title: TDG_degron_dTAG_iN3_d7_AraC_S1_ENDseq

description: Library name: Sample 10

data_processing:
Raw reads were trimmed by Trimmomatic or Trim Galore!.
Trimmed reads were mapped to reference genome using bowtie with --best -n 3 -l 50 -k 1.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization
Bigwig files in Purkinje END-seq data were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM
Assembly: hg19, mm10
Supplementary files format and content: bw files include normliazed value for each sample

extract_protocol:
For S1/END-seq, to dissociate iPSC-derived iNs or mouse cortical neurons, cells were washed with PBS/5mM EDTA, treated with Trypsin/EDTA for 4 minutes, and neutralized with cold PBS/EDTA/10% FBS. After pelleting and resuspending in neutralization buffer, cells were processed for END-seq or S1-END-seq. For S1-END-seq, cells were embedded in agarose plugs, lysed with Proteinase K, treated with RNase A, and equilibrated in S1 nuclease buffer. S1 nuclease was added to the plugs, incubated on ice for 15 minutes, then at 37°C for 20 minutes before terminating the reaction with EDTA.
For S1/END-seq, plugs were processed through the standard END-seq protocol.

value: TDG-degron

value: dTAG13 and AraC for 8 hr


title: day0_iPSCs_CRISPRi_AX227_replicate2

status: Public on May 13 2025

type: SRA

city: Bethesda

first: Chuanyuan

last: Chen

state: MD

address: 9000 Rockville Pike, Building 37

department: National Cancer Institute

country: USA

institute: National Institutes of Health

description: Library name: Sample 2

library_source: genomic

data_processing:
sgRNA sequences were counted and normalized by MAGeCK (v 0.5.7) count subcommand. Beta score was calculated to select negatively/positively regulated genes by MAGeCK-MLE subcommand.
Assembly: hg19
Supplementary files format and content: xlsx file from CRISPRi_Screen includes beta score
Library strategy: CRISPR Screen

molecule: genomic DNA

organism: Homo sapiens

source_name: iPSCs

growth_protocol: Human iPSC lines (WTC11) were cultured on Matrigel-coated dishes in Essential 8 Medium (E8) supplemented with 10 μM ROCK inhibitor at 37°C and 5% CO2. The medium was replaced every 1–2 days, and cells were passaged using Accutase and replated in E8 with ROCK inhibitor to promote survival, with the inhibitor removed once colonies formed. For iPSC-derived i3Neuron differentiation, NGN2-expressing iPSCs were plated in N2 medium with doxycycline and ROCK inhibitor. After two days, the cells were replated onto poly-L-ornithine-coated plates and cultured in iN Culture Media, including BrainPhys media, BDNF, NT-3, laminin, and doxycycline. The media was changed twice a week from day 6 onwards. For primary cortical neurons, cortices were dissected from E16.5 mouse embryos, digested with Papain and DNase I, and triturated in Neurobasal complete medium. The cells were then filtered, seeded on poly-d-lysine and laminin-coated plates, and aphidicolin was added to eliminate dividing cells.

extract_protocol:
For CRISPRi-screen, genomic DNA was extracted from transduced iPSCs using the DNeasy Blood & Tissue Kit (QIAGEN). The extracted DNA was then amplified by PCR to enrich target fragments for sequencing.
For CRISPRi-screen, the PCR reaction included 10 μg of DNA, 1 μM of each forward and reverse primer containing Illumina sequencing indices, and 1× KAPA HiFi HotStart Ready Mix (Roche). The amplification process involved an initial 3-minute denaturation at 95°C, followed by 20 cycles of 30 seconds at 95°C, 30 seconds at 55°C, and 30 seconds at 72°C, concluding with a final 5-minute extension at 72°C. The amplified DNA was purified using AMPure XP beads (Beckman Coulter) with a 2× size selection, and the quality was assessed using the Agilent High Sensitivity D5000 ScreenTape System.

tag: cell line

value: iPSCs

tag: cell type

tag: genotype

value: WT transduced with CRISPRi sgRNA library AX227

tag: treatment

value: sgRNA library AX227 transduction


title: day3_iNs_CRISPRi_AX227_replicate2

description: Library name: Sample 5

source_name: iPSC-derived i3Neurons

value: iPSC-derived i3Neurons

value: Neurons


title: 30_abH3K36me3_empty_Rep2

city: Mainz

first: Frank

last: Rühle

address: Ackermannweg 4

department: Bioinformatics Core Facility

country: Germany

institute: Institute of Molecular Biology (IMB)

description:
Library name: Sample 6
abH3K36me3_empty_Rep2

data_processing:
Raw reads were mapped to the ensembl AgamP4 genome with bowtie2 (v2.3.4)
Multimapping reads and PCR duplicates were removed with Picard (v2.2) and Samtools (v1.9).
Coverage signal tracks (bigWigs) of alignments were generated using DeepTools (v3.1)
Assembly: AgamP4
Supplementary files format and content: bigWig files, containing CPM normalized coverage signals of primary alignments.

organism: Anopheles gambiae

growth_protocol: Ag55 cells were cultured in Leibovitz L15 media with 10% FBS (Gibco, 10270-10,6 Lot: 2260092) and 1x penicillin-streptomycin (Gibco, 15140122) at 27°C at 80% humidity.

extract_protocol:
The cells were detached, washed in DPBS and counted. Next, 50 mln cells were resuspended in 1 ml PBS with 1.8% formaldehyde and incubated for 12 min at room temperature with occasional mixing by inversion. After 12 min, glycine was added to a final concentration of 0.25 M to stop the fixation. The cells were pelleted (3000 rpm) and washed twice: once with PBS and 0.25M glycine, once with PBS only. Cell pellets were then flash frozen before further processing.
Cell pellets were resuspended in 0.6 mL of Farnham buffer (10 mM Tris (pH 8), 85 mM KCl, 0.5% IGEPAL-CA630 with a protease inhibitor cocktail and transferred to a 1 mL AFA Fibre Covaris Tube. Nuclei were isolated in Covaris S200 with the following settings: Duty Cycle/Factor 2%, 200 Bursts, 75 Watt, 6°C for a total of 14.5 min. Pellets were centrifuged at 2000g for 2 min and resuspended in 500 µl of Chromatin Shearing Buffer (10 mM Tris (pH 8), 0.2% SDS, 1 mM EDTA, 50 mM NaCl). Chromatin was sheared with Covaris S200 using the following settings: Duty Factor/Cycle 20%, 200 Bursts, 150 Watt in 1 ml AFA Fibre tube in 0.5 ml of buffer for a total of 27 minutes.
10 µl of the sheared chromatin was taken as input for later processing. Samples were flash frozen. Upon thawing, chromatin was centrifuged at full speed for 5 min in 4°C. the supernatant was diluted to 20 µg of chromatin in final buffer with 0.05% SDS, 125 mM NaCl, 10 mM Tris (pH 8), 1 mM EDTA. Next, the material was incubated with 1 µl of respective histone modification antibody overnight (H3K27ac: Abcam, ab4729, lot: GR243994-1; H3K36me3: Abcam, ab9050 , lot: GR20245-2). The bound antibody-protein-DNA complexes were captured using Protein G dynabeads (1 h at 4 °C) followed by 3 washes in RIPA (25 mM HEPES pH 7.6, 150 mM NaCl, 1 mM EDTA, 1% Triton-X 100, 0.1% SDS, 0.1% DOC and protease inhibitors), 1 wash in LiCl buffer (250 mM LiCl, 10 mM Tris-HCl, 1 mM EDTA, 0.5% NP-40 and 0.5% DOC) and 2 washes in TE buffer. The immunoprecipitated DNA was decrosslinked by an overnight incubation at 65°C with shaking. Next day, samples were incubated with 1 µl of Rnase A for 30 min at 37°C and then with 2.5 µl of 20% SDS and 1 µl of Proteinase K for 1h at 65°C. DNA was extracted using magnetic beads.
ChIP-seq libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit with standard protocols and 12 PCR cycles. Libraries were cleaned up using 1.8 volume and pooled in equimolar ratios aiming at 10 Mio reads per library. The pool was sequenced on a NextSeq 500 (high output, 150 cycles) flow cell, paired end for 2x79 cycles plus 8 cycles for the single index read.

treatment_protocol: 50 Mio Ag55 cells were seeded in a 15-cm dish. After 16 hours, 9 ml of an empty baculovirus in Sf-900 media was added to the cells. Cells were collected for further processing 48h later.

tag: antibody

tag: ectopic expression

value: HA-tagged empty control


title: 29_abH3K36me3_empty_Rep1

description:
Library name: Sample 5
abH3K36me3_empty_Rep1


title: TDG_degron_iN3_d7_AraC_S1_ENDseq

description: Library name: Sample 9

value: AraC for 8 hr


title: day3_iNs_CRISPRi_AX227_replicate3

description: Library name: Sample 6


title: 23_abH3K27ac_empty_Rep1

description:
Library name: Sample 3
abH3K27ac_empty_Rep1


title: 06_input_empty_Rep2

description:
Library name: Sample 2
input_empty_Rep2


title: BMDC, WT, Control, rep1

status: Public on May 14 2025

city: Ann Arbor

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

institute: University of Michigan

description: Library name: 2_ZJJ_WT

library_source: transcriptomic

data_processing:
Reads were mapped to the reference genome GRCm39 using HISAT.
Reads were mapped to reference genes using Bowtie2
Assembly: GCF_000001635.27_GRCm39
Supplementary files format and content: Tab-delimited text file contains FPKM, TPM, and raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: BMDC

extract_protocol:
RNA was isolated using the miRNeasy Micro Kit (Qiagen, 1071023)
RNA libraries were prepared by BGI genomics for their DNBSEQ platform for PE150 RNA resequencing

value: BMDC

value: WT

value: Control


title: 05_input_empty_Rep1

description:
Library name: Sample 1
input_empty_Rep1


title: 24_abH3K27ac_empty_Rep2

description:
Library name: Sample 4
abH3K27ac_empty_Rep2


title: Sorted Thy1.1- (Areg-non-producing) Lung Treg cells, Exp1_Control/IAV-5dpi/Bleo-12dpi, scRNA-seq, GEXrun1

city: New York

first: Nicholas

last: Arpaia

state: NY

department: Microbiology & Immunology

institute: Columbia University

library_source: transcriptomic single cell

data_processing:
Cell Ranger v5.0.0
Assembly: GRCh38
Supplementary files format and content: Processed RDS object for Experiment 1 (2021); full TCR sequences and V(D)J usage information is included in metadata within RDS file
Supplementary files format and content: Processed RDS object for Experiment 2 (2022); full TCR sequences and V(D)J usage information is included in metadata within RDS file

source_name: lung

extract_protocol:
10X Genomics Chromium Platform
10X Genomics Chromium Single Cell 5’ V(D)J with Feature Barcoding Reagent Kits (CG000186)

treatment_protocol: Thy1.1- (Areg non-producing) and Thy1.1+ (Areg-producing) lung Treg cells were sorted and prepared for single cell RNA-seq

tag: tissue

value: lung

value: Treg cells

value: C57BL/6 male; Foxp3GFPAregThy1.1/Thy1.1

value: Control/Influenza A Virus/Bleomycin


title: D7_cortical_AraC_RNA_seq_rep3

description: Library name: Sample 45

data_processing:
Raw reads were trimmed by Trim Galore!.
Trimmed reads were mapped to reference genome using STAR.
Bigwig files were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM
Assembly: hg19, mm10
Supplementary files format and content: bw files include normliazed value
Supplementary files format and content: csv files include raw count expression matrix

source_name: Embryonic cerebral cortex

extract_protocol:
For RNA-seq, total RNA was extracted from cells using TRIzol reagent (Thermo Fisher, 15596018) following the manufacturer’s instructions.
For RNA-seq, libraries were prepared using the NEBNext® Ultra II Directional RNA Library Prep Kit for Illumina (NEB; cat. No. E7760).

