title: seedling OE, mock, rep2

status: Public on Feb 20 2025

city: Hannover

first: Maximilian

last: Fuchs

address: Carl-Neuberg-Str. 1

department: IMTTS

institute: Hanover Medical School

hyb_protocol: 1.65 ug of Cy3-labelled cRNA (specific activity >8.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Arabidopsis Genome Oligo Microarrays for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: Slides were scanned on the Agilent DNA Microarray Scanner using one color scan setting for 1x44k array slides (Scan Area 61x21.6 mm, XDR, Scan resolution 5 µm, Dye channel is set to Green and Green PMT is set to 100%).

data_processing:
The scanned images were analyzed with feature extraction software package (v11.5.1.1/ Agilent Technologies) using default parameters (protocol GE1_1105_Oct12 and Grid: 012391_D_20060331) to obtain background subtracted and spatially detrended Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.
Background correction and normalization were carried out using the limma package, with quantile normalization applied to ensure consistency across arrays

organism: Arabidopsis thaliana

source_name: seedling OE, mock

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Hilden, GER).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

growth_protocol: plants were grown in liquid MS medium containing 3% sucrose under 9 h light/15 h dark with gentle shaking

extract_protocol: RNA extraction was performed using Nucleozol (Machery and Nagel) and purified using the RNeasy Plant kit (Qiagen, Hilden, GER) according to the manufacturer's instructions.

treatment_protocol: 11 d old seedlings were treated with 75 µM prostaglandin A1 or mock and harvested after 4 h

value: seedlings

value: over expressor

value: mock


title: EV3686, Oxaliplatin

type: SRA

city: Tokyo

first: Atsushi

last: Sakai

address: 1-1-5 Sendagi, Bunkyo-ku

country: Japan

institute: Nippon Medical School

description: Library name: Sample24

library_source: transcriptomic

data_processing:
Read data were analyzed using BaseSpace Sequence Hub (Illumina). The reads were aligned to the human genome (hg38) using RNAseq alignment and then gene expression was quantified using Cufflinks Assembly & DE.
Assembly: hg38
Supplementary files format and content: Excel files include values for TPM, fold change and statistics

molecule: total RNA

organism: Homo sapiens

source_name: EV

extract_protocol:
Total RNA was extracted using RNAiso plus (Takara Bio).
For cell samples, a strand-specific cDNA library was synthesized using an NEB Next Ultra Directional RNA Kit from Illumina (New England Biolabs). For EV samples, a strand-specific cDNA library was synthesized using an NEB Next Ultra II Directional RNA Kit from Illumina (New England Biolabs).

treatment_protocol: 7 days treatment with oxaliplatin (0.1 ug/ml)

