T cell
24L012462

value: SD


title: brain_BalbC_SD_act_37_41

description:
sequencing data from FACS-sorted T cell
24L012422


title: Control 1

description:
Library name: Sample 1
RSA_VS_Control.xlsx

value: Normal


title: hypo_BL6_HFD_act_72_76

description:
sequencing data from FACS-sorted T cell
24L012458


title: Control 3

description:
Library name: Sample 3
RSA_VS_Control.xlsx


title: mod[07570]_[L8] replicate1

description: Library name: Sample 10


title: hypo_BL6_SD_act_11_15

description:
sequencing data from FACS-sorted T cell
24L012466


title: mod[07570]_[L8] replicate2

description: Library name: Sample 11


title: TFBS screen, round 1, replicate A

description: Library name: OTX2_12TFBS_round1_repA.amplicon

value: TFBS screen, round 1


title: hypo_BL6_HFD_act_33_37

description:
sequencing data from FACS-sorted T cell
24L012461


title: TFBS screen, round 0, replicate C

description: Library name: OTX2_12TFBS_round0_repC.amplicon

value: TFBS screen, round 0


title: TFBS screen, round 1, replicate C

description: Library name: OTX2_12TFBS_round1_repC.amplicon


title: Control 2

description:
Library name: Sample 2
RSA_VS_Control.xlsx


title: GNP ATACseq

city: Kingston

first: James

last: Purzner

state: Ontario

address: 76 Stuart Street

department: Surgery

country: Canada

institute: Queen's University

data_processing:
Adaptor prunning was done using trimmomatic, keeping only reads with > 28 BP for ChIPseq and > 92 BP for RNAseq.
For ChIP-seq reads were aligned to mm9 genome using Bowtie2 and reads with a MAPQ < 2 were discarded.  Peaks were called using EPIC and per gene promoter quantification were done by extending the from the TSS to include adjacent peaks.
Assembly: mm9
Supplementary files format and content: .bw bigwig ChIP seq signal track
Supplementary files format and content: _norm.bedgraph.gz ChIP seq normalized signal track generated using align2rawsignal (Kundaje)

source_name: cerebellum

extract_protocol:
GNPs and MB cells were purified using established percol fractionation protocol.   For crosslinking ChIPseq the single cell suspension was fixed in 1% foraldehyde for 10 min.  The chromatin was sheared using a Bioruptor.  ChIP was performed using Protein G agarose beads. For native ChIP GNPs or MB was incubated in MNase for 20 min and mononucleosomes wers isolated by centrifugation, ChIP was performed using Potein G agarose beads with an IgG/IgM linker.  Following elution DNA was purified by phenol chloroform extraction.
ChIP-seq libraries were prepared using NEBNext ChIP-Seq Library Prep (New England Biolabs).  Sequencing was performed using HiSeq 2500 (Illumina Inc).