value: Embryonic cerebral cortex

value: AraC for 16hr


title: D7_cortical_AraC_RNA_seq_rep2

description: Library name: Sample 44


title: day9_iNs_AraC_CRISPRi_AX227_replicate3

description: Library name: Sample 12

value: sgRNA library AX227 transduction and AraC treatment for 3 days


title: iNeuron_d7_AraA_RNA-seq

description: Library name: Sample 39

value: AraA overnight


title: iNeuron_d7_AraC_RNA-seq

description: Library name: Sample 38

value: AraC overnight


title: D7_cortical_NT_RNA_seq_rep2

description: Library name: Sample 41


title: day0_iPSCs_CRISPRi_AX227_replicate3

description: Library name: Sample 3

value: iPSCs

value: WT transduced with CRISPRi sgRNA library AX227

value: sgRNA library AX227 transduction


title: D7_cortical_NT_RNA_seq_rep1

description: Library name: Sample 40

value: Neurons


title: WB_AraC_gH2AX_pos_571_RNA_seq_replicate2

description: Library name: Sample 26

source_name: Whole brain without cerebellum

value: Whole brain without cerebellum

value: One cycle of AraC


title: WB_AraC_gH2AX_pos_570_RNA_seq_replicate1

description: Library name: Sample 25

value: WT


title: Golgi_AraC_574_RNA_seq_replicate6

description: Library name: Sample 24

source_name: Cerebellum

value: Cerebellum


title: Golgi_AraC_570_RNA_seq_replicate2

description: Library name: Sample 20


title: Golgi_AraC_573_RNA_seq_replicate5

description: Library name: Sample 23


title: WB_AraC_gH2AX_pos_574_RNA_seq_replicate3

description: Library name: Sample 27


title: Golgi_AraC_571_RNA_seq_replicate3

description: Library name: Sample 21


title: Golgi_AraC_569_RNA_seq_replicate1

description: Library name: Sample 19


title: Golgi_PBS_563_RNA_seq_replicate1

description: Library name: Sample 13

value: One cycle of PBS


title: Golgi_PBS_564_RNA_seq_replicate2

description: Library name: Sample 14


title: Golgi_PBS_567_RNA_seq_replicate5

description: Library name: Sample 17


title: Golgi_PBS_568_RNA_seq_replicate6

description: Library name: Sample 18


title: Golgi_PBS_565_RNA_seq_replicate3

description: Library name: Sample 15


title: Purkinje_AraC_573_batch2_RNA_seq_replicate5

description: Library name: Sample 11


title: Purkinje_AraC_572_batch2_RNA_seq_replicate4

description: Library name: Sample 10


title: D7_cortical_AraC_RNA_seq_rep1

description: Library name: Sample 43


title: Purkinje_AraC_571_batch1_RNA_seq_replicate3

description: Library name: Sample 6


title: Purkinje_PBS_567_batch2_RNA_seq_replicate5

description: Library name: Sample 8


title: Purkinje_PBS_566_batch2_RNA_seq_replicate4

description: Library name: Sample 7


title: Purkinje_AraC_569_batch1_RNA_seq_replicate1

description: Library name: Sample 4


title: Purkinje_PBS_564_batch1_RNA_seq_replicate2

description: Library name: Sample 2


title: D7_cortical_NT_RNA_seq_rep3

description: Library name: Sample 42


title: Purkinje_AraC_570_batch1_RNA_seq_replicate2

description: Library name: Sample 5


title: Purkinje_PBS_565_batch1_RNA_seq_replicate3

description: Library name: Sample 3


title: Golgi_NT_H3K27ac_CUT&RUN

description: Library name: Sample 2

data_processing:
Raw reads were trimmed by Trim Galore!.
Trimmed reads were mapped to mouse genome (mm10) using bowtie2 with -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Bigwig files were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM
Assembly: mm10
Supplementary files format and content: bw files include normliazed value for each sample
Library strategy: CUT&Run

extract_protocol:
For CUT&RUN, Purkinje or Golgi nuclei were washed a total of two times with wash buffer (20 mM HEPES–KOH (pH 7.5), 150 mM NaCl, 0.5 mM spermidine, Roche complete Protease Inhibitor tablet EDTA-free) and bound to activated Concanavalin A beads (Polysciences) for 10 min at room temperature. Cell permeabilization was done in 200 μl of digitonin buffer (0.05% digitonin and 0.1% BSA in wash buffer) followed by incubation with 1 μg of the antibody against H3K27ac (Abcam, ab4729) overnight at 4°C. After antibody incubation, cells were washed with digitonin buffer, followed by incubation with purified hybrid protein A-protein G-micrococcal nuclease (pAG-MNase) at 4°C for 1 hour. Samples were washed again in digitonin buffer, resuspended in 150 μl digitonin buffer, and equilibrated to 0°C on ice water for 5 minutes. To start with MNase cleavage, 3 μl of 100 mM CaCl2 was added to cells, and after 1 hour of digestion, reactions were stopped with the addition of 150 μl 2× stop buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.02% digitonin, 50 μg/ml RNase A, and 50 μg/ml glycogen). Samples were incubated at 37°C for 10 minutes to release DNA fragments and centrifuged at 16,000g for 5 minutes. Supernatants were collected, and a mix of 1.5 μl (20%) SDS/2.25 μl (20 mg/ml) proteinase K was added to each sample, followed by incubation at 65°C for 35 minutes. DNA was precipitated with ethanol and sodium acetate, pelleted by centrifugation at 4°C, washed, air-dried, and resuspended in 18 μl 0.1× TE.
For CUT&RUN, the library was prepared by using the standard ChIP-seq protocol.

value: NT


title: Golgi_AraC_572_RNA_seq_replicate4

description: Library name: Sample 22


title: Purkinje_PBS_563_batch1_RNA_seq_replicate1

description: Library name: Sample 1


title: WT_Purkinje_gDNA_ITPR1_5loci_PS-seq

description: Library name: Sample 5

data_processing:
Paired-end raw reads were mapped to reference genome using BSMAP with -w 2 -v 0 -q 30.
Assembly: hg19, mm10
Supplementary files format and content: bw files include normliazed value for each sample

extract_protocol:
For pyridine borane-sequencing, genomic DNA was extracted from day 7 iNs or sorted Purkinje nuclei using DNeasy® Blood & Tissue (QIAGEN; cat. No. 69504) following the manufacturer’s instructions.
For pyridine borane-sequencing, 200 ng genomic DNA was used in a 50 μl reaction containing 600 mM sodium acetate solution (3M, pH = 4.5) (Quality Biological, cat. No. 351-309-101) and 1 M pyridine borane (Alfa Aesar, cat. No. L13178-09), and incubated for 16 hours at 37°C in an Eppendorf ThermoMixer shaking at 850 rpm. The product was purified by the QIAquick Nucleotide Removal Kit (QIAGEN, cat. No. 28306). The primers targeting the desired neuronal enhancer regions containing CpG sites were designed and the PCR amplicons were generated using the PyroMark PCR kit (QIAGEN, cat. No. 978703).


title: TDG_PCP2Cre_positive_Purkinje_gDNA_ITPR1_5loci_PS-seq

description: Library name: Sample 7

value: Pcp2-Cre TDG fl/fl


title: Purkinje_NT_H3K27ac_CUT&RUN

description: Library name: Sample 1


title: WT_Purkinje_gDNA_Grid2_6loci_PS-seq

description: Library name: Sample 6


title: Purkinje_AraC_574_batch2_RNA_seq_replicate6

description: Library name: Sample 12


title: Purkinje_PBS_END_seq

description: Library name: Sample 3


title: TDG_PCP2Cre_positive_Purkinje_gDNA_Grid2_6loci_PS-seq

description: Library name: Sample 8


title: Golgi_PBS_566_RNA_seq_replicate4

description: Library name: Sample 16


title: Purkinje_second20mice_AraC_END_seq_replicate2

description: Library name: Sample 2


title: Purkinje_PBS_568_batch2_RNA_seq_replicate6

description: Library name: Sample 9


title: Purkinje_first20mice_AraC_END_seq_replicate1

description: Library name: Sample 1


title: day7_WT_Ms_cortical_neurons_AraC_ENDseq

description: Library name: Sample 12

value: AraC for 18hr


title: FACS_sorted_Ms_Purkinje_neurons_NT_41_ATAC_seq

description: Library name: Sample 2

data_processing:
Raw reads were trimmed by Trim Galore!.
Trimmed reads were mapped to mouse genome (mm10) using bowtie2 with -N 1 -L 25 -X 2000 --no-mixed --no-discordant.
Bigwig files were generated with bacmCoverage function from deepTools with -bs=1 -normalizeUsing BPM
Assembly: mm10
Supplementary files format and content: bw files include normliazed value for each sample

extract_protocol:
For ATAC-seq, the nuclei pellet was resuspended in 190μl transposition reaction mix (10mM Tris-HCl pH 7.5, 5mM MgCl2, 10% Dimethylformamide) by pipetting up/down 10 times. 10μl of pre-assembled Tn5 transposome with ATAC adapters was added. Tubes were gently agitated to mix all components and incubated at 37°C for 30 minutes at 1200 rpm in an Eppendorf Thermomixer. ATAC reactions were terminated by adding 1mL Zymo DNA binding buffer and vortexed. Reactions were purified according to the manufacturer’s instructions using the DNA Clean and Concentrator-5 kit (ZYMO RESEARCH, cat. No. D4004) and eluted in 15μl nuclease-free water.
For ATAC-seq, eluted ATAC DNA was gap repaired, purified by the DNA Clean and Concentrator-5 kit, and eluted in 25μl nuclease-free water. Eluted ATAC DNA was amplified and barcoded in 50μl PCR reactions (25μl 2x Kapa HiFi HotStart Ready Mix, 22μl eluted ATAC DNA, 1.5μl 10μM i5 index primer, 1.5μl 10μM i7 index primer) with the following PCR thermocycler program: 98°C 45 s; 10 cycles of 98°C 15 s, 62°C 30 s, 72°C 30 s; final extension 72°C 2 min; hold at 4°C. PCR reactions were cleaned by AMPure XP beads.


title: FACS_sorted_Ms_Purkinje_neurons_AraC_839_ATAC_seq

description: Library name: Sample 4

value: AraC for 5 days


title: FACS_sorted_Ms_Purkinje_neurons_NT_40_ATAC_seq

description: Library name: Sample 1


title: DpnII Hi-C on asynchronous C2C12 cells R2

city: München

first: Marlies

middle: E

last: Oomen

address: Feodor-Lynen-Strasse 21

department: Institute of Epigenetics and Stem Cells

institute: Helmholtz Zentrum München

description: Library name: MOHiC-C2C12-NS-R2T1

data_processing:
Sequence data was mapped to mm10 or hg38 and processed using the publicly available distiller-nf pipeline and cooltools
For more information see methods section of associated publication
Assembly: mm10 and hg38
Supplementary files format and content: multitire cooler files '.mcool' of all interactions

source_name: Myoblast

growth_protocol: For culture conditions see methods of associated publication

extract_protocol:
Cells were fixed with 1% formaldehyde and stored at -80C until optional FACS sorting and further processing according to Hi-C protocol
DpnII Hi-C2.0 protocol as published by Belaghzal et al 2017 Methods

treatment_protocol: Mitotic cells for mESC and C2C12 were obtained using 50ng/mL Nocodazole (6hr and 8hr respectively) followed by a gentle shake off. HeLa cells were synchronized in G2 for 24 hours in 9uM RO-3306, followed by a wash and release into nocodazole (100ng/mL) for 2, 4, and 8hrs. Floating cells were collected. Both HeLa and C2C12 mitotic cells were sorted by FACS

value: Myoblast

value: Myoblasts

value: Untreated

tag: batch

value: paired-end


title: DpnII Hi-C on mitotic synchronized and sorted C2C12 cells R2

description: Library name: MOHiC-C2C12-MC-R2T1

value: 8hr Nocodazole


title: day7_WT_Ms_cortical_neurons_NT_ENDseq

description: Library name: Sample 11

value: Embryonic cerebral cortex


title: DpnII Hi-C on mitotic synchronized and sorted C2C12 cells R1

description: Library name: MOHiC-C2C12-MC-R1T1


title: WT_day7_iNs_RNA_seq_replicate2

description: Library name: Sample 49

value: iPSC-derived i3Neurons


title: WT_day17_iNs_RNA_seq_replicate1

description: Library name: Sample 50

value: Neurons


title: WT_day17_iNs_RNA_seq_replicate2

description: Library name: Sample 51


title: WT_day7_iNs_RNA_seq_replicate1

description: Library name: Sample 48


title: iN_day7_WT_SAR_seq

description: Library name: Sample 1

data_processing:
Reads were mapped to reference genome using bowtie with -n 2 -l 50 -m 1.
BedGraph files were generated by bedtools genomecov, normalized by reads per million (RPM) and then converted to bigWig files using bedGraphToBigWig from UCSC pre-compiled utilities for visualization
Assembly: hg19
Supplementary files format and content: bw files include normliazed value

extract_protocol:
For SAR-seq, day7 iNs were incubated with 20 μM EdU for 18 hr. Cells were harvested and washed with PBS and incubated with accutase for 5-10 minutes. Cells were then collected using a cell scrapper (Corning), pelleted at 200xg for 5 minutes and resuspended in cold 0.1% BSA in PBS. Cold methanol was then added dropwise into all samples during slow vortexing to 80% final concentration. Cells were permeabilized on ice for 10 min and resuspended in 1 mL of Click-iT reaction solution for 2 hrs shaking at room temperature. Cells were then lysed with Proteinase K overnight at 37C. DNA was extracted with UltraPure Phenol:Chloroform:Isoamyl Alcohol (25:24:1, v/v) (Invitrogen) according to manufacturer’s instructions
For SAR-seq, DNA was sonicated to 150-200 bp fragments using a Covaris S220 sonicator. Biotin-EdU labeled DNA fragments were pulled down using MyOne Streptavidin C1 Beads (ThermoFisher, cat. No. 650-01) and incubated at 24C shaking in a ThermoMixer C at 800 rpm for 30 min. Dynabeads were washed 3x in W&B (10 mM Tris-HCl pH 7.5, 1 mM EDTA, 1 M NaCl, 0.1% Tween (freshly added)), 2x in EB (10 mM Tris-HCl pH 8.0), and 1x T4 DNA Ligase Buffer (NEB). Dynabeads were resuspended in end-repair reaction and incubated at 24C shaking at 800 rpm for 30 min. Dynabeads were washed 1x in 1X W&B, 2x EB, and 1x NEBuffer 2 (NEB) and resuspended in A-tailing reaction mix (NEB), followed by incubation at 37C shaking at 800 rpm for 30 min. Dynabeads were washed 1x in NEBuffer 2 and resuspended in ligation reaction mix (NEB), 5 nM annealed TruSeq truncated adapter and incubated at 25C shaking at 600 rpm for 20 min. Ligation reaction was stopped by adding 50 mM EDTA, and Dynabeads were washed 3x in 1X W&B, 3x EB. PCR amplified for 16 cycles with Kapa HiFI HotStart Ready Mix using TruSeq index adapters. PCR products were separated from DynaBeads and cleaned using AMPure Beads XP.