tag: tissue

value: EV

tag: cell line

tag: cell type

value: Primary sensory neuron

tag: treatment

value: Oxaliplatin


title: EV3382, Oxaliplatin

description: Library name: Sample22


title: EV3681, Oxaliplatin

description: Library name: Sample23


title: EV2490, Oxaliplatin

description: Library name: Sample21


title: EV1005, Oxaliplatin

description: Library name: Sample19


title: seedling OE, PGA, rep2

type: RNA

country: Germany

source_name: seedling OE, PGA

tag: genotype

value: prostaglandin A1


title: EV1231A, Oxaliplatin

description: Library name: Sample20


title: seedlings mutant2, PGA, rep3

source_name: seedlings mutant2, PGA

value: EMS mutant


title: seedling OE, mock, rep1


title: seedling OE, mock, rep3


title: Col-0 seedlings, PGA, rep3

source_name: Col-0 seedlings, PGA

value: wild type


title: seedlings mutant2, mock, rep1

source_name: seedlings mutant2, mock


title: mutant seedlings, mock, rep3

source_name: mutant seedlings, mock

value: T-DNA insertion mutant


title: mutant seedlings, PGA, rep3

source_name: mutant seedlings, PGA


title: mutant seedlings, PGA, rep1


title: mutant seedlings, mock, rep1


title: seedling OE, PGA, rep3


title: Col-0 seedlings, PGA, rep1


title: Col-0 seedlings, mock, rep2

source_name: Col-0 seedlings, mock


title: mutant seedlings, PGA, rep2


title: Col-0 seedlings, mock, rep1


title: mutant seedlings, mock, rep2


title: Col-0 seedlings, PGA, rep2


title: seedlings mutant2, mock, rep2


title: seedlings mutant2, PGA, rep1


title: seedlings mutant2, mock, rep3


title: seedlings mutant2, PGA, rep2


title: seedling OE, PGA, rep1


title: Col-0 seedlings, mock, rep3


title: EV3382, Control

description: Library name: Sample16

value: Control


title: EV3681, Control

description: Library name: Sample17


title: EV3686, Control

description: Library name: Sample18


title: EV2490, Control

description: Library name: Sample15


title: Cell3681, Oxaliplatin

description: Library name: Sample11

source_name: Cell

value: Cell


title: EV1005, Control

description: Library name: Sample13


title: Cell3382, Oxaliplatin

description: Library name: Sample10


title: Cell2490, Oxaliplatin

description: Library name: Sample9


title: Cell1231A, Oxaliplatin

description: Library name: Sample8


title: Cell3681, Control

description: Library name: Sample5


title: Cell3382, Control

description: Library name: Sample4


title: Cell1005, Oxaliplatin

description: Library name: Sample7


title: Cell3686, Control

description: Library name: Sample6


title: Cell2490, Control

description: Library name: Sample3


title: Cell1231A, Control

description: Library name: Sample2


title: Cell1005, Control

description: Library name: Sample1


title: Sri Lankan CL lesion, 48i

city: York

first: Paul

middle: M

last: Kaye

state: North Yorkshire

address: University of York, Heslington

country: United Kingdom

institute: Hull York Medical School, University of York

description:
Library name: 61_48i
10x Visium for FFPE spatial transcriptomics

data_processing:
Raw sequencing data was used to generate FASTQ files using default settings
Spatial 3' v1 chemistry using spaceranger-1.3.0 was used to align reads to GrCh38-2020-A genome using the Visium Human Transcriptome Probe Set to obtain gene expression matrices
Assembly: GRCh38-2020-A
Supplementary files format and content: .h5: Feature barcode matrices file in the HDF5 format
Supplementary files format and content: _detected_tissue_image.jpg: Image showing spots over tissue section
Supplementary files format and content: _scalefactors_json.json: Json file for scalefactors
Supplementary files format and content: _tissue_hires_image.png: tissue section image in high resolution
Supplementary files format and content: _tissue_lowres_image.png: tissue section image in low resolution
Supplementary files format and content: _tissue_positions_list.csv: spatial barcodes and their xy co-ordinates on tissue
Library strategy: Spatial Transcriptomics

molecule: polyA RNA

source_name: Skin

extract_protocol:
Biopsies were formalin-fixed and embedded in paraffin. 5μm sections were cut with a microtome and placed on 10x Visium spatial transcriptomics slide
Manufacturer's instructions (10x Visium for FFPE) were followed to prepare sequencing libraries