value: cerebellum

value: Cerebellar granule neuron precursors


title: TFBS screen, round 1, replicate B

description: Library name: OTX2_12TFBS_round1_repB.amplicon


title: hypo_BL6_SD_act_67_71

description:
sequencing data from FACS-sorted T cell
24L012457

value: act


title: TFBS screen, round 0, replicate B

description: Library name: OTX2_12TFBS_round0_repB.amplicon


title: MB input 2

value: Ptch1 heterozygous


title: TFBS screen, round 0, replicate A

description: Library name: OTX2_12TFBS_round0_repA.amplicon


title: MB H3K27me3 replicate 2


title: MB input 1


title: hypo_BL6_HFD_act_06_10

description:
sequencing data from FACS-sorted T cell
24L012456

value: hypothalamus


title: RSA 2

description:
Library name: Sample 5
RSA_VS_Control.xlsx


title: MB H3K27me3 replicate 1


title: PNL2932

city: Hangzhou

first: Lidan

last: Hu

address: No.268 Kaixuan Road

department: School of Medicine

institute: Zhejiang University

description: Library name: Sample8

data_processing:
Raw sequencing data were processed using fastp v0.23.4 to filter out low-quality and low-complexity reads and remove adapter sequences. Cleaned reads were aligned to the hg38 reference genome in paired-end mode using bowtie2 (v2.5.1). The resulting BAM files were converted to bigWig format using bamCoverage from deeptools (v3.5.3) for chromosome coverage visualization. Custom R scripts were utilized to generate chromosome coverage plots.
Metagene plots were created using computeMatrix and plotProfile functions from deeptools (v3.5.3). Peak calling was performed with MACS2 (v2.2.9.1) using the callpeak function, and highly reproducible peaks across replicates were identified using IDR (v2.0.4.2). After quality control checks, data from replicates were merged to generate a combined set of peaks for each group.
The overlap and intersection of peaks between cell lines were assessed using Venn diagrams generated by the intersect function in bedtools (v2.27.1). Motif analysis was conducted with MEME (v5.0.2), restricting motif length to 6–10 bp and retaining motifs with significant E-values (< 10-3). Peak annotation, including overlapping gene locations, was performed with bedtools (v2.27.1) and reference gene annotation data from encode regions. Functional annotation of genes was done using the DAVID online database (https://david.ncifcrf.gov/; last accessed October 2023), focusing on cell cycle, apoptosis, and transcription regulation-related genes. Genomic distribution of peaks was visualized using IGV (v2.16.2).
Assembly: hg38
Supplementary files format and content: csv files include FPKM values for each sample

growth_protocol: HCT116 cells were cultured in McCoy’s 5A medium (Meilunbio, MA0314) , while HEK293T cells were cultured in DMEM medium (Sigma, D5546). All media were supplemented with 10% fetal bovine serum (FBS; Yeasen, 40131ES), 100 U/mL penicillin, and 100 μg/mL streptomycin (Beyotime, C0222). Cells were maintained at 37°C in a humidified incubator with 5% CO2.

extract_protocol:
10 million cells were collected and lysed in RIP buffer (20 mM Tris-HCl pH=7.4, 100 mM KCl, 1.5 mM MgCl2, 0.2 mM EDTA, 1% NP-40, 100U RNase inhibitor, 1×cocktail), and lysates were incubated with 6 μg anti-PNLDC1 antibody-coated beads (Proteintech, 25559-1-AP) overnight at 4°C. Immunocomplexes were washed with washing buffer for 3 times (20 mM Tris-HCl pH=7.4, 100 mM KCl, 1.5 mM MgCl2, 0.2 mM EDTA), treated with proteinase K, and RNA was extracted using phenol/chloroform/isoamyl alcohol (125:24:1). Clean reads were aligned to the hg38 genome using bowtie2 (v2.5.1). Both input and RIP samples were prepared for next-generation sequencing.
RIP sequencing libraries were prepared using Illumina TruSeq-stranded-mRNA following manufactors' protocols.

treatment_protocol: Immunoprecipitation were performed by using IgG and PNLDC1 antibodies and agarose beads.

value: Human embryonic kidney cells

value: PNLDC1 binding

tag: rip antibody


title: PNL2931

description: Library name: Sample7

value: anti-PNLDC1 antibody-coated beads (Proteintech, 25559-1-AP)