title: WT_iPSCs_RNA_seq_replicate1

description: Library name: Sample 46


title: iNeuron_d7_Gem40uM_Replicate3_RNA-seq

description: Library name: Sample 35

value: Gemcitabine overnight


title: iNeuron_d7_NT_Replicate1_RNA-seq

description: Library name: Sample 28


title: WT_iPSCs_RNA_seq_replicate2

description: Library name: Sample 47


title: iNeuron_d7_Gem40uM_Replicate2_RNA-seq

description: Library name: Sample 32


title: d7_iNs_dTAG_loci_1and2_PS-seq

description: Library name: Sample 3

value: TDG-degron

value: dTAG13 for 24 hr


title: iNeuron_d7_Gem80uM_Replicate2_RNA-seq

description: Library name: Sample 33

value: WT


title: d7_iNs_dTAG_loci_4and5_PS-seq

description: Library name: Sample 4


title: d7_iNs_NT_loci_1and2_PS-seq

description: Library name: Sample 1


title: iNeuron_d7_Gem40uM_Replicate1_RNA-seq

description: Library name: Sample 29


title: d7_iNs_NT_loci_4and5_PS-seq

description: Library name: Sample 2


title: iNeuron_d7_NT_Replicate3_RNA-seq

description: Library name: Sample 34


title: iNeuron_d7_Gem80uM_Replicate1_RNA-seq

description: Library name: Sample 30


title: iNeuron_d7_NT_Replicate2_RNA-seq

description: Library name: Sample 31


title: TDG_degron_dTAG_iN3_d7_Gemcitabine_S1_ENDseq

description: Library name: Sample 19

value: Gemcitabine for 18 hr


title: FACS_sorted_Ms_Purkinje_neurons_AraC_597_ATAC_seq

description: Library name: Sample 3

value: Cerebellum


title: TDG_degron_WT_iN3_d7_Gemcitabine_S1_ENDseq

description: Library name: Sample 18


title: day7_sgXRCC1_iNs_Gemcitabine_END_seq

description: Library name: Sample 17

value: XRCC1 knockdown


title: WT_day7_iNs_Gemcitabine_S1_ENDseq

description: Library name: Sample 15


title: iNeuron_d7_Gem80uM_Replicate3_RNA-seq

description: Library name: Sample 36


title: day7_WT_iNs_DMOG_AraC_ENDseq

description: Library name: Sample 14

value: DMOG for 19 hr, AraC for 18hr


title: day7_TDG_degron_iNs_AraC_ENDseq

description: Library name: Sample 7

value: AraC for 18 hr


title: day7_WT_iNs_AraC_ENDseq_control_for_DMOG

description: Library name: Sample 13

value: AraC for 18hr


title: WT_day8_iNs_B2M_VLP_AraC_ENDseq

description: Library name: Sample 6

value: B2M-VLP for 2 days, AraC fo 18 hr


title: day7_TDG_degron_iNs_dTAG13_AraC_ENDseq

description: Library name: Sample 8

value: dTAG13 for 20 hr, AraC for 18 hr


title: WT_day7_iNs_AraC_ENDseq

description: Library name: Sample 5


title: DpnII Hi-C on G2 synchronized HeLa cells released for 4hr in Nocodazole

description: Library name: MOHiC-HeLa-4hr-Noco-R1T1

source_name: Adenocarcinoma cells

value: Adenocarcinoma cells

value: HeLa

value: 4hr Nocodazole

value: paired-end


title: WT_day7_iNs_AraC_S1_ENDseq

description: Library name: Sample 4

value: iPSC-derived i3Neurons

value: Neurons


title: DpnII Hi-C on G2 synchronized HeLa cells released for 8hr in Nocodazole

description: Library name: MOHiC-HeLa-8hr-Noco-R1T1

value: 8hr Nocodazole


title: DpnII Hi-C on G2 synchronized HeLa cells released for 2hr in Nocodazole

description: Library name: MOHiC-HeLa-2hr-Noco-R1T1

value: 2hr Nocodazole


title: 4C_HS40_aWT_B4

city: Cambridge

first: Larry

last: Melidis

state: Not US or Canada

address: Robinson Way

department: CRUK-CI

country: United Kingdom

institute: University of Cambridge

data_processing:
library strategy: 4C
CUT&Tag and CUTAC read mapping and processing
Libraries were demultiplexed using demuxFQ (flags: -c -d -i -e -t 1 -r 0.01 -R -l 9). FASTQC- version 0.11.8 was used to assess the read quality and bases with a quality score below 20 were trimmed from both reads using cutadapt (cutadapt -q 20). For CUTAC libraries, reads greater than 120bp in length were removed alignment.  Reads were aligned to the hg38 reference genome using bwa mem with default parameters. Sorted bam files with duplicates removed were generated with SAMtools (version 1.15.1), and converted to bigwig using deepTools bamCoverage (parameters: --normalizeUsing CPM, --binSize 10, 5 or 3 with 12nt smoothing function). Statistical comparisons between WT and mutants were performed by two-sided t-test, using cpm signal summed over 1kb regions. Sample size for CUT&Tag;
4C-seq data was analysed using the pipe4C pipeline (https://github.com/deLaatLab/pipe4C) in R (version 4.3.0) Read 1 sequencing reads were used as input for the pipe4C pipeline and all reads mapped to the viewpoint chromosome were scaled to 1 million reads. An average running mean window size was set at 21 fragment ends. 4C plots were generated using peakC74 (https://github.com/deWitLab/peakC) where two biological replicates were used as input into the peakC program and subsequently plotted with ggplot2 in R. Biological replicates were processed on the same day and sequenced on the same flow cell. Samples for comparison were sequenced together in a single run.
Assembly: hg38
Supplementary files format and content: bigWig, counts

source_name: myelogenous leukemia

growth_protocol: K562 cells were cultured in RPMI1640 (Glutamine plus, Life Technologies) with 10% of fetal bovine serum (Life Technologies) at 37°C with 5% CO2. Cell cultures were routinely checked for mycoplasma infection.

extract_protocol:
First round PCR for specific enhancer sites was performed in four (for HS2 and HS3 viewpoints) or ten (for HS-40 viewpoint) parallel reactions per enhancer site using 25 uL NEBNext High-Fidelity 2X PCR Master Mix (M0541 New England Biolabs), 2 uL 10 mM 4C forward primer, 2 uL 10 mM 4C reverse primer and 200 ng of 4C template in total 50 uL volume, under the following conditions; 72 ºC for 3 min, 98 ºC for 1 min followed by 16 cycles of 98 ºC for 10 sec, primer specific Ta for 30 sec, 72 ºC for 1 min and final extension at 72 ºC for 2 min. Four reactions were pooled and purified with 1.3X Ampure XP Beads (A63882, Beckman Coulter Life Sciences) and eluted in 100 uL 10 mM Tris-HCl pH 8.0. For addition of Illumina adaptor sequences and dual indexes to amplified 4C template, DNA from round 1 PCR was divided in four 21 uL volumes to which 25 uL NEBNext High-Fidelity 2X PCR Master Mix, 2 uL 10mM forward adaptor primer, 2 uL 10mM reverse adaptor primer was added to each reaction and amplified under conditions; 98 ºC for 30 sec, followed by 12 cycles of 98 ºC for 10 sec, 63 ºC for 10 sec, 72 ºC for 30 sec and final extension at 72 ºC for 2 min. Reactions were pooled and purified with 1.3X Ampure XP Beads. Library size distribution was analysed on a Tapestation 2200 (Agilent Technologies) and library concentrations were quantified by NEBNext Library Quant Kit for Illumina (E7630, New England BioLabs). 4C libraries were multiplexed for next-generation sequencing on the NextSeq 500 or 2000 platform (single-end 76bp). Biological replicates were performed together and sequenced together in a single run.
30 million cells per sample were crosslinked in 2% formaldehyde for 10 min at room temperature and quenched with 0.125 M glycine for 5 min. Cells were washed once in 50 mL of ice-cold PBS and centrifuged at 1500 rpm for 10 min at 4 ºC. Nuclei were extracted by incubation in 50 mL cell lysis buffer (10 mM Tris-HCl pH 8, 10 mM NaCl, 0.2% IGEPAL CA-630 (18896, Sigma-Aldrich), one tablet protease inhibitor (11873580001, Roche cOmplete, EDTA-free) for 30 min on ice and centrifuged at 1800 rpm for 5 min at 4 ºC. Nuclei were overlayed once with 500 uL of 1.25X NEBuffer r3.1 (B6003S, New England Biolabs), buffer was removed, pellet was resuspended in 1 uL of 1.25X NEBuffer r3.1, and aliquoted in 250 uL volumes. To each aliquot 108 uL of 1.25X NEBuffer r3.1 was added followed by 11 uL of 10% SDS (V6551, Promega) and incubated at 37 ºC for 1 hr in a thermomshaker (Eppendorf) at 950 rpm. 75 uL of 10% Triton X-100 (93443, Sigma-Aldrich) was added to each tube and incubated for 1 hr at 37 ºC at 950 rpm. 500 U of DpnII (R0543M, New England Biolabs) was added to each tube and incubated overnight at 37 ºC. After centrifugation at 2500 rpm at 4 ºC for 5 min, the pellet was resuspended in 950 uL of 1X ligation buffer (15224-025, Invitrogen), 50 uL of 1U/uL T4 DNA ligase (15224-025, Invitrogen) was added and incubated at 16 ºC for 4 hr, without shaking. Crosslinks were removed by addition of 60 uL 10 mg/mL Proteinase K (03115879001, Roche) and incubating overnight at 65 ºC with shaking at 800 rpm. Another 60 uL 10 mg/mL Proteinase K was adding the following day and incubated at 65 ºC at 800 rpm for 2 hr. 10 uL of 10 mg/mL Rnase A (10109142001, Roche) was then added followed by incubation at 37 ºC at 800 rpm for 1 hr. Reaction volumes were pooled and DNA was purified by phenol:chloroform extraction; equal volume of phenol pH 8.0 (P4557, Sigma-Aldrich) was added, vortexed for 1 min and centrifuged at 3500 rpm for 10 min at room temperature. Aqueous phase was transferred to a new tube and extraction repeated as above with equal volume of phenol:chloroform pH 8.0 (P3803, Sigma-Aldrich). DNA was precipitated in 1/10 volume 3M sodium acetate over 34 mL of ethanol overnight at -20 ºC. Precipitated DNA was centrifuged at 3900 rpm at 4 ºC for 30 min and resuspended in 400 uL of 1X TE buffer. DNA was purified again with an equal volume of phenol:chloroform as above, this was repeated twice in total and DNA was precipitated in 0.1X volume of 3M sodium acetate over 1 mL of ethanol overnight at -20 ºC. Precipitated DNA was centrifuged at 14000 rpm at 4 ºC for 30 min, washed three times with 1 mL of 70% ethanol and resuspended in 25 uL of 1X TE buffer. For the second restriction enzyme digestion, DNA was incubated with 500 U of DdeI (R0175L, New England Biolabs) in 1X NEBuffer r3.1 in 500 uL total volume overnight at 37 ºC at 500 rpm. Enzyme was heat inactivated by incubating for 20 min at 65 ºC. Ligation reaction was performed in 1X ligation buffer and 50 U 1U/mL T4 DNA ligase in total volume of 5 mL overnight at 16 ºC, without shaking. DNA was purified by phenol:chloroform following steps outlined above.