value: Skin

value: Clinical infection


title: Sri Lankan CL lesion, 47i

description:
Library name: 59_47i
10x Visium for FFPE spatial transcriptomics


title: Sri Lankan CL lesion, 53i

description:
Library name: 054_53i
10x Visium for FFPE spatial transcriptomics


title: Sri Lankan CL lesion, 40i

description:
Library name: 59_40i
10x Visium for FFPE spatial transcriptomics


title: Sri Lankan CL lesion, 30i

description:
Library name: 59_30i
10x Visium for FFPE spatial transcriptomics


title: Sri Lankan CL lesion, 35i

description:
Library name: 59_35i
10x Visium for FFPE spatial transcriptomics


title: Indian PKDL lesion, 575

description:
Library name: 059_575
10x Visium for FFPE spatial transcriptomics


title: Brazilian CL lesion, 010

description:
Library name: 78_010
10x Visium for FFPE spatial transcriptomics


title: Brazilian CL lesion, 002

description:
Library name: 78_002
10x Visium for FFPE spatial transcriptomics


title: Brazilian CL lesion, 009

description:
Library name: 78_009
10x Visium for FFPE spatial transcriptomics


title: Indian PKDL lesion, 543

description:
Library name: 77_543
10x Visium for FFPE spatial transcriptomics


title: Cell3686, Oxaliplatin

description: Library name: Sample12


title: EV1231A, Control

description: Library name: Sample14


title: shTFRC-rIgG-3

city: Beijing

first: Qizhi

last: Wang

address: Chaoyang District

country: China

institute: Chinese Academy of Sciences

description:
Library name: shTFRC-rIgG-3
shTFRC_rIgG.bw

library_source: genomic

data_processing:
Low quality sequencing reads and adapters were removed by Trim Galore
All clean reads were aligned to human hg38 genome using Bowtie2
Multiple mapped reads and PCR duplicates were removed to generate uniquely mapped reads by JAVA picard MarkDuplicates
Assembly: hg38
Supplementary files format and content: bw
Library strategy: CUT&Tag

molecule: genomic DNA

extract_protocol:
For each sample, 1×105 cells were harvested and the nucleus were isolated with nuclear extraction buffer according to the manufacturer of Hyperactive Universal CUT&Tag Assay Kit of Illumina
Add N5 and N7 connectors, establish and amplify the library using PCR

tag: antibody

value: rIgG


title: shTFRC-rIgG-2

description:
Library name: shTFRC-rIgG-2
shTFRC_rIgG.bw


title: shTFRC-rIgG-1

description:
Library name: shTFRC-rIgG-1
shTFRC_rIgG.bw


title: shTFRC-TfR1-3

description:
Library name: shTFRC-TfR1-3
shTFRC_TfR1.bw


title: shTFRC-TfR1-2

description:
Library name: shTFRC-TfR1-2
shTFRC_TfR1.bw


title: shTFRC-TfR1-1

description:
Library name: shTFRC-TfR1-1
shTFRC_TfR1.bw


title: scARC library, group 49, 6hr_GEX

city: Evanston

first: Jubao

last: Duan

state: IL

address: 1001 University Place

department: Center for Psychiatric Genetics

country: USA

institute: NorthShore University HealthSystem

description:
Library name: GEX_scARC_Library_49_6
Library 49, 6 hr post stimulation, contains cell lines CD0000049, CD000058, CD000032, CD000061

library_source: transcriptomic single cell

data_processing:
10x Genomics Chromium single cell Multiome sequencing libraries were sequenced at UMGC on Novaseq S4 platform targeting pair-end (2 x 150bp) 50k reads per nuclei for ATAC library and 25K reads per nuclei for gene expression library. Briefly, after raw data collection, Illumina’s BCL2FASTQ software was used to de-multiplex and assemble the fastq files corresponding to reads (R1/R2) and indices (i5/i7) for Cell Ranger ARC. The fastq files were subsequently processed by 10x Genomics Cell Ranger ARC (v2.0.2) and aligned twice to both the human GRCh38.p14 genome and a contingent of human GRCh38.p14 and mouse GRCm38 provided by 10x Genomics for efficient identification and removal of rodent astrocytes. For snATAC-seq, the per-library Transcription Start Sites (TSS) enrichment score is usually between 7-9 and the Fraction of high-quality Reads overlapping Peaks (FRiP) is usually between 40%-80%. We excluded cells with >15% of the reads mapped to mitochondrial genes, cells with > 8,000 or < 400 number of features, and cells with > 40,000 or <500 number of UMI counts (filtered by 400 < nCount < 8,000 using Seurat).
For each library that contains cells derived from 3-4 iPSC lines, barcode-level identification was performed separately for snRNA-seq (GEX) and snATAC-seq data with genotyping information of all donors. Briefly, the BAM files generated from GEX and ATAC assays (gex_possorted_bam.bam and atac_possorted_bam.bam) were processed by demuxlet (Kang et al., 2018) with known genotype information provided as .vcf files. Barcodes (cells) identified as singlets with P1 likelihood (p1LLK) < 1x10-8 were collected, and only barcodes positively identified in both GEX and ATAC assays were retained for downstream analysis.
snRNA-seq (GEX) data were processed by extracting gene expression data from the .h5 files generated by Cell Ranger ARC. Only barcodes (cells) confidently assigned to individual iPSC lines were retained. With Seurat 5.1.0(Hao et al., 2024), for cell type assignmentsTo assign cell type identity, Leiden clustering was performed at the library level based on the first 30 PCs (or appropriate as determined by the elbowplot) and subsequently by comparing cell clusters and their marker gene expressions (GAD1, GAD2, SLC17A6, SLC17A7, NEFM) and added as metadata. The library-level gene expression matrices were subsequently collated in Seurat 5.1.0(Hao et al., 2024) as one large object with cell line-specific metadata assigned. Harmony (Korsunsky et al., 2019) was used to integrate the library-level gene matrices and removed sequencing batch-derived effects.
For snATAC-seq data, the aggregation function of Cell Ranger ARC was used to merge and generate new fragment files for MACS2-based peak calling with the CallPeaks() function in Signac(Stuart et al., 2021) with default settings. We made two merged fragment files, one containing all libraries from batch 024 (18 cell lines) and the other from batch 018, 024, 025, and 029 (76 cell lines). From each fragment file, we iterated througugh the combinations of cell types (NEFM+ glut, NEFM- glut, GABA) and stimulation stages (0 hr, 1 hr, 6 hr), which generated nine peak sets (cell type x time). We further generated a union peak set from batch 024 by setting CallPeaks(combine.peaks = TRUE) for peak analysis across different cell types. Finally, peaks that fell within the ENCODE blacklisted regions were removed. We also removed peaks that fall within chromosomes X and Y and the mitochondrial genome regions.
Assembly: hg38/GRCh38
Supplementary files format and content: CellRanger 2.0.2 output directory sans .bam files
Supplementary files format and content: h5, count matrices snATAC and snRNA-seq
Supplementary files format and content: .cloupe, 10x Genomics Loupe data file