title: GNP MIRAseq replicate 3

value: WT


title: GNP MIRAseq input 2


title: IgG2932

description: Library name: Sample6

value: IgG binding

value: anti-IgG


title: GNP MIRAseq replicate 2


title: GNP MIRAseq input 1


title: IgG2931

description: Library name: Sample5


title: brain_BL6_HFD_act_77_80

description:
sequencing data from FACS-sorted T cell
24L012434

value: brain

value: HFD


title: brain_BL6_HFD_act_33_37

description:
sequencing data from FACS-sorted T cell
24L012435


title: GNP input 6


title: PNL1162

description: Library name: Sample4

value: Colorectal Cancer cells


title: brain_BL6_SD_act_01_05

description:
sequencing data from FACS-sorted T cell
24L012432

value: SD


title: GNP Ring1 ChIPseq replicate 2


title: brain_BL6_SD_act_62_66

description:
sequencing data from FACS-sorted T cell
24L012428


title: PNL1161

description: Library name: Sample3


title: GNP input 5


title: GNP RNA pol2 Ser5-phospho replicate 2


title: brain_BL6_SD_act_67_71

description:
sequencing data from FACS-sorted T cell
24L012423


title: GNP input native


title: hypo_BL6_SD_act_43_47

description:
sequencing data from FACS-sorted T cell
24L012454


title: GNP MIRAseq input 3


title: GNP RNA pol2 Ser5-phospho replicate 1


title: GNP H2Aubi119 ChIPseq replicate 2


title: IgG1161

description: Library name: Sample1


title: Healthy donor #3 naïve CD4 T cells, TCR-stimulated, 0.4mM Gln

city: NYC

first: Lei

last: Huang

address: 701 W 168th St Rm 1404 HHSC

institute: Columbia University

description: Library name: JH018

data_processing:
Libraries were sequenced using Element AVITI at JP Sulzberger Columbia Genome Center with paired end reads at 75bp length targeting 40 million reads per sample.
Bases2fastq version 1.5.0.962525890 was used for converting BCL to fastq format, coupled with adaptor trimming.
Assembly: A pseudoalignment was performed to a kallisto index created from transcriptomes (Ensembl v96, Human:GRCh38.p12) using kallisto (0.44.0).
Supplementary files format and content: tab-delimited text filw includes raw counts for each sample

source_name: Primary human T cells

growth_protocol: Human naïve CD4 T cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, 1% of penicilin-streptomycin, and glutamine in a humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
RNA was isolated using a miRNAeasy kit (Qiagen) according to the manufacturer’s instructions, including on-column DNaseI treatment.
The Clontech Ultra Low v4 kit (Takara Bio) was used for cDNA synthesis and Nextera XT kit (Illumina) was used for library preparation.

treatment_protocol: Naïve CD4 T cells were cultured in RPMI-complete with different glutamine concentrations at physiologic levels (0.4mM), or supraphysiologic levels (2mM), in the presence of MACSiBead particles loaded with biotinylated antibodies against human CD2, CD3, CD28 (Miltenyi Biotec) for 3 days, with 25ng/ml recombinant human IL-2 (Peprotech).

value: Primary human T cells


title: Healthy donor #2 naïve CD4 T cells, TCR-stimulated, 0.4mM Gln

description: Library name: JH017


title: GNP input 4


title: GNP H3K36me3 ChIPseq replicate 1


title: brain_BL6_HFD_act_38_42

description:
sequencing data from FACS-sorted T cell
24L012421


title: GNP H3K27ac ChIPseq replicate 1


title: GNP H3K27me3 ChIPseq replicate 2


title: BA3

city: yangzhou

first: Liu

middle: zi

last: yu

address: shuangqiao

institute: Yangzhou University

data_processing:
Illumina Novaseq 6000 platform used for basecalling.
Clean reads were obtained by removing adapters, high contents of unknown bases reads and low quality reads
The clean reads were mapped to the reference genome of Chinese white pear deposited in the GDR database (https://www.rosaceae.org/rosaceae_downloads/Pyrus_x_bretschneideri/Pbretschneideri-genome.v1.1/assembly/pbr.v1.1.chr.fa.gz) using Hisat2
Gene expression levels were estimated according to Fragments Per Kilobase of transcript sequence per Millions (FPKM)
Genome_build: Pyrus x bretschneideri ‘DangshanSuli’  Genome(assembly Pbr_v1.1)
Supplementary_files_format_and_content: Excel files include genes read count and FPKM values for each sample (.xls)

organism: Pyrus pyrifolia

source_name: Cuiguan

growth_protocol: Seven-year-old  ‘Cuiguan’ pears growing in an orchard in Yizheng, Jiangsu, China.

extract_protocol:
Total RNA was extracted by the ethyl ammonium bromide (CTAB) method using skin tissues collected from fruits with control and fruit bagging treatment 115 DAFB with three biological replicates.
RNA-Seq library was generated with NEB Next® UltraTM RNA Library Prep Kit for Illumina (NEB, USA) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

treatment_protocol: Half of the pear fruitlets were covered with Kobayashi paper bags. Single-layer white bags (F-PK2) were used 20 days after full bloom (DAFB) and double-layer yellow-white bags were used 40 DAFB. The other fruits without fruit bagging were set as control. Fruit samples were collected at  115 DAFB.