treatment_protocol: not applicable

value: myelogenous leukemia

value: K562 aWT


title: 4C_HS40_aWT_B3


title: 4C_HS40_aWT_B1


title: RNAseq_bWT_HS3del_B4

description: cDNA derived from mRNA

data_processing:
CUT&Tag and CUTAC read mapping and processing
Libraries were demultiplexed using demuxFQ (flags: -c -d -i -e -t 1 -r 0.01 -R -l 9). FASTQC- version 0.11.8 was used to assess the read quality and bases with a quality score below 20 were trimmed from both reads using cutadapt (cutadapt -q 20). For CUTAC libraries, reads greater than 120bp in length were removed alignment.  Reads were aligned to the hg38 reference genome using bwa mem with default parameters. Sorted bam files with duplicates removed were generated with SAMtools (version 1.15.1), and converted to bigwig using deepTools bamCoverage (parameters: --normalizeUsing CPM, --binSize 10, 5 or 3 with 12nt smoothing function). Statistical comparisons between WT and mutants were performed by two-sided t-test, using cpm signal summed over 1kb regions. Sample size for CUT&Tag;
4C-seq data was analysed using the pipe4C pipeline (https://github.com/deLaatLab/pipe4C) in R (version 4.3.0) Read 1 sequencing reads were used as input for the pipe4C pipeline and all reads mapped to the viewpoint chromosome were scaled to 1 million reads. An average running mean window size was set at 21 fragment ends. 4C plots were generated using peakC74 (https://github.com/deWitLab/peakC) where two biological replicates were used as input into the peakC program and subsequently plotted with ggplot2 in R. Biological replicates were processed on the same day and sequenced on the same flow cell. Samples for comparison were sequenced together in a single run.
Assembly: hg38
Supplementary files format and content: bigWig, counts

extract_protocol:
500 ng RNA was used as input for library preparation with NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (E7760S, New England Biolabs), following manufacturer’s instructions. Polyadenylated transcripts were enriched using the NEBNext Poly(A) mRNA Magnetic Isolation Module (E7490, New England Biolabs) as per the manufacturer’s protocol. Libraries were sequenced in paired-end mode on a NextSeq 2000 (51 bp paired-end).
RNA from 1 million cells was extracted with RNeasy Plus Mini Kit (74136, Qiagen) following manufacturer’s instructions

value: K562 bWT HS3del


title: WT_day7_iNs_Gemcitabine_ENDseq

description: Library name: Sample 16

value: WT

value: Gemcitabine for 18 hr


title: 4C_HS40_aMut2_B1

value: K562 aMut2


title: RNAseq_bWT_HS3del_B2

description: cDNA derived from mRNA


title: 4C_HS40_aRes_B2

value: K562 aRes


title: 4C_HS40_aRes_B1


title: 4C_HS40_aMut1_B2

value: K562 aMut1


title: 4C_HS40_aWT_B2


title: RNAseq_bWT_HS3del_B1

description: cDNA derived from mRNA


title: RNAseq_bWT_B4

description: cDNA derived from mRNA

value: K562 bWT


title: 4C_HS40_aMut1_B1


title: RNAseq_bWT_B3

description: cDNA derived from mRNA


title: RNAseq_bWT_B2

description: cDNA derived from mRNA


title: RNAseq_bWT_B1

description: cDNA derived from mRNA


title: RNAseq_bMut2_B1

description: cDNA derived from mRNA

value: K562 bMut2


title: RNAseq_bMut1_HS3del_B1

description: cDNA derived from mRNA

value: K562 bMut HS3del


title: RNAseq_bMut2_B2

description: cDNA derived from mRNA


title: RNAseq_bMut1_HS3del_B2

description: cDNA derived from mRNA


title: RNAseq_bMut1_B4

description: cDNA derived from mRNA

value: K562 bMut1


title: RNAseq_bMut1_HS3del_B3

description: cDNA derived from mRNA


title: RNAseq_bMut2_B3

description: cDNA derived from mRNA


title: RNAseq_bMut2_B4

description: cDNA derived from mRNA


title: 4C_HS40_aMut2_B2


title: RNAseq_bWT_HS3del_B3

description: cDNA derived from mRNA


title: RNAseq_bMut1_B3

description: cDNA derived from mRNA


title: RNAseq_aWT_B8

description: cDNA derived from mRNA


title: RNAseq_aWT_B7

description: cDNA derived from mRNA


title: RNAseq_bMut1_B1

description: cDNA derived from mRNA


title: RNAseq_bMut1_B2

description: cDNA derived from mRNA


title: RNAseq_aWT_B2

description: cDNA derived from mRNA


title: RNAseq_aWT_B3

description: cDNA derived from mRNA


title: RNAseq_aRes4_B3

description: cDNA derived from mRNA

value: K562 aRes4


title: RNAseq_aWT_B1

description: cDNA derived from mRNA


title: RNAseq_aRes4_B2

description: cDNA derived from mRNA


title: RNAseq_aWT_B4

description: cDNA derived from mRNA


title: RNAseq_aWT_B5

description: cDNA derived from mRNA


title: RNAseq_aRes3_B4

description: cDNA derived from mRNA

value: K562 aRes3


title: RNAseq_aWT_B6

description: cDNA derived from mRNA


title: RNAseq_aRes3_B3

description: cDNA derived from mRNA


title: RNAseq_aRes3_B2

description: cDNA derived from mRNA


title: RNAseq_aRes3_B1

description: cDNA derived from mRNA


title: RNAseq_aRes2_B8

description: cDNA derived from mRNA

value: K562 aRes2


title: RNAseq_aRes4_B1

description: cDNA derived from mRNA


title: RNAseq_aRes2_B7

description: cDNA derived from mRNA


title: RNAseq_aRes2_B4

description: cDNA derived from mRNA


title: RNAseq_aRes2_B6

description: cDNA derived from mRNA


title: RNAseq_aRes2_B2

description: cDNA derived from mRNA


title: RNAseq_aRes2_B3

description: cDNA derived from mRNA


title: RNAseq_aRes2_B5

description: cDNA derived from mRNA


title: RNAseq_aRes2_B1

description: cDNA derived from mRNA


title: RNAseq_aRes1_B8

description: cDNA derived from mRNA

value: K562 aRes1


title: RNAseq_aRes1_B6

description: cDNA derived from mRNA


title: RNAseq_aRes1_B7

description: cDNA derived from mRNA


title: RNAseq_aRes4_B4

description: cDNA derived from mRNA


title: RNAseq_aRes1_B4

description: cDNA derived from mRNA


title: RNAseq_aRes1_B3

description: cDNA derived from mRNA


title: RNAseq_aRes1_B2

description: cDNA derived from mRNA


title: RNAseq_aRes1_B1

description: cDNA derived from mRNA


title: RNAseq_aMut2_B3

description: cDNA derived from mRNA


title: RNAseq_aMut2_B2

description: cDNA derived from mRNA


title: RNAseq_aMut1_B3

description: cDNA derived from mRNA


title: RNAseq_aMut1_B4

description: cDNA derived from mRNA


title: RNAseq_aMut2_B1

description: cDNA derived from mRNA


title: RNAseq_aMut1_B5

description: cDNA derived from mRNA


title: RNAseq_aMut1_B6

description: cDNA derived from mRNA


title: RNAseq_aMut1_B7

description: cDNA derived from mRNA


title: RNAseq_aMut1_B1

description: cDNA derived from mRNA


title: RNAseq_aMut2_B4

description: cDNA derived from mRNA


title: SG4_bWT_B2.t1

data_processing:
library strategy: CUT&Tag
CUT&Tag and CUTAC read mapping and processing
Libraries were demultiplexed using demuxFQ (flags: -c -d -i -e -t 1 -r 0.01 -R -l 9). FASTQC- version 0.11.8 was used to assess the read quality and bases with a quality score below 20 were trimmed from both reads using cutadapt (cutadapt -q 20). For CUTAC libraries, reads greater than 120bp in length were removed alignment.  Reads were aligned to the hg38 reference genome using bwa mem with default parameters. Sorted bam files with duplicates removed were generated with SAMtools (version 1.15.1), and converted to bigwig using deepTools bamCoverage (parameters: --normalizeUsing CPM, --binSize 10, 5 or 3 with 12nt smoothing function). Statistical comparisons between WT and mutants were performed by two-sided t-test, using cpm signal summed over 1kb regions. Sample size for CUT&Tag;
4C-seq data was analysed using the pipe4C pipeline (https://github.com/deLaatLab/pipe4C) in R (version 4.3.0) Read 1 sequencing reads were used as input for the pipe4C pipeline and all reads mapped to the viewpoint chromosome were scaled to 1 million reads. An average running mean window size was set at 21 fragment ends. 4C plots were generated using peakC74 (https://github.com/deWitLab/peakC) where two biological replicates were used as input into the peakC program and subsequently plotted with ggplot2 in R. Biological replicates were processed on the same day and sequenced on the same flow cell. Samples for comparison were sequenced together in a single run.
Assembly: hg38
Supplementary files format and content: bigWig, counts

extract_protocol:
Sequencing libraries were generated by mixing 25 uL NEBNext High Fidelity 2X PCR Master Mix (M0541, New England Biolabs), 2 uL of P5 indexing primer (10 mM), 2 uL of P7 indexing primer (10 mM) with 21 uL of purified DNA in a PCR reaction under the following conditions: 72 ºC for 5 min, 98 ºC for 30 sec followed by n cycles of 98 ºC 10 sec, 63 ºC for 10 sec, and a final extension at 72 ºC for 1 min. For BG4 and SG4 libraries n=8 cycles were used, for all other CUT&Tag libraries n=10 was used. Libraries were purified using Ampure XP beads (A63882, Beckman Coulter Life Sciences) by incubation with 0.4X ratio of beads for 15 min, followed by supernatant incubation with 1.4X ratio of beads for 15 min. Beads were washed twice with 800 mL 80% ethanol and eluted in 25 uL of 10mM Tris-HCl pH 8.0. Library size distribution was analysed on a Tapestation 2200 (Agilent Technologies) and library concentrations were quantified by NEBNext Library Quant Kit for Illumina (E7630, New England BioLabs). Individual libraries were pooled for optimal read balancing and sequenced paired end with NextSeq 2000 P2 or P3 Reagents 100 Cycles v3 (20046811, 20040559, Illumina, Inc.) on the NextSeq 2000 platform (Illumina, Inc.).
Dynabeads MyOne Streptavidin T1 beads (65601, Thermo Fisher Scientific) were incubated with Concanavalin A (C2272, biotin conjugate, Sigma-Aldrich) in ratio of 10 mg/mL beads to 1.15 mg/mL Concanavalin A at 22 ºC for 30 min at 400 rpm on a thermoshaker (Eppendorf). Volume sufficient for 10 µL beads per reaction was prepared. Beads were washed with 1 mL of binding buffer (20mM HEPES pH 7.5, 10mM KCl, 1mM CaCl2, 1mM MnCl2) and resuspended in volume of binding buffer sufficient for 10 uL beads per reaction. Cells were fixed in 0.1% formaldehyde (28906, Thermo Fisher Scientific) in 1X PBS for 2 min at room temperature and quenched with 0.075M glycine. Cells were centrifuged at 1300xg 4 ºC for 4 min and resuspended in wash buffer (20mM HEPES pH 7.5, 150mM KCl, 0.5mM spermidine (S0266, Sigma-Aldrich), one tablet protease inhibitor (11873580001, Roche cOmplete, EDTA-free)) at 500 cells/mL. 10 uL beads were incubated with 100 uL of cell suspension at 25 ºC for 10 min at 600 rpm, washed twice with 100 uL wash buffer and resuspended in 50 uL of antibody buffer (2mM EDTA, 0.1% BSA (A8577, Sigma-Aldrich), 0.05% digitonin (300410, Merck Millipore) in wash buffer). Primary antibody was added and incubated at 4 ºC at 600rpm overnight. Primary antibodies used include; BG4 scFv (made in house) at 0.5 mM per reaction, SG4 (made in house) at 1 mM per reaction, anti-H3K4me1 antibody (710795, Thermo Fisher Scientific), anti-H3K27ac antibody (ab4729, Abcam), anti-Ser5 phosphorylated Rpb1 antibody (#13523, Cell Signaling Technology), anti-GATA1 antibody (ab181544, Abcam), anti-BRG1 antibody (ab110641, Abcam), anti-P300 antibody (sc-48343, Santa Cruz Biotechnology), Normal Rabbit IgG (2729, Cell Signaling Technology)). Cells were washed twice with 100 uL dig wash buffer (0.05% digitonin in wash buffer) and resuspended in 50 uL of dig-wash buffer. Secondary antibody was then added and incubated at 25 ºC at 600 rpm for 1 hr. For BG4 and SG4 samples, 2 uL of rabbit anti-FLAG antibody (#2368, Cell Signaling Technology) was added, for all other rabbit primary antibodies 0.5 uL of Guinea Pig anti-rabbit IgG antibody (ABIN101961, antibodies-online.com) was added, and for mouse primary antibodies 0.5 uL of Rabbit Anti-mouse IgG H&L (ab46540, Abcam) was added per reaction. Cells were then washed three times with 500 uL dig-wash buffer and resuspended in 50 uL dig-300 buffer (20mM 20mM HEPES pH 7.5, 300mM KCl, 0.5mM spermidine, 0.01% digitonin, one tablet protease inhibitor). pA-Tn5 (2 mM, made in house) was added in 1:250 dilution to each sample and incubated at 25 ºC at 600 rpm for 1 hr. Cells were washed three times with 500 uL dig-300 buffer and resuspended in 300 uL tagmentation buffer (10mM MgCl2 in dig-300 buffer) and incubated at 37 ºC at 600 rpm for 1 hr. Cells were then washed twice with 500 uL TAPS wash buffer (10 mM TAPS (J63268.AE, Thermo Fisher Scientific) and resuspended in 100 uL of proteinase K solution (0.5 mg/mL Proteinase K (EO0491, Thermo Fisher Scientific), 0.5% SDS in 10mM Tris-HCl pH 8.0). Samples were vortexed on full and incubated at 55 ºC for 1 hr at 800 rpm. DNA was extracted using DNA Clean & Concentrator 5 (D4013, Zymo Research) following the manufacturer’s instructions, DNA was eluted in 25 uL DNA elution buffer.