source_name: Neuron

growth_protocol: We differentiated iPSC lines into both excitatory and inhibitory neurons and co-cultured with rate glial cells. For excitatory neuron differentiation, we used the method to derive Ngn2-glutamatergic neuron {Zhang, 2013 #6824}  with minor modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 5 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor, together with appropriate amount of rtTA virus and Ngn2-puro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. On DIV2 - DIV4, cells were treated with neural culture media (Neuralbasal media with 1x B27Plus and 1x Glutamax) supplemented with 2g/ml puromycin, 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, puromycin was withdrawn and cells were treated with neural culture media with 2ug/ml doxycycline. On DIV7, cells would be ready for replating. For generating excitatory neurons, we used the method to derive Ascl1/Dlx2-GABAergic neurons {Yang, 2017 #7817} with minopr modifications. On DIV0, 60-80% confluent iPSCs were dissociated into single cells using accutase and replated into Matrigel-coated 6-w plate at 7 x 105 cells per well in mTeSRPlus media with 5M ROCK inhibitor together with rtTA virus, Ascl1-puro virus and Dlx2-hygro virus. On DIV1, media was refreshed with mTeSRplus containing 5M ROCK inhibitor and 2g/ml doxycycline. From DIV2 - DIV4, cells were treated with neural culture media supplemented with 2g/ml puromycin, 150g/ml hygromycin and 2g/ml doxycycline to remove non-transduced cells. On DIV5 - DIV6, cells were treated with neural culture media with 2g/ml doxycycline and 2M AraC. Cells would be ready for replating on DIV7. To co-culture the excitatory and inhibitory neurons,  on DIV7, separately cultured Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and primary rat cortical astrocytes (Thermofisher; N7745100) were dissociated using accutase at 37C for 15-20min. Ngn2-glutamatergic neurons, Ascl1/Dlx2-GABAergic neurons and astrocytes were replated at 5:5:1 ratio onto Matrigel pre-coated 12-well plate in neural culture media supplemented with 2g/ml doxycycline, 10ng/ml BDNF, 10ng/ml GDNF, 10ng/ml NT-3 and 1% FBS. For each co-culture,  we pooled cells from 3-4 donor lines with equal proportion. On DIV8, we refilled cells with more media. From DIV9 – DIV33, media was refreshed every three days with half volume change. Doxycycline was withdrawn at DIV14 and 1uMµM AraC was added in the media from DIV8-DIV17 to ensure neuron purity. DIV33 neurons were used for KCI stimulation.