value: pear fruit harvested 115 DAFB with fruit bagging treatment

tag: organ

value: fruit skin


title: GNP H2Aubi119 ChIPseq replicate 1

value: cerebellum

value: Cerebellar granule neuron precursors


title: BA2


title: Healthy donor #1 naïve CD4 T cells, TCR-stimulated, 0.4mM Gln

description: Library name: JH016


title: IgG1162

description: Library name: Sample2


title: GNP Ring1 ChIPseq replicate 1


title: BA1


title: GNP input 3


title: CARD11 patient #628 naïve CD4 T cells, TCR-stimulated, 0.4mM Gln

description: Library name: JH015


title: GNP MIRAseq replicate 1


title: GNP input 2


title: CARD11 patient #651 naïve CD4 T cells, TCR-stimulated, 0.4mM Gln

description: Library name: JH014


title: CG2

value: pear fruit harvested 115 DAFB without treatment


title: brain_BL6_SD_act_11_15

description:
sequencing data from FACS-sorted T cell
24L012426

value: act


title: GNP H3K4me1 ChIPseq replicate 2


title: GNP H3K27ac ChIPseq replicate 2


title: GNP H3K4me1 ChIPseq replicate 1


title: CARD11 patient #650 naïve CD4 T cells, TCR-stimulated, 0.4mM Gln

description: Library name: JH013


title: GNP input 1


title: GNP H3K4me3 ChIPseq replicate 1


title: Healthy donor #3 naïve CD4 T cells, TCR-stimulated, 2mM Gln

description: Library name: JH012


title: MB RNAseq replicate 3

data_processing:
Adaptor prunning was done using trimmomatic, keeping only reads with > 28 BP for ChIPseq and > 92 BP for RNAseq.
For RNA-seq reads were aligned with Tophat.  GNP specific transcript models were generated by merging UCSC mm9 and Ensembl 67 mouse annotations to generate a large number of TSS.  The TSS were filtered using H3K4me3 ChIP and by overlap with models created from our data using Stringtie. Quantification was done using HTSEQ.
Assembly: mm9
Supplementary files format and content: _GNP_tss_model_uniq_filtered_counts.txt  RNAseq quantified using HTSEQ from a custom transcript model

extract_protocol:
GNPs and MB cells were purified using established percol fractionation protocol.   For RNAseq the cells were immediately lysed in Trizol.  Purified RNA was then DNase treated and cleaned up with an RNEasy column (Qiagen).  mRNA was purifid using NEBNext Poly A selection beads (NEB).
RNAseq libararies were prepared using Illumina TruSeq v2 library preperation kit (Illumina Inc).  Sequencing was performed using HiSeq 2500 (Illumina Inc).

value: Medulloblastoma cells

value: Ptch1 heterozygous


title: GNP H3K27me3 ChIPseq replicate 1


title: naïve mice, LHb, rep3

first: Liang

last: Yang

state: Zhejiang

address: 866 Yuhangtang Road

department: Medicine

description: Library name: N_3

library_source: transcriptomic single cell

data_processing:
The snRNA-seq libraries were checked for quality using the Agilent Bioanalyzer High Sensitivity chip.
Sequencing results were converted to FASTQ files using Illumina bcl2fastq software (version 5.0.1).
Raw data were demultiplexed, barcode and mapped to the goat reference genome using the Cell Ranger package (version 7.2.0).
Feature-barcode raw digital gene expression matrix (UMI counts per gene per cell) was filtered and normalized by using the R package Seurat  (Version 4.1.1).
Genes detected in fewer than one cell were filtered out, and cells were removed if they expressed fewer than 500 detected genes, UMI counts less than Inf, and the percent of mitochondrial-DNA derived gene-expression < 25%. The Doublet Finder package was also used to remove doublets.
Assembly: GRCm39
Supplementary files format and content: barcodes.tsv.gz
Supplementary files format and content: matrix.mtx.gz
Supplementary files format and content: features.tsv.gz