title: SG4_bWT_B2.t3


title: RNAseq_aMut1_B2

description: cDNA derived from mRNA


title: SG4_bWT_B2.t2


title: SG4_bWT_B1.t2


title: SG4_bWT_B1.t1


title: SG4_bMut1_B2.t2


title: SG4_bWT_B1.t3


title: RNAseq_aRes1_B5

description: cDNA derived from mRNA


title: SG4_bMut1_B1.t2


title: SG4_bMut1_B1.t3


title: SG4_aRes_B2_t2


title: SG4_bMut1_B1.t1


title: SG4_aWT_B1_t1


title: SG4_aWT_B2_t2


title: SG4_aRes_B1_t1


title: SG4_aMut1_B1_t1


title: SG4_aMut1_B2_t2


title: RNAPII_5SP_bWT_B2_t1


title: RNAPII_5SP_bWT_B1_t2


title: RNAPII_5SP_bMut2_B1_t1


title: RNAPII_5SP_bMut2_B2_t1


title: RNAPII_5SP_bMut2_B1_t2


title: RNAPII_5SP_bMut1_B1.t2


title: RNAPII_5SP_bMut1_B2.t2


title: RNAPII_5SP_bMut1_B2.t1


title: RNAPII_5SP_bWT_B1_t1


title: RNAPII_5SP_aWT_B4


title: RNAPII_5SP_aWT_B3


title: RNAPII_5SP_aWT_B1


title: RNAPII_5SP_aWT_B2


title: SG4_bMut1_B2.t3


title: RNAPII_5SP_aMut1_B4


title: RNAPII_5SP_aRes_B4


title: RNAPII_5SP_aRes_B3


title: RNAPII_5SP_aRes_B1


title: RNAPII_5SP_aRes_B2


title: RNAPII_5SP_aMut1_B1


title: H3K4me1_WT_HS3del_B2_t2


title: H3K4me1_WT_HS3del_B1_t2


title: H3K4me1_WT_HS3del_B2_t1


title: H3K4me1_bWT_B1


title: H3K4me1_WT_HS3del_B1_t1


title: RNAPII_5SP_bMut1_B1.t1


title: H3K4me1_bMut_HS3del_B2_t1


title: H3K4me1_bMut1_B1


title: H3K4me1_bMut_HS3del_B1_t1


title: H3K27ac_bWT_B2


title: H3K4me1_bMut2_B1


title: H3K27ac_WT_HS3del_B1_t1


title: RNAPII_5SP_bMut2_B2_t2


title: H3K4me1_bMut_HS3del_B2_t2


title: H3K27ac_WT_HS3del_B1_t2


title: H3K27ac_WT_HS3del_B2_t1


title: H3K27ac_bMut_HS3del_B2_t2


title: H3K27ac_WT_HS3del_B2_t2


title: H3K27ac_bMut_HS3del_B2_t1


title: H3K27ac_bMut_HS3del_B1_t2


title: RNAPII_5SP_aMut1_B2


title: H3K27ac_bWT_B1


title: RNAPII_5SP_aMut1_B3


title: H3K27ac_bMut1_B1


title: H3K27ac_aWT_B1


title: H3K27ac_bMut_HS3del_B1_t1


title: H3K27ac_bMut1_B2


title: H3K27ac_bMut2_B1


title: H3K27ac_aMut1_B2


title: H3K27ac_aWT_B2


title: CUTAC_WT_B3

extract_protocol:
Sequencing libraries were generated by mixing 25 uL NEBNext High Fidelity 2X PCR Master Mix (M0541, New England Biolabs), 2 uL of P5 indexing primer (10 mM), 2 uL of P7 indexing primer (10 mM) with 21 uL of purified DNA in a PCR reaction under the following conditions: 72 ºC for 5 min, 98 ºC for 30 sec followed by 10 cycles of 98 ºC 10 sec, 63 ºC for 10 sec, and a final extension at 72 ºC for 1 min. Libraries were purified using Ampure XP beads (A63882, Beckman Coulter Life Sciences) by incubation with 0.4X ratio of beads for 15 min, followed by supernatant incubation with 1.4X ratio of beads for 15 min. Beads were washed twice with 800 mL 80% ethanol and eluted in 25 uL of 10mM Tris-HCl pH 8.0. Library size distribution was analysed on a Tapestation 2200 (Agilent Technologies) and library concentrations were quantified by NEBNext Library Quant Kit for Illumina (E7630, New England BioLabs). Individual libraries were pooled for optimal read balancing and sequenced paired end with NextSeq 2000 P2 or P3 Reagents 100 Cycles v3 (20046811, 20040559, Illumina, Inc.) on the NextSeq 2000 platform (Illumina, Inc.).
Cleavage Under Targeted Accessible Chromatin (CUTAC) was performed following the CUT&Tag procedure outlined above with the following changes. The primary antibody used for all CUTAC samples was anti-dimethyl-Histone H3 (lys4) (07-030, Merck Millipore) 1:50 per reaction. pA-Tn5 catalysed tagmentation was performed in 300 uL CUTAC buffer (10 mM TAPS (J63268.AE, Thermo Fisher Scientific) pH 8.5, 5 mM MgCl2) at 37 ºC at 600 rpm for 20 min.

value: K562 WT


title: CUTAC_aMut1_B1

value: myelogenous leukemia


title: CUTAC_bMut2_B1


title: CUTAC_bMut2_B2


title: BG4_aWT_B2_t3

value: K562 aWT


title: BG4_aWT_B3_t2


title: CUTAC_aMut1_B2


title: CUTAC_WT_B1


title: CUTAC_bMut2_B3


title: BG4_aWT_B2_t2


title: CUTAC_aRes_B1


title: CUTAC_aRes_B3


title: BG4_aWT_B2_t1


title: BG4_aWT_B1_t3


title: BG4_aRes_B2_t3


title: CUTAC_WT_B2


title: BG4_aRes_B3_t3


title: H3K4me1_bMut_HS3del_B1_t2


title: BG4_aWT_B1_t2


title: CUTAC_aRes_B2


title: BG4_aWT_B3_t1


title: BG4_aRes_B1_t3


title: BG4_aRes_B1_t2


title: BG4_aRes_B3_t2


title: BG4_aRes_B2_t2


title: BG4_aRes_B3_t1


title: CUTAC_aMut1_B3


title: BG4_aWT_B3_t3


title: BG4_aRes_B2_t1


title: BG4_aWT_B1_t1


title: BG4_aRes_B1_t1


title: BG4_aMut1_B3_t3


title: BG4_aMut1_B2_t3


title: BG4_aMut2_B2_t1


title: BG4_aMut2_B1_t2


title: BG4_aMut2_B2_t2


title: BG4_aMut1_B3_t1


title: BG4_aMut2_B1_t1


title: BG4_aMut1_B1_t3


title: BG4_aMut1_B3_t2


title: BG4_aMut1_B1_t1


title: MCF7 Mnase-seq

first: Pedro

middle: J

last: Batista

address: 37 Convent Street Bldg 37

data_processing:
The paired-end reads were merged using PEAR then mapped on human genome reference hg19 with bowtie2 (https://doi.org/10.1038/nmeth.1923).  The positions of 16,161 protein-coding genes – ranging from 1 to 200 kb – were extracted from NCBI RefSeq. Sub-nucleosomal DNA fragments of length 80-140 bp were intersected with these 16,161 protein-coding genes using bedtools. For each gene, the count of nucleosomal fragments was normalized by the total count of fragments mapped in each sample.
Assembly: hg19
Supplementary files format and content: MN-EXO_METTL7A.xlsx

extract_protocol:
Cells were harvested at 80% confluency using a cell scraper, centrifuged at 125g for 5 min and washed once with cold phosphate-buffered saline. Cells were then resuspended in cold RSB buffer (10 mM Tris-HCl, pH 8.0, 10 mM NaCl, 3 mM MgCl2) containing 0.5% Nonidet P-40, 1 mM PMSF and put on ice. The cell suspensions were homogenized by 20 strokes of pestle B in a Dounce homogenizer over 30 min on ice. Release nuclei were centrifuged in Sorvall X Pro centrifuge at 150g, 4ºC for 5 min, nuclei pellet was resuspended in cold RSB buffer supplemented with 1 mM PMSF. Before digestion, 1x10 6 nuclei in RSB buffer with 1 mM PMSF were supplemented with 2 mM CaCl2 and kept at 37ºC for 5 min. 5 units of Micrococcal nuclease (Nuclease S7 Micrococcal Nuclease, cat# 10107921001; Roche Applied Science) with 200 units ExoIII (cat# M0206S; New England Biolabs) were added to each nuclei aliquot and incubated for 10 min at 37ºC. The reaction was stopped by adding EDTA to a final concentration of 5 mM.
Digested nuclei were centrifuged at 4,600g in a Sorvall Legend Micro tabletop centrifuge, supernatant S1 was removed and discarded. Pellet was resuspended in cold TE buffer, (10 mM Tris-HCl pH 8.0, 1 mM EDTA), gently pipetted and incubated on ice for 10 min. After centrifugation supernatant S2 was collected, pelleted material was resuspended in TE buffer, and after third centrifugation supernatant S3 was collected. Supernatants 2 and 3 were analyzed on 1% agarose gel in TAE buffer to confirm the release of DNA fragments of various length, then combined and treated with 1% SDS and 20 µg of proteinase K (New England Biolabs, #P8107S). The reaction was incubated for 1 h at 55ºC. DNA was extracted with phenol-chloroform-isoamyl alcohol, precipitated in 2.5 volumes of 100% alcohol supplemented with 50 mM sodium-acetate and left at -80ºC for overnight. Samples were centrifuged at 17,000g at a tabletop centrifuge, pellet was rinsed in 70% alcohol, air dried and dissolved in TE buffer (10 mM Tris-HCl, pH 8.0, 0.2 mM EDTA). Total DNA was sequenced on Illumina NextSeq2000 for a 100 bp pair-ended run to obtain 300 million reads per sample.

value: Breast Cancer


title: MCF7 DpVp ATAC-seq Replicate 2

data_processing:
Fastq files analyzed from raw data to called peaks using PEPATAC pipeline against hg38 build of human genome.
Reads trimmed using skewer.
Reads aligned to hg38 using Bowtie2
Deduplicated using samblaster
Peak calling with MACS2
Differntial accessibility determined with DEseq2. De novo and known motif enrichment analysis performed with HOMER. Changes in TF occupancy between cell states performed with BagFoot.
Assembly: hg38
Supplementary files format and content: PEPATAC_METTL7A_hg38_peaks_coverage.tsv, contains called peaks from ATAC-seq

source_name: MCF7 DpVp

extract_protocol:
Cells suspended in cold ATAC-Resuspension Buffer and incubated on ice for 3 minutes. Nuclei then pelleted at 500 RCF for 10min at 4C.
Nuclei resuspended in 50uL transposition mix and incubated at 37C for 30min in thermomixer shaking at 1000RPM. Reactions stopped by adding EDTA and then purified using Zymo DNA Clean and Concentrate kit, and PCR amplified for 5 cycles, and purified with the same Zymo DNA clean and Concentrator kit.
Library pool size selected for 100-1000 bp on 1% Agarose gel, and sequenced on Illumina NextSeq2000 for a 100bp pair-ended run to obtain 100 million reads per sample.