extract_protocol:
After stimulation, cells were briefly washed with 1x PBS and dissociated in accutase at 37C for 40min with gentle shaking. After accutase incubation, we pipetted cells multiple times and filtered suspension twice with 40m tip filter (Sigma# BAH136800040-50EA) to obtain single cells. The washed cells were subjected to fresh nuclei isolation following 10x Genomics’ protocols (CG000365 and CG000338). For each library, around 15,000 freshly isolated nuclei were loaded for GEM capture targeting 10,000 nuclei recovery.
The pre-amplified DNAs (for snATAC-seq) and cDNAs (for snRNA-seq) were shipped to University of Minnesota Genomics Center  (UMGC) for sn-multiomics sequencing library construction following 10x Genomics’ standard protocol.

treatment_protocol: To model neuron activation, we followed previously used protocol to treat the cells with KCI {Boulting, 2021 #8234}. Briefly, 24hr before stimulation, old media was aspirated and DIV33 neuron co-culture were silenced in neural culture media supplemented with 1M TTX and 100M DL-AP5. The next day, we added fresh culture media with warmed depolarization solution (10mM HEPES, 170mM KCl, 1mM MgCl2, 2mM CaCl2) to initiate KCI stimulation. We prepared three conditions with different treatment duration (0hr, 1hr and 6hr). After stimulation, cells were dissociated for 10x Genomics’ sn-Multiomics sequencing library preparation.

value: Neuron

value: cultured glutamatergic and GABAergic neurons derived from iPS cells

tag: batch


title: scARC library, group 49, 1hr_GEX

description:
Library name: GEX_scARC_Library_49_1
Library 49, 1 hr post stimulation, contains cell lines CD0000049, CD000058, CD000032, CD000061


title: scARC library, group 49, 0hr_GEX

description:
Library name: GEX_scARC_Library_49_0
Library 49, unstimulated, contains cell lines CD0000049, CD000058, CD000032, CD000061


title: scARC library, group 44, 6hr_GEX

description:
Library name: GEX_scARC_Library_44_6
Library 44, 6 hr post stimulation, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: scARC library, group 44, 1hr_GEX

description:
Library name: GEX_scARC_Library_44_1
Library 44, 1 hr post stimulation, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: scARC library, group 44, 0hr_GEX

description:
Library name: GEX_scARC_Library_44_0
Library 44, unstimulated, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: scARC library, group 39, 6hr_GEX

description:
Library name: GEX_scARC_Library_39_6
Library 39, 6 hr post stimulation, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: scARC library, group 39, 1hr_GEX

description:
Library name: GEX_scARC_Library_39_1
Library 39, 1 hr post stimulation, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: Brazilian CL lesion, 006

description:
Library name: 78_006
10x Visium for FFPE spatial transcriptomics


title: scARC library, group 39, 0hr_GEX

description:
Library name: GEX_scARC_Library_39_0
Library 39, unstimulated, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: scARC library, group 36, 6hr_GEX

description:
Library name: GEX_scARC_Library_36_6
Library 36, 6 hr post stimulation, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: scARC library, group 22, 1hr_GEX

description:
Library name: GEX_scARC_Library_22_1
Library 22, 1 hr post stimulation, contains cell lines CD0000022, CD000037, CD000023, CD000040


title: scARC library, group 22, 6hr_GEX

description:
Library name: GEX_scARC_Library_22_6
Library 22, 6 hr post stimulation, contains cell lines CD0000022, CD000037, CD000023, CD000040


title: scARC library, group 36, 0hr_GEX

description:
Library name: GEX_scARC_Library_36_0
Library 36, unstimulated, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: scARC library, group 36, 1hr_GEX

description:
Library name: GEX_scARC_Library_36_1
Library 36, 1 hr post stimulation, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: scARC library, group 49, 0hr_ATAC

description:
Library name: scARC_Library_49_0
Library 49, unstimulated, contains cell lines CD0000049, CD000058, CD000032, CD000061

library_source: genomic single cell


title: scARC library, group 44, 6hr_ATAC

description:
Library name: scARC_Library_44_6
Library 44, 6 hr post stimulation, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: scARC library, group 22, 0hr_GEX

description:
Library name: GEX_scARC_Library_22_0
Library 22, unstimulated, contains cell lines CD0000022, CD000037, CD000023, CD000040