source_name: brain tissue

extract_protocol:
The LHb tissues were transferred to a Petri dish (Petri dish was placed on wet ice) pre-spiked with 1×PBS (without RNase and Ca, Mg ions) and washed with 1XPBS to remove blood stains, grease and other adherents from the tissue surface. The tissue was then cut into 0.5 mm2 pieces and washed again with 1×PBS. The washed pieces were added with dissociation solvent (0.35% collagenase IV5, 2 mg/ml papain, 120 Units/ml DNase I) and reacted for 20 min at 37°C in a water bath shaker (100 rpm). PBS (containing 10% fetal bovine serum) was used to terminate the dissociation. The cells were repeatedly puffed 5-10 times with a pipette gun (gentle handling to prevent cell death due to shear force). The cell suspension was filtered through a 70-30um cell sieve and subsequently centrifuged at 300g for 5 min at 4°C. After centrifugation, the cell sediment was collected and the cells were resuspended by adding 100ul of 1× PBS (0.04% BSA) solution. To remove erythrocytes, 1 ml of 1X erythrocyte lysis solution (MACS 130-094-183, 10×) was added and reacted at room temperature or on wet ice for 2-10 min. After lysis, the cells were centrifuged at 300g for 5 min at 4°C, and the cell precipitate was collected after centrifugation. Add 100μl of Dead Cell Removal MicroBeads (MACS 130-090-101), mix well and incubate for 15min at room temperature. At the end of incubation, Binding Buffer was added, after MS Columns (130-042-201) to remove reagents, and dead cells.Cell precipitates were collected by centrifugation at 300g for 5min at 4°C. Subsequently 1×PBS (0.04% BSA) was used to resuspend the cell precipitate and centrifuged at 4°C 300g for 5min (repeated twice). The candidate cells were obtained after tissue dissociation, lysis of erythrocytes and removal of dead cells, and 100 μl of 1×PBS (0.04% BSA) was added to form a cell suspension. The cell activity was detected by trypan blue staining method, and the cell activity was required to be >85%. The number of cells was counted using a hemocytometer or Countess II Automated Cell Counter, and the cell concentration was 700-1200 cells/μl.
The scRNA-seq libraries were constructed using the 10x Genomics 3' Reagent Kits v3.

value: brain tissue

tag: strain

value: naive


title: CG1


title: naïve mice, LHb, rep2

description: Library name: N_2


title: Healthy donor #1 naïve CD4 T cells, TCR-stimulated, 2mM Gln

description: Library name: JH010


title: GNP RNAseq P14 replicate 2

value: WT

tag: age


title: GNP RNAseq P14 replicate 3


title: Healthy donor #2 naïve CD4 T cells, TCR-stimulated, 2mM Gln

description: Library name: JH011


title: CG3


title: MB RNAseq replicate 2


title: MB RNAseq replicate 1


title: GNP RNAseq P7 replicate 1


title: GNP RNAseq P14 replicate 1


title: CARD11 patient #628 naïve CD4 T cells, TCR-stimulated, 2mM Gln

description: Library name: JH009


title: GNP RNAseq P7 replicate 3


title: GNP RNAseq P7 replicate 2


title: naïve mice, LHb, rep1

description: Library name: N_1


title: CRS mice, LHb, rep3

description: Library name: CRS_3

value: CRS


title: CARD11 patient #651 naïve CD4 T cells, TCR-stimulated, 2mM Gln

description: Library name: JH008


title: CRS mice, LHb, rep2

description: Library name: LC_14d_2


title: GNP RNAseq P1 replicate 2


title: GNP RNAseq P1 replicate 1


title: CARD11 patient #650 naïve CD4 T cells, TCR-stimulated, 2mM Gln

description: Library name: JH007


title: Healthy donor #3 naïve CD4 T cells, non-stimulated

description: Library name: JH006


title: GNP RNAseq E15.5 replicate 3


title: CRS mice, LHb, rep1

description: Library name: LC_14d_1


title: GNP RNAseq E15.5 replicate 2


title: CRS mice, LH, rep3

description: Library name: CL3

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Mus musculus reference genome(ftp://ftp.ensembl.org/pub/release-103/gtf/mus_musculus/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8).
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by edgeR software between two different group and two different samples. The genes/transcripts with the parameter of pvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: GRCm39
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.