value: MCF7 DpVp

value: Breast cancer


title: MCF7 ATAC-seq Replicate 1


title: MCF7 DpVp Mnase-seq

value: Romidepsin resistant


title: MCF7 ATAC-seq Replicate 2


title: HuT78 DpVp ATAC-seq Replicate 2

source_name: HuT78 DpVp

value: HuT78 DpVp

value: T-lymphocyte


title: HuT78 DpVp ATAC-seq Replicate 1


title: HuT78 ATAC-seq Replicate 1


title: MCF7 DpVp ATAC-seq Replicate 1


title: P037, Bulk CD4, TCRb

city: Besançon

first: Olivier

last: Adotévi

state: Franche-Comté

address: 8 rue du Dr JFX Girod

department: Oncology

country: France

institute: Université de Franche-Comté

description:
Library name: P037_S20_R1_001
SEQTR

data_processing:
TCR sequences processed using an adhoc Perl script (:https://doi.org/10.1016/j.crmeth.2023.100459). The TCR sequences were aligned and analyzed using the IMGT database as the reference. The alignment and annotation were performed using MixCR.
MiXCR upstream analysis ouput were used as input for the immunarch v.0.9 package. The distribution of clones was done by repExplore (method = "volume"). Clonality analysis was assessed using repClonality (method = "homeo") function and diversity evaluation was done by repDiversity function (method = d50"). The trackClonotypes function (col = ‘aa+v’) was used to track clonotypes across vaccine time points.
Assembly: IMGT
Supplementary files format and content: Tab-separate values files
Library strategy: TCR-seq

molecule: polyA RNA

source_name: PBMC

extract_protocol:
IFNγ secreting cells were sorted by using IFNγ secretion-detection assay (Mitenyi) before cell sorting on MACSQuant Tyto (Miltenyi Biotec, Germany). IFNγ+CD4+ T cells were lysed in 300µL Lysis/Binding Buffer for Dynabeads™ mRNA Purification Kits and stored at -80°C (A33562, Invitrogen).
The TCR products were purified, quantified and loaded on MiSeq or NextSeq1000 instruments (Illumina) for the deep sequencing of theTCRa/b chain.

treatment_protocol: PBMC from selected patients were thawed and in vitro stimulated during 6 days with vaccinated-derived peptides

value: PBMC

value: CD4+ T

tag: age


title: HuT78 ATAC-seq Replicate 2


title: P037, CD4+IFN+, Priming vaccination, TCRb

description:
Library name: P037_S19_R1_001
SEQTR


title: P020, CD4+IFN+, Priming vaccination, TCRb

description:
Library name: P020_S13_R1_001
SEQTR


title: BG4_aMut1_B2_t2

value: K562 aMut1


title: BG4_aMut1_B2_t1


title: Effect of everolimus treatment on subcutaneous tumors in mice rep4

city: Shanghai

first: Xin

last: Lou

state: Shanghai

address: 688 Hongqu Road

department: Department of Pancreatic Surgery

country: China

institute: Fudan University Shanghai Cancer Center

description:
Library name: Everolimus4
exp2.txt

data_processing:
Data filtering The sequencing data was filtered with SOAPnuke  by (1) Removing reads containing sequencing adapter; (2) Removing reads whose low-quality base ratio (base quality less than or equal to 15) is more than 20%; (3) Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format. The subsequent analysis and data mining were performed on Dr. Tom Multi-omics Data mining system (https://biosys.bgi.com).
RNA identification Bowtie2 was applied to align the clean reads to the gene set, in which known and novel, coding and noncoding transcripts were included.
Gene Quantification Differential Expression Analysis Expression level of gene was calculated by RSEM (v1.3.1) . The heatmap was drawn by pheatmap (v1.0.8)  according to the gene expression difference in different samples. Essentially, differential expression analysis was performed using the DESeq2(v1.4.5)  (or DEGseq or PoissonDis)with Q value ≤ 0.05 (or FDR ≤ 0.001).
Gene Annotation To take insight to the change of phenotype, GO (http://www.geneontology.org/) and KEGG (https://www.kegg.jp/) enrichment analysis of annotated different expression gene was performed by Phyper based on Hypergeometric test. The significant levels of terms and pathways were corrected by Q value with a rigorous threshold (Q value ≤ 0.05) .
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: subcutaneous tumor

extract_protocol:
1. Experimental Procedures 1.1 Sample Lysis 1.1.1 Transfer appropriate tissue sample into corresponding tissue grinding tube (tissue≤30 mg, cell≤1×107). 1.1.2 Add 600 μL Buffer RLT Plus. Homogenize the lysate for using a rotor–stator homogenizer, stay at room temperature for 5 min. 1.1.3 Centrifuge at 12,000×g for 3 min in room temperature, transfer the supernatant to AllPrep DNA spin column. 1.1.4 Centrifuge 12,000×g for 30 s in room temperature, transfer the solution from the collection tube for the RNA purification. 1.1.5 Transfer the DNA spin column to the new collection tube for DNA purification. 1.2 DNA Purification 1.2.1 Add 500μL Buffer AW1 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.2 Add 500μL Buffer AW2 to AllPrep DNA spin column, centrifuge at 10,000×g for 30 s and discard the filtrate. 1.2.3 Centrifuge at 16,000×g for 2 min, transfer the AllPrep DNA spin column to 1.5mL centrifuge tube. 1.2.4 Add 50μL Buffer EB to AllPrep DNA spin column, stay at room temperature for 1 min. 1.2.5 Centrifuge at 16,000×g for 2 min and collect the DNA. 1.3 RNA Purification 1.3.1 Add the equal volume of 70% ethanol to the collection tube, mix by pipetting. 1.3.2 Transfer 700 μL mixed solution, to a RNeasy spin column placed in a 2 mL collection tube. 2.3.3 Centrifuge at 10,000×g for 30 s and allow it to empty by gravity flow. 1.3.4 Add 700 μL Buffer RW1 to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.5 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.6 Add 500 μL Buffer RPE to RNeasy spin column. Centrifuge at 10,000×g for 30 s and discard the filtrate. 1.3.7 Centrifuge at 16,000×g for 2 min and transfer the RNeasy spin column to the 1.5 mL centrifuge tube. 1.3.8 Add 35 μL RNase-free water to RNeasy spin column. Stay at room temperature for 1min. 1.3.9 Centrifuge at 16,000×g for 2 min at room temperature to collect RNA.
After total RNA was extracted, mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase, which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I, RNase H and dUTP Solution. An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina Novaseq™ 6000 (LC-Bio Technology CO., Ltd., Hangzhou, China) following the vendor's recommended protocol.

value: subcutaneous tumor

value: subcutaneous tumor tissue cells

value: Everolimus


title: Effect of everolimus treatment on subcutaneous tumors in mice rep3

description:
Library name: Everolimus3
exp2.txt


title: Effect of everolimus treatment on subcutaneous tumors in mice rep2

description:
Library name: Everolimus2
exp2.txt


title: BG4_aMut1_B1_t2


title: P020, Bulk CD4, TCRb

description:
Library name: P020_S14_R1_001
SEQTR


title: Effect of everolimus treatment on subcutaneous tumors in mice rep1

description:
Library name: Everolimus1
exp2.txt


title: P005, CD4+IFN+, Priming vaccination, TCRb

description:
Library name: P005_S11_R1_001
SEQTR


title: Effect of temozolomide treatment on subcutaneous tumors in mice rep4

description:
Library name: TMZ4
exp2.txt

value: TMZ


title: P005, Bulk CD4, TCRb

description:
Library name: P005_S12_R1_001
SEQTR


title: Effect of temozolomide treatment on subcutaneous tumors in mice rep3

description:
Library name: TMZ3
exp2.txt


title: P023, Bulk CD4, 4years post-vaccination,TCRb

description:
Library name: P023_S18_R1_001
SEQTR


title: Effect of temozolomide treatment on subcutaneous tumors in mice rep1

description:
Library name: TMZ1
exp2.txt


title: P023, CD4+IFN+, Priming vaccination,TCRb

description:
Library name: P023_S15_R1_001
SEQTR


title: P023, Bulk CD4, Baseline, TCRb

description:
Library name: P023_BulkCD4_BSL
SEQTR

extract_protocol: PMBCs were thawed in RPMI 20% human serum, centrifuged 7 min 200g. CD4+ T cells were sorted using magnetic column after labelling with CD4 MicroBeads (130- 096-553, Miltenyi Biotec). CD4+ T cells were lysed in 300µL Lysis/Binding Buffer for Dynabeads mRNA Purification Kits and stored at -80C (A33562, Invitrogen).


title: Effect of sunitinib treatment on subcutaneous tumors in mice rep1

description:
Library name: Sunitinib1
exp2.txt

value: Sunitinib


title: LIG4_KO_c40_11_day9_iNs_NT_chr19_amplicon_seq

description: Library name: Sample 38

data_processing:
For Amplicon-seq, Miseq reads were joined using the fastq-join tool with default parameters, then the joined reads were aligned to the reference sequence hg19 using Burrows-Wheeler aligner (BWA) mem.
Assembly: hg19
Supplementary files format and content: bw files from Amplicon_seq include deletion signal for each condition after subtracting the signal in NT

extract_protocol:
For Targeted deep sequencing (amplicon-seq), collected neurons and extracted genomic DNA using DNeasy Blood & Tissue Kits (QIANGEN cat. No. 69506) following the manufacturer’s protocol.
For Targeted deep sequencing (amplicon-seq), amplification of targeted regions in a 25μl PCR reaction (12.5μl 2x Kapa HiFi HotStart Ready Mix, 1μg of genomic DNA, 1μM of each forward and reverse primer, and ddH2O to make 25μl) with the following PCR thermocycler program: 95°C 3min; 25 cycles of 95°C 30s, 60/64°C 15s (adjust according to Tm of primers), 72°C 30s; final extension 72°C 5min; hold at 4°C. Separated the PCR products on a 2% agarose gel and recovered the targeted DNA band by the QIAquick Gel Extraction Kit (QIANGEN, cat. No. 28704). Subsequently, Nextera index sequences were added by performing another round of PCR in 50μl reactions (25μl 2x Kapa HiFi HotStart Ready Mix, 100ng of purified DNA, 5μl of each Nextera XT index i5 and i7 primers, and ddH2O to make 50μl) with the following PCR thermocycler program: 95°C 3min; 8 cycles of 95°C 30s, 55°C 30s, 72°C 30s; final extension 72°C 5min; hold at 4°C. PCR products were separated on a 2% agarose gel and the targeted DNA band was recovered by the QIAquick Gel Extraction Kit.

value: iPSC-derived i3Neurons

value: Neurons

value: Lig4 knockout clone 40

value: NT


title: LIG4_KO_c40_11_day9_iNs_AraC_chr19_amplicon_seq

description: Library name: Sample 39

value: AraC treatment for 3 days


title: Effect of sunitinib treatment on subcutaneous tumors in mice rep3

description:
Library name: Sunitinib3
exp2.txt


title: LIG4_KO_c13_day9_iNs_AraC_chr19_amplicon_seq

description: Library name: Sample 37

value: Lig4 knockout clone 13


title: Effect of surufatinib treatment on subcutaneous tumors in mice rep4

description:
Library name: Surufatinib4
exp2.txt

value: Surufatinib


title: LIG4_KO_c13_day9_iNs_NT_chr19_amplicon_seq

description: Library name: Sample 36


title: Effect of sunitinib treatment on subcutaneous tumors in mice rep2

description:
Library name: Sunitinib2
exp2.txt


title: Subject_J, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day28

city: Rockville

first: Johannes

last: Goll

address: 401 N Washington St

department: Bioinformatics Service Group

institute: The Emmes Company

data_processing:
Gene expression quantification was conducted on the gene level using the function featureCounts within the Subread v1.4.6 software counting mapped paired-reads to obtain fragment counts per gene. Fragments that overlapped with multiple genes or had multiple mapping locations on the reference genome were excluded.
Supplementary files format and content: tab-delimited text includes raw counts of each ENSEMBL Gene ID for each Sample
Assembly: Paired-end reads were mapped against the human reference genome (GRCh38) using TopHat2 (Version 2.1.1). Human gene models and annotations were obtained from ENSEMBL v84, (March 2016).

extract_protocol:
Mononuclear cells from fresh breast milk and whole blood and extract total RNA from fresh mononuclear cells were extracted using Trizol ® (Invitrogen, Life Technologies Corporation) according to the manufacturer’s instructions
The integrity of all RNA samples was checked using an Agilent 2100 Bioanalyzer. RNA-seq libraries were prepared using the Illumina TruSeq Stranded mRNA Sample Prep Kit.