title: scARC library, group 44, 0hr_ATAC

description:
Library name: scARC_Library_44_0
Library 44, unstimulated, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: scARC library, group 49, 6hr_ATAC

description:
Library name: scARC_Library_49_6
Library 49, 6 hr post stimulation, contains cell lines CD0000049, CD000058, CD000032, CD000061


title: scARC library, group 39, 6hr_ATAC

description:
Library name: scARC_Library_39_6
Library 39, 6 hr post stimulation, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: scARC library, group 39, 0hr_ATAC

description:
Library name: scARC_Library_39_0
Library 39, unstimulated, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: scARC library, group 36, 6hr_ATAC

description:
Library name: scARC_Library_36_6
Library 36, 6 hr post stimulation, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: scARC library, group 39, 1hr_ATAC

description:
Library name: scARC_Library_39_1
Library 39, 1 hr post stimulation, contains cell lines CD0000047, CD000039, CD000048, CD000042


title: scARC library, group 22, 6hr_ATAC

description:
Library name: scARC_Library_22_6
Library 22, 6 hr post stimulation, contains cell lines CD0000022, CD000037, CD000023, CD000040


title: scARC library, group 49, 1hr_ATAC

description:
Library name: scARC_Library_49_1
Library 49, 1 hr post stimulation, contains cell lines CD0000049, CD000058, CD000032, CD000061


title: scARC library, group 22, 0hr_ATAC

description:
Library name: scARC_Library_22_0
Library 22, unstimulated, contains cell lines CD0000022, CD000037, CD000023, CD000040


title: CON-3

city: Shanghai

first: Yang

last: Zheng

state: --- Select One ---

address: No.115, Jinzun Road, Pudong District

institute: Department of Oral and Maxillofacial-Head Neck Oncology, Shanghai Ninth People's Hospital

description:
Library name: Sample 5
RNAseq data for control

data_processing:
The original fluorescence image files obtained from Illumina platform are transformed to short reads (Raw data) by base calling and these short reads are recorded in FASTQ format, which contains sequence information and corresponding sequencing quality information.
Assembly: The reads were mapped to human reference genome (hg38) using STAR v2.7.10. Gene expression was quantified by cufflinks v2.2.1. The differential gene expression analysis was performed using limma package.
Supplementary files format and content: tab-delimited text file includes FPKM for all Sample

growth_protocol: HN4 cells were maintained in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal bovine serum (FBS), 100x penicillin/streptomycin, and incubated in a humidified atmosphere with 5% CO2 at 37°C.

extract_protocol:
TRIzol was used to isolate total RNA from samples. Ensure the RNA is of high quality by checking the RNA integrity number (RIN) using an Agilent Bioanalyzer.
RNA-seq profiling of FADD overexpression cells were conducted by standard Illumina TruSeq library preparation followed by Illumina sequencing using MiSeq.

treatment_protocol: HN4 cells were stably transfected with full-length FADD plasmids or control.

value: head and neck squamous cell carcinoma

value: CON


title: scARC library, group 44, 1hr_ATAC

description:
Library name: scARC_Library_44_1
Library 44, 1 hr post stimulation, contains cell lines CD0000057, CD000046, CD000044, CD000031


title: CON-1

description:
Library name: Sample 4
RNAseq data for control


title: scARC library, group 22, 1hr_ATAC

description:
Library name: scARC_Library_22_1
Library 22, 1 hr post stimulation, contains cell lines CD0000022, CD000037, CD000023, CD000040


title: OE-3

description:
Library name: Sample 3
RNAseq data for FADD overexpression

value: OE


title: OE-2

description:
Library name: Sample 2
RNAseq data for FADD overexpression


title: OE-1

description:
Library name: Sample 1
RNAseq data for FADD overexpression


title: KO-2

first: Amina

middle: Hospital Capital Medical

last: Saleem

state: Chaoyang

address: 2Anzhen Road

department: Pathology and Pathophysiology

institute: Capital Medical University

description: Library name: KO2

data_processing:
Use HISAT2 to align Clean Reads to the reference genome, obtaining positional information on the reference genome or genes, as well as sequence-specific characteristics of the sequencing sample.
This project utilizes the reference genome from the Ensembl database.
We converted the BAM files, obtained from aligning reads to the reference genome, into TDF format files recognizable by IGV. Through the IGV software, we visualized the distribution of reads across various chromosomes and displayed the distribution of functional regions annotated in the genome, such as exons, introns, and intergenic regions.
Assembly: GRCh38.109
Supplementary files format and content: fpkm.annot.xlsx