title: GNP RNAseq E15.5 replicate 1


title: CRS mice, LH, rep2

description: Library name: CL2


title: Healthy donor #2 naïve CD4 T cells, non-stimulated

description: Library name: JH005


title: CARD11 patient #628 naïve CD4 T cells, non-stimulated

description: Library name: JH003


title: Reinduction, EZHi, H3K27me3, rep2

city: Oxford

first: Pawel

last: Mikulski

address: South Parks Road

department: Biochemistry

institute: University of Oxford

data_processing:
The raw reads (fastq) were downloaded from Basespace servers (Illumina) using basespace-cli and concatenated per sample using base unix. Read quality was assessed using Basespace (Illumina) and FastQC software.
The reads were mapped to hg38 genome with Bowtie2, adjusting trimming conditions dependent on the read quality.
SAM to BAM conversion, BAM sorting and indexing were performed with Samtools v1.1. Read duplicates were removed with Picard (MarkDuplicates command).
Sorted and duplicate-removed BAM files were subjected to read count, normalization (CPM) and conversion to bigwig format with Deeptools v2 (bamcoverage command).
Assembly: hg38
Supplementary files format and content: bigwig
Library strategy: Cut&Run-seq

source_name: Hela Kyoto

growth_protocol: The cells were grown in Dulbecco's Modified Eagle Medium (DMEM) containing high glucose and pyruvate (ThermoFisher, 41966-029) supplemented with 10% NCS (newborn calf serum, ThermoFisher, 16010-159) and 1% Penicillin–Streptomycin (ThermoFisher, 15140-122) at 37°C, 5% CO2.

extract_protocol:
Cut&Run-seq was performed using CUTANA v3 kit (Epicypher) according to the manufacturer’s protocol and with mild crosslinking (1 min incubation with 1% formaldehyde at room temperature).
Sequencing libraries were performed with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB) according to the published protocol (Nan Liu 2021. Library Prep for CUT&RUN with NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645). protocols.io https://dx.doi.org/10.17504/protocols.io.bagaibse). The samples were multiplexed with NEBNext Multiplex Oligos for Illumina (Index Primers Set 1 and 2) (NEB). Size selection steps were performed with Ampure XP beads (Beckman Coulter) and adjusted for nucleosomal DNA fragment size (150bp, excluding adapters).

treatment_protocol: The cells were primed with 50 ng/ml IFNγ (Merck) or left untreated for 24 h, followed by IFNγ washout with DPBS (ThermoFisher) and trypsinization by TrypLE (ThermoFisher) to harvest cells. Cells were cultured with fresh medium for another 48 h unless stated otherwise. Next, naïve and primed cells were induced by IFNγ for 24 h. After 24 h, cells were trypsinized and harvested, and the pellets were processed for subsequent experiments.

value: Hela Kyoto

value: Cervical cancer

tag: cut&run antibody

value: H3K27me3 (Cell Signaling Technology, #9733)


title: Reinduction, DMSO, H3K27me3, rep2


title: naïve mice, LH, rep3

description: Library name: NL3


title: Healthy donor #1 naïve CD4 T cells, non-stimulated

description: Library name: JH004


title: CARD11 patient #651 naïve CD4 T cells, non-stimulated

description: Library name: JH002


title: Priming, DMSO, H3K27me3, rep2


title: Reinduction, EZHi, H3K27me3, rep1


title: Priming, EZHi, H3K27me3, rep1


title: Reinduction, DMSO, H3K27me3, rep1


title: Priming, EZHi, H3K27me3, rep2


title: naïve mice, LH, rep2

description: Library name: NL2


title: CARD11 patient #650 naïve CD4 T cells, non-stimulated

description: Library name: JH001


title: Priming, DMSO, H3K27me3, rep1


title: Primed, GFPneg, H3K27me3, rep2


title: Primed, GFPneg, H3K27me3, rep3


title: Primed, GFPneg, H3K27me3, rep1


title: naïve mice, LH, rep1

description: Library name: NL1


title: GNP RNAseq P1 replicate 3


title: CRS mice, mPFC, rep3

description: Library name: CC3


title: Priming, GFPneg, H3K27me3, rep3


title: Priming, GFPneg, H3K27me3, rep2


title: CRS mice, mPFC, rep2

description: Library name: CC2


title: Priming, GFPneg, H3K27me3, rep1


title: Primed, GFPplus, H3K27me3, rep3


title: CRS mice, LH, rep1

description: Library name: CL1


title: Primed, GFPplus, H3K27me3, rep2


title: naïve mice, mPFC, rep3

description: Library name: NC3


title: Primed, GFPplus, H3K27me3, rep1