tag: day


title: Effect of sunitinib treatment on subcutaneous tumors in mice rep4

description:
Library name: Sunitinib4
exp2.txt


title: P023, CD4+IFN+, 4years post-vaccination,TCRb

description:
Library name: P023_S17_R1_001
SEQTR


title: LIG4_KO_c40_11_day9_iNs_AraC_chr6_amplicon_seq

description: Library name: Sample 33


title: Effect of temozolomide treatment on subcutaneous tumors in mice rep2

description:
Library name: TMZ2
exp2.txt


title: Subject_J, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day0


title: Effect of surufatinib treatment on subcutaneous tumors in mice rep1

description:
Library name: Surufatinib1
exp2.txt


title: Subject_J, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day8

source_name: breast milk lymphocyte (BML)

value: breast milk lymphocyte (BML)


title: LIG4_KO_c40_11_day9_iNs_NT_chr6_amplicon_seq

description: Library name: Sample 32


title: WT_day9_iNs_NT_chr19_amplicon_seq_controlforLIG4KO

description: Library name: Sample 34

value: WT


title: LIG4_KO_c13_day9_iNs_NT_chr6_amplicon_seq

description: Library name: Sample 30


title: Effect of surufatinib treatment on subcutaneous tumors in mice rep2

description:
Library name: Surufatinib2
exp2.txt


title: LIG4_KO_c13_day9_iNs_AraC_chr6_amplicon_seq

description: Library name: Sample 31


title: WT_day9_iNs_AraC_chr6_amplicon_seq_controlforLIG4KO

description: Library name: Sample 29


title: Effect of octreotide treatment on subcutaneous tumors in mice rep4

description:
Library name: Octreotide4
exp2.txt

value: Octreotide


title: WT_day9_iNs_NT_chr6_amplicon_seq_controlforLIG4KO

description: Library name: Sample 28


title: LIG4_KO_c40_11_day9_iNs_AraC_chr1_amplicon_seq

description: Library name: Sample 27


title: Effect of octreotide treatment on subcutaneous tumors in mice rep3

description:
Library name: Octreotide3
exp2.txt


title: Effect of octreotide treatment on subcutaneous tumors in mice rep2

description:
Library name: Octreotide2
exp2.txt


title: LIG4_KO_c40_11_day9_iNs_NT_chr1_amplicon_seq

description: Library name: Sample 26


title: Effect of surufatinib treatment on subcutaneous tumors in mice rep3

description:
Library name: Surufatinib3
exp2.txt


title: Subject_J, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day2


title: WT_day9_iNs_AraC_chr19_amplicon_seq_controlforLIG4KO

description: Library name: Sample 35


title: LIG4_KO_c13_day9_iNs_AraC_chr1_amplicon_seq

description: Library name: Sample 25


title: Effect of octreotide treatment on subcutaneous tumors in mice rep1

description:
Library name: Octreotide1
exp2.txt


title: Subject_C, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: Effect of rapamycin treatment on subcutaneous tumors in mice rep4

description:
Library name: Rapamycin4
exp2.txt

value: Rapamycin


title: Subject_J, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day28


title: WT_day9_iNs_AraC_chr1_amplicon_seq__controlforLIG4KO

description: Library name: Sample 23


title: Subject_C, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day0


title: WT_day9_iNs_NT_chr1_amplicon_seq_controlforLIG4KO

description: Library name: Sample 22


title: Subject_C, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28


title: Col-0 SUC2:.CO:CIT aba1-6 ChIP biol rep.2

city: Milano

first: Lucio

last: Conti

address: Via Celoria 26

country: Italy

institute: Università degli Studi di Milano

description: Library name: Unknown_CE349-003R0008

data_processing:
Mapping of raw reads and peak calling followed the greenscreen pipeline (Klasfeld et al., 2022) with slight modifications. The adapted code is available at https://github.com/beaLando/chipseq_aba.git. In brief, fastp (Chen et al., 2018) was used to trim and filter reads after quality checks in fastqc (Andrews S., 2010). Mapping of filtered reads was then executed with Bowtie2 with TAIR10.1 as reference genome. Peak calling was done in macs2 (Gaspar, 2018) for each replicate separately using input samples as background. Peaks found for each replicate were then processed with irreproducible discovery rate (IDR) to retain reproducible peaks and with a global IDR (FDR corrected) greater or equal to -log10(0.1). This list was then further filtered to retain only peaks falling outside greenscreen’s blacklisted regions. Further quality checks were executed with qualimap (García-Alcalde et al., 2012) and deeptools (Ramírez et al., 2014). Finally, ChIPseeker (Yu et al., 2015) was used to estimate how frequently peaks would fall within gene promoters or other genomic regions.
Assembly: TAIR10.1
Supplementary files format and content: fastq (raw reads ChIP-Seq samples) and narrowpeak (called, unfiltered, peaks on ChIP-Seq samples)

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Murashige and Skoog (MS) medium was prepared by dissolving the MS salt mix (Duchefa) in distilled water. After adjusting the pH solution to 5.8, agar (Duchefa) was added to a final concentration of 0.8% w/v. Sterilized seeds (70% v/v ethanol and 1% w/v Sodium Dodecyl Sulphate, SDS for 10 minutes) were spread onto solidified agar plates, stratified for 2-3 days (4°C and dark) and then moved to the growth chamber. Temperature range in the growth chamber fluctuated between 24 °C during the day and 21 °C in the night and air humidity was about 60%.Long day conditions (LDs, 16 h light / 8 h dark) were kept constant throughout the experiment.

extract_protocol:
5 grams (fresh weight) of whole seedlings were used for each genotype/replicate. A bioruptor sonicator (Diagenode, B01020001) was used to shear the chromatin using the following settings: 40 Cycles, 30 sec ON, 30 sec OFF at high power. With these conditions the size of sheared DNA is below 100 bp. GFP-Trap magnetic nanobodies (Chromotek) were used.
Inputs and ChIP samples (two biological replicates) were quantified with Qubit dsDNA Quantification High sensitivity Assay Kit (Invitrogen). For library preparation, the VAHTS Universal Plus DNA Library Prep Kit for Illumina (ND617-02, Vazyme, Nanjing, China) was used, following the manufacturer’s recommendations without fragmentation. Library quality control was performed using the QSep-400 (BiOptic, Taipei, China) and Qubit 3.0 (Thermo Fisher Scientific, Wilmington, USA). The qualified library was sequenced on the Illumina Novaseq X platform (Illumina, San Diego, USA) with paired-end 150 bp (PE150) mode. Library construction and sequencing were performed at Biomarker Technologies (BMKGENE) GmbH.

value: whole seedling

value: Col-0 SUC2:.CO:CIT aba1-6

tag: chip nanobody

value: GFP-Trap


title: Effect of rapamycin treatment on subcutaneous tumors in mice rep3

description:
Library name: Rapamycin3
exp2.txt

value: subcutaneous tumor

value: subcutaneous tumor tissue cells


title: WT_day9_iNs_AraC_DNA_PKi_chr19_amplicon_seq

description: Library name: Sample 21

value: AraC and DNA-PKi treatment for 3 days


title: Effect of rapamycin treatment on subcutaneous tumors in mice rep2

description:
Library name: Rapamycin2
exp2.txt


title: Subject_C, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day8


title: Col-0 SUC2:.CO:CIT aba1-6 Input biol rep.2

description: Library name: Unknown_CE349-003R0007


title: Col-0 SUC2:.CO:CIT aba1-6 ChIP biol rep.1

description: Library name: Unknown_CE349-003R0006


title: Col-0 SUC2:.CO:CIT aba1-6 Input biol rep.1

description: Library name: Unknown_CE349-003R0005


title: Effect of rapamycin treatment on subcutaneous tumors in mice rep1

description:
Library name: Rapamycin1
exp2.txt


title: Subject_J, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day0


title: Col-0 SUC2:.CO:CIT ChIP biol rep.2

description: Library name: Unknown_CE349-003R0004

value: Col-0 SUC2:.CO:CIT


title: LIG4_KO_c13_day9_iNs_NT_chr1_amplicon_seq

description: Library name: Sample 24

value: iPSC-derived i3Neurons

value: Neurons


title: Subject_C, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day0


title: WT_day9_iNs_AraC_DNA_PKi_chr6_amplicon_seq

description: Library name: Sample 18


title: Subject_L, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: Col-0 SUC2:.CO:CIT Input biol rep.2

description: Library name: Unknown_CE349-003R0003


title: WT_day9_iNs_AraC_chr6_amplicon_seq_controlforPKi

description: Library name: Sample 17


title: Col-0 SUC2:.CO:CIT ChIP biol rep.1

description: Library name: Unknown_CE349-003R0002


title: Effect of PBS treatment on subcutaneous tumors in mice rep3

description:
Library name: Control3
exp2.txt

value: Control


title: Effect of PBS treatment on subcutaneous tumors in mice rep2

description:
Library name: Control2
exp2.txt


title: Subject_L, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day0


title: WT_day9_iNs_NT_chr6_amplicon_seq_controlforPKi

description: Library name: Sample 16

value: NT


title: WT_day9_iNs_AraC_chr19_amplicon_seq_controlforPKi

description: Library name: Sample 20

value: AraC treatment for 3 days


title: Col-0 SUC2:.CO:CIT Input biol rep.1

description: Library name: Unknown_CE349-003R0001


title: Subject_L, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28


title: Effect of PBS treatment on subcutaneous tumors in mice rep1

description:
Library name: Control1
exp2.txt


title: 48-hour treatment of HUVECs with APOE rep3

description:
Library name: APOE3
exp1.txt

source_name: HUVEC

value: HUVEC

value: Human Umbilical Vein Endothelial Cells

value: APOE


title: Subject_L, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day8

value: breast milk lymphocyte (BML)


title: WT_day9_iNs_AraC_DNA_PKi_chr1_amplicon_seq

description: Library name: Sample 15

value: WT


title: WT_day9_iNs_AraC_chr1_amplicon_seq_controlforPKi

description: Library name: Sample 14


title: 48-hour treatment of HUVECs with APOE rep2

description:
Library name: APOE2
exp1.txt


title: Subject_L, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day2


title: Effect of PBS treatment on subcutaneous tumors in mice rep4

description:
Library name: Control4
exp2.txt


title: Subject_C, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day2


title: WT_day9_iNs_NT_chr19_amplicon_seq_controlforPKi

description: Library name: Sample 19


title: WT_day9_iNs_NT_chr1_amplicon_seq_controlforPKi

description: Library name: Sample 13


title: AD, High P, brain, 5

city: shanghai

first: jiaxue

last: cha

address: Siping Road 1239

institute: Tongji university

description: Library name: AD High P 5

data_processing:
The Clean Reads were rapidly and accurately aligned to the reference genome using the HISAT2 software.
Assembly: mm10
Supplementary files format and content: The txt file named gene_fpkm_all.txt contains FPKM data for all samples.

source_name: brain

extract_protocol:
RNA-seq was performed at Beijing Novozymes Co including library preparation, fragmentation, and PCR enrichment of target mRNA according to strand-specific protocols. RNA integrity was assessed using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA).
Total RNA was used as input material for the RNA sample preparations. Briefly, mRNA was purified from total RNA using poly-T oligo-attached magnetic beads. Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H. Remaining overhangs were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, Adaptor with hairpin loop structure were ligated to prepare for hybridization. In order to select cDNA fragments of preferentially 370-420 bp in length, the library fragments were purified with AMPure XP system. Then PCR was performed with Phusion High-Fidelity DNA polymerase, Universal PCR primers and Index (X) Primer. At last, PCR products were purified (AMPure XP system) and library quality was assessed on the Agilent Bioanalyzer 2100 system.

value: brain

value: AD

value: High P


title: WT_day9_iNs_AraC_chr19_amplicon_seq

description: Library name: Sample 12

source_name: iPSC-derived i3Neurons


title: 48-hour treatment of HUVECs with APOE rep1

description:
Library name: APOE1
exp1.txt


title: AD, High P, brain, 4

description: Library name: AD High P 4


title: Subject_L, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day0


title: Subject_B, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day28


title: AD, High P, brain, 2

description: Library name: AD High P 2


title: WT_day9_iNs_NT_chr19_amplicon_seq

description: Library name: Sample 11


title: Subject_B, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day0


title: 48-hour treatment of HUVECs with DMSO rep3

description:
Library name: DMSO3
exp1.txt

value: DMSO


title: 48-hour treatment of HUVECs with DMSO rep2

description:
Library name: DMSO2
exp1.txt


title: WT_day9_iNs_AraC_chr17_amplicon_seq

description: Library name: Sample 10


title: AD, High P, brain, 1

description: Library name: AD High P 1


title: WT_day9_iNs_NT_chr17_amplicon_seq

description: Library name: Sample 9


title: AD, Low P, brain, 4

description: Library name: AD Low P 4

value: Low P


title: WT_day9_iNs_AraC_chr9_amplicon_seq

description: Library name: Sample 8


title: 48-hour treatment of HUVECs with DMSO rep1

description:
Library name: DMSO1
exp1.txt


title: AD, Low P, brain, 5

description: Library name: AD Low P 5


title: 293T, HA-ATXN1::DUX4 delAXH, replicate 1 (February 2025 Dataset)

city: San Francisco

first: Ross

last: Okimoto

address: 513 Parnassus Ave

institute: University of California, San Francisco

description: Library name: C1

data_processing:
FASTQ files were aligned to GRCh38 using STAR (version 2.7.11b).
Gene counts were extracted during alignment using STAR parameter --quantMode GeneCounts
Differental expression analysis was performed in R (version 4.2.2) with edgeR (version 3.40.2).
Log2(cpm) data were obtained from TMM-normalized data using edgeR with the cpm function (log = T) which with this version of edgeR adds an average prior count of 2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file, STAR gene counts for all samples, data taken from column 4 of STAR output due to the strandedness of the library prep kit used. File name = counts_Feb2025.txt
Supplementary files format and content: Tab-delimited text file, log2(counts per million) measurements for all samples after edgeR processing. File name = logcpm_Feb2025.txt

growth_protocol: 293T cells were maintained in DMEM (high glucose, +L-Glutamine, +Sodium Pyruvate) with 10% fetal bovine serum (FBS) and 1% Pen-Strep (100 U/mL Penicillin, 100 ug/mL Streptomycin) at 37C in a 5% CO2 humidified incubator.