source_name: Cardioomyocytes

growth_protocol: C3H 10T1/2 mesenchymal cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). 1.3 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using SMARTER mRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Adipogenic differentiation was induced by treatment of 2-day post confluent cells (designated day 0, D0) with 10ug/ml insulin (Sigma).

value: Cardioomyocytes

value: Cardiomyocytes


title: KO-3

description: Library name: KO3


title: KO-1

description: Library name: KO1


title: WT-2

description: Library name: WT12


title: WT-1

description: Library name: WT11


title: SU-DIPG-XVII_vorinostat_H3K27me3_rep2

city: Tianjin

first: Yu

last: Kong

address: 22nd Qixiangtai Road

institute: Tianjin Medical University

data_processing:
ChIP-seq reads were aligned to the reference human genome assembly hg38 using Bowtie2 with default parameters. Low mapping quality reads (mapping quality < 20) and duplicates were discarded.
Signal tracks for each sample were generated using the MACS2 (v2.1.1.20160309) pile-up function and were normalized to 1 million reads (RPM).
Quantitation of enrichment of H3K27ac was determined by spike-in normalization of the mapped reads.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

source_name: SU-DIPG-XVII

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a BioRuptor sonicator (Diagenode).
The DNA Library of ChIP were prepared with a TruePrep DNA Library Prep Kit according to the manufacturer’s instructions (TD503, Vazyme).

value: SU-DIPG-XVII

value: H3F3A K27M

value: vorinostat


title: SU-DIPG-XVII_combine_H3K27me3_rep2


title: SU-DIPG-XVII_EC-8042_H3K27me3_rep2


title: SU-DIPG-XVII_EC-8042_H3K27me3_rep1


title: SU-DIPG-XVII_vorinostat_H3K27me3_rep1


title: SU-DIPG-XVII_combine_H3K27me3_rep1


title: SU-DIPG-XVII_control_H3K27me3_rep2

value: DMSO


title: SU-DIPG-XVII_control_H3K27me3_rep1


title: scARC library, group 36, 1hr_ATAC

description:
Library name: scARC_Library_36_1
Library 36, 1 hr post stimulation, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: SU-DIPG-XVII_SP1_rep2

data_processing:
CUT&Tag reads were first processed using TrimGalore (v0.4.4_dev) to trim adaptor and low-quality reads.
Trimmed reads were then aligned to the mouse genome build mm10 using bowtie2 (v2.4.2) with parameters --local --very-sensitive --no-mixed --no-discordant --phred33 -I 10 -X 700.
Low mapping quality reads (mapping quality < 30) and duplicates were discarded.
Biological replicates passed quality control were pooled together.
Heatmap, profile and signal tracks for each sample were generated using deeptools V3.5.1. ChIP-seq peaks were identified by MACS2.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)
Library strategy: CUT&Tag

extract_protocol:
Cells were wahed and harvested by wash buffer and incubated with activated beads. Then primary antibody was added, followed by Guinea Pig anti-Rabbit IgG antibody. After incubation, pA-Tn5 adapter complex was added. The purified DNA was amplified, then 200-1,000bp fragments were enriched for sequencing.
CUT&Tag libraries were prepared by Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyem, TD903-01 )


title: scARC library, group 36, 0hr_ATAC

description:
Library name: scARC_Library_36_0
Library 36, unstimulated, contains cell lines CD0000038, CD000043, CD000036, CD000045