extract_protocol:
RNA was harvested with the Qiagen RNeasy Mini kit including on-column DNAse digestion with additional purification using the Monarch Spin RNA Cleanup Kit (NEB).
Libraries were constructed by Novogene by polyA-enriching RNA and then using the NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (NEB).

treatment_protocol: 293T cells were reverse transfected with plasmids encoding no (empty vector) or the described inserts using Fugene 6 and Opti-MEM. 500,000 cells per condition were transfected on separate days for separate replicates, and RNA was harvested approximately 48 hours later.

value: human embryonic kidney

tag: genetic modification

value: HA-ATXN1::DUX4 delAXH overexpression


title: 293T, HA-ATXN1::DUX4 delAXH, replicate 2 (February 2025 Dataset)

description: Library name: C2


title: Subject_B, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day0


title: Subject_B, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day2


title: WT_day9_iNs_AraC_chr6_amplicon_seq

description: Library name: Sample 6

value: iPSC-derived i3Neurons


title: 293T, HA-ATXN1::DUX4, replicate 2 (February 2025 Dataset)

description: Library name: B2

value: HA-ATXN1::DUX4 overexpression


title: Subject_A, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: 293T, HA-ATXN1::DUX4, replicate 1 (February 2025 Dataset)

description: Library name: B1


title: U3, UUO kidneys

city: Fuzhou

first: Zhimin

address: Chazhong Road NO.20

institute: the First Affiliated Hospital, Fujian Medical University, Fuzhou

description: Library name: Sample 1

data_processing:
The gel beads and the oil droplets are ruptured and PCR amplification was performed using the generated cDNA as a template. The products of all GEMs were mixed and a standard sequencing library is constructed. The cDNA was first enzymatically digested into fragments of about 200 – 300 base pairs (bp), together with the library building process of traditional second-generation sequencing such as sequencing junction and primers. Finally the DNA library was generated by PCR amplification.
Cell capture was performed using the official library kit (10X Genomics Chromium Single-Cell 3' kit, V3) according to manufacturer’s instructions.
Assembly: GRCm38
Supplementary files format and content: U3-matrix-data.txt

source_name: kidney

growth_protocol: C57BL/6 mice (8 – 10 weeks, 22 – 26 g, male) were obtained from the pathogen-free (SPF) facility of Fujian Medical University. All animal experiments were approved by the Laboratory Animal Management and Ethics Committee of Fujian Medical University and were performed in accordance with the "China Guide for the Protection and Use of Laboratory Animals". All mice were housed in a specific pathogen-free facility with a 12-hour light/dark cycle.

extract_protocol:
Harvested cells at the required densities were combined with gel beads containing the barcoded information along with a mixture of cells and enzymes. Oil surfactant droplets in a microfluidic "double-cross" system were used for encapsulation to generate Gel Beads-In-Emulsions (GEMs). GEMs were passed through a reservoir and collected while the gel beads were lysed to release the barcode sequence. The cDNA fragment was then reverse transcribed before the sample was labeled.
10X Genomics Chromium protocol

treatment_protocol: Kidneys were placed on ice-cold Dulbecco’s phosphate buffered saline (DPBS), debrided, cut longitudinally, and coronally sectioned. The renal pelvis portion of the kidney was then excised with a sterile razor, and the remaining tissue was washed in a 6 cm Petri dish with 1×DPBS to remove residues such as blood stains. Subsequently, the tissue was sheared to a size of 5×5 mm3. The cleaned samples were then transferred to 5 mL centrifuge tubes with 1×DPBS and placed on ice to rapidly shear the tissues to 1 – 3 mm3. Next, 10 times the volume of 1×DPBS was added to the sheared tissues which were cleaned by gentle blowing with a Pap sieve five times, and collected by filtering through a 70 μm cell sieve. The collected tissues were transferred into the prepared digestive enzyme solution (collagen II 2 mg/mL, collagen IV 2 mg/mL) and incubated for 30 min at 37 ℃, 100 rpm; the dissociated solution mixed with tissues and cells was transferred into 2 – 3 times the volume of 1×DPBS, washed by blowing with a Bass pipette and passed through a 40 μm cell sieve before the filtrate was collected. The filtered cell suspension was centrifuged at 300 g for 5 min at 12 °C. The supernatant was discarded and the remaining cells were collected. Any erythrocytes remaining in the cell fractions were removed by lysis in erythrocyte lysate for 3 – 10min. Subsequently, the precipitate was resuspended in 1×DPBS using 10 times the volume of cell suspension used in the previous step, washed 1 – 2 times, centrifuged again as previously described (300 g at 12 °C for 5 min). Cell densities were adjusted to 700 – 1200 cells/μL with 1640 (+5% (v/v) fetal bovine serum (FBS)) before analysis.

value: kidney

value: UUO


title: AD, Low P, brain, 2

description: Library name: AD Low P 2


title: WT_day9_iNs_NT_chr9_amplicon_seq

description: Library name: Sample 7

value: Neurons

value: NT


title: AD, High P, brain, 3

description: Library name: AD High P 3


title: AD, Low P, brain, 3

description: Library name: AD Low P 3


title: Subject_B, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day8


title: WT_day9_iNs_NT_chr6_amplicon_seq

description: Library name: Sample 5


title: AD, Low P, brain, 1

description: Library name: AD Low P 1


title: 293T, empty vector, replicate 2 (February 2025 Dataset)

description: Library name: A2

value: empty vector transfected


title: Subject_A, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day0


title: AD, Veh, brain, 5

description: Library name: AD Veh 5

value: Veh


title: WT_day9_iNs_AraC_chr4_amplicon_seq

description: Library name: Sample 4

value: AraC treatment for 3 days


title: WT_day9_iNs_NT_chr4_amplicon_seq

description: Library name: Sample 3

value: WT


title: Subject_A, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28

value: breast milk lymphocyte (BML)


title: AD, Veh, brain, 4

description: Library name: AD Veh 4

value: brain

value: AD


title: Subject_B, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day28


title: 293T, HA-CIC::LEUTX, replicate 3

description: Library name: G3

data_processing:
FASTQ files were aligned to GRCh38 using STAR (version 2.7.11b).
Gene counts were extracted during alignment using STAR parameter --quantMode GeneCounts
Differental expression analysis was performed in R (version 4.2.2) with edgeR (version 3.40.2).
Log2(cpm) data were obtained from TMM-normalized data using edgeR with the cpm function (log = T) which with this version of edgeR adds an average prior count of 2.
Assembly: GRCh38
Supplementary files format and content: Tab-delimited text file, STAR gene counts for all samples, data taken from column 4 of STAR output due to the strandedness of the library prep kit used. File name = counts_May2024.txt
Supplementary files format and content: Tab-delimited text file, log2(counts per million) measurements for all samples after edgeR processing. File name = logcpm_May2024.txt

treatment_protocol: 293T cells were reverse transfected with plasmids encoding no (empty vector) or the described inserts using Fugene 6 and Opti-MEM. 300,000 cells per condition were transfected on separate days for separate replicates, and RNA was harvested approximately 48 hours later.

value: HA-CIC::LEUTX overexpression


title: Subject_A, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day8


title: AD, Veh, brain, 3

description: Library name: AD Veh 3


title: Subject_A, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day2


title: WT_day9_iNs_AraC_chr1_amplicon_seq

description: Library name: Sample 2


title: Subject_A, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day0


title: AD, Veh, brain, 2

description: Library name: AD Veh 2


title: 293T, HA-CIC::LEUTX, replicate 2

description: Library name: G2


title: WT_day9_iNs_NT_chr1_amplicon_seq

description: Library name: Sample 1


title: Subject_P, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day28


title: AD, Veh, brain, 1

description: Library name: AD Veh 1


title: 293T, HA-CIC(ex18)::NUTM1(ex3), replicate 2

description: Library name: F2

value: HA-CIC(ex18)::NUTM1(ex3) overexpression


title: 293T, HA-CIC(ex18)::NUTM1(ex3), replicate 3

description: Library name: F3

value: human embryonic kidney


title: WT, High P, brain, 4

description: Library name: WT High P 4

value: High P


title: WT, High P, brain, 5

description: Library name: WT High P 5


title: Subject_P, live attenuated influenza vaccine (LAIV), peripheral blood mononuclear cells (PBMC), Day0


title: 293T, HA-CIC(ex20)::NUTM1(ex6) E mutant, replicate 3

description: Library name: E3

value: HA-CIC(ex20)::NUTM1(ex6) E mutant overexpression


title: WT, High P, brain, 3

description: Library name: WT High P 3


title: 293T, HA-CIC(ex18)::NUTM1(ex3), replicate 1

description: Library name: F1


title: Subject_P, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day8


title: Subject_P, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day28


title: 293T, empty vector, replicate 1 (February 2025 Dataset)

description: Library name: A1


title: 293T, HA-CIC(ex20)::NUTM1(ex6) E mutant, replicate 2

description: Library name: E2


title: Subject_P, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day2


title: Subject_P, live attenuated influenza vaccine (LAIV), breast milk lymphocyte (BML), Day0


title: 293T, HA-CIC(ex20)::NUTM1(ex6) E mutant, replicate 1

description: Library name: E1


title: WT, High P, brain, 1

description: Library name: WT High P 1


title: 293T, HA-CIC(ex20)::NUTM1(ex6) dTAD, replicate 3

description: Library name: D3


title: WT, Veh, brain, 5

description: Library name: WT Veh 5


title: Subject_E, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day0


title: Subject_E, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day28


title: WT, Veh, brain, 4

description: Library name: WT Veh 4


title: 293T, HA-CIC::LEUTX, replicate 1

description: Library name: G1


title: 293T, HA-CIC(ex20)::NUTM1(ex6) dTAD, replicate 1

description: Library name: D1


title: Subject_E, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day28


title: Subject_E, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day2


title: 293T, HA-CIC(ex20)::NUTM1(ex6), replicate 2

description: Library name: C2

value: HA-CIC(ex20)::NUTM1(ex6) overexpression


title: WT, Veh, brain, 1

description: Library name: WT Veh 1


title: Subject_E, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day0


title: WT, High P, brain, 2

description: Library name: WT High P 2


title: WT, Veh, brain, 3

description: Library name: WT Veh 3


title: 293T, HA-CIC(ex20)::NUTM1(ex6), replicate 3

description: Library name: C3


title: Subject_E, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day8


title: 293T, HA-CIC(ex20)::NUTM1(ex6), replicate 1

description: Library name: C1


title: 293T, HA-CIC::DUX4, replicate 3

description: Library name: B3

value: HA-CIC::DUX4 overexpression


title: Subject_F, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day28


title: Subject_F, trivalent inactivated influenza vaccine (TIV), peripheral blood mononuclear cells (PBMC), Day0


title: 293T, HA-CIC::DUX4, replicate 2

description: Library name: B2


title: Costim GFP

city: St. Louis

first: Macee

last: Owen

state: MO

address: 660 S Euclid

institute: Washington University School of Medicine

description:
Library name: 4_Macee
MO1_postQC.rds

data_processing:
Alignment with Cell Ranger V6
QC and Filtering with Seurat V4
Unsupervised Clustering with Seurat V4
Assembly: mm10
Supplementary files format and content: .rds objects

source_name: heart

extract_protocol: Chromium Single Cell 3ʹ Reagent v3.1 kit from 10X Genomics

value: heart

value: heart transplant


title: Subject_F, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day28


title: 293T, HA-CIC::DUX4, replicate 1

description: Library name: B1


title: WT, Veh, brain, 2

description: Library name: WT Veh 2


title: Subject_F, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day8


title: CSA GFP

description:
Library name: 2_Macee
MO1_postQC.rds


title: IRF8

description:
Library name: IRF8
MO2_postQC.rds


title: 293T, empty vector, replicate 3

description: Library name: A3


title: Costim myeloid

description:
Library name: 3_Macee
MO1_postQC.rds


title: WT

description:
Library name: WT
MO2_postQC.rds


title: 293T, HA-CIC(ex20)::NUTM1(ex6) dTAD, replicate 2

description: Library name: D2


title: 293T, empty vector, replicate 2

description: Library name: A2


title: Subject_F, trivalent inactivated influenza vaccine (TIV), breast milk lymphocyte (BML), Day0


title: CSA myeloid

description:
Library name: 1_Macee
MO1_postQC.rds


title: 293T, empty vector, replicate 1

description: Library name: A1