title: SU-DIPG-IV_SP1_rep2

value: HIST1H3B K27M


title: SU-DIPG-XVII_SP1_rep1


title: SU-DIPG-IV_SP1_rep1


title: hPPC-180606_SP1_rep2

value: WT


title: hPPC-180606_SP1_rep1


title: SU-DIPG-XVII_H3K27me3_rep2


title: SU-DIPG-IV_H3K27me3_rep2


title: SU-DIPG-XVII_H3K27me3_rep1


title: SU-DIPG-IV_H3K27me3_rep1


title: hPPC-180606_H3K27me3_rep2


title: hPPC-180606_H3K27me3_rep1


title: SU-DIPG-XVII_combine_SP1_rep1


title: WT-3

description: Library name: WT13


title: SU-DIPG-XVII_vorinostat_SP1_rep1


title: SU-DIPG-XVII_combine_SP1_rep2


title: SU-DIPG-XVII_control_SP1_rep1


title: SU-DIPG-XVII_ATAC_rep2

data_processing:
ATAC-seq reads were trimmed using TrimGalore (v0.4.4_dev).
Normalized reads were aligned to the hg38 reference assembly using Bowtie2 v2.1.0. Peaks were defined using MACS2 (parameters: --nomodel -f BAMPE).
Peaks separated by fewer than 150 bp were merged. Differential peak calling was performed using the DESeq2 R package.
Chipseeker was employed for functional gene set analysis.
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

extract_protocol:
50,000 cells were used for ATAC-seq. After being washed by PBS, the cells were resuspended in lysis buffer.
After spinning down, the pellets of cells were resuspended in transposome mix. The reaction was incubated at 37℃ for 0.5 h in a PCR cycler, before 1 ml 0.5M EDTA, 1 ml proteinase K (20 mg/ml) and 5 ml 10% SDS were added to stop the reaction. After another incubation at 50℃ for 1 h, DNA was purified.


title: SU-DIPG-XIII_ATAC_rep2

source_name: SU-DIPG-XIII-FL

value: SU-DIPG-XIII-FL


title: SU-DIPG-XIII_ATAC_rep1


title: SU-DIPG-IV_ATAC_rep1

source_name: SU-DIPG-IV

value: SU-DIPG-IV


title: SU-DIPG-XVII_EC-8042_SP1_rep2


title: hPPC-180606_ATAC_rep2


title: SU-DIPG-XVII_EC8042-1_ATAC_rep2


title: hPPC-180606_ATAC_rep1


title: SU-DIPG-XVII_EC8042-1_ATAC_rep1


title: SU-DIPG-XVII_control-1_ATAC_rep2


title: SU-DIPG-XVII_EC-8042_rep2

data_processing:
Library construction and sequencing were carried out by Novogene.
RNA-seq reads were aligned to mouse genome build mm10 or human genome assembly hg38 using Hisat2 V2.1.0.
Expression levels for all RefSeq transcripts were quantified to fragment per kilobase million (FPKM) using StringTie v2.1.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

extract_protocol:
RNA was harvested using, 1 mg of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using  oligo -dT beads


title: SU-DIPG-XVII_control-1_ATAC_rep1


title: SU-DIPG-IV_EC-8042_rep1


title: SU-DIPG-IV_EC-8042_rep2


title: Human_FT_Non-BRCAm_C-23-8

city: Grand Rapids

first: Ian

last: Beddows

state: MI

address: 333 Bostwick

institute: Van Andel Institute

data_processing:
Expression counts from RNA-seq sequencing relied on a pipeline based on STAR and RSEM. Specifically, prior to alignment, reads were quality filtered using fastp with default settings 63. Next, reads were aligned to an rRNA reference using bwa with the putative rRNA mapped reads removed from downstream analyses 64. Using STAR, the remaining non-rRNA reads were mapped to the GRCh38.90 reference. We utilized the expected counts for genes from RSEM.
Assembly: hg38
Supplementary files format and content: level3_RNA_counts_N94.tsv contains raw gene/feature counts

source_name: Fallopian tube

extract_protocol:
Qiagen Allprep DNA/RNA FFPE kit following the manufacturer’s protocol for recovering total RNA, including small RNAs
500 ng of total RNA using the KAPA RNA HyperPrep Kit (Kapa Biosystems, Wilmington, MA USA). Ribosomal RNA material was reduced using the QIAseq FastSelect –rRNA HMR Kit (Qiagen, Germantown, MD, USA). RNA was sheared to 300-400 bp and was converted to cDNA. cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA)). Following adapter ligation, 8 cycles of PCR were performed.

value: Fallopian tube

value: Non-BRCAm

tag: race

value: White

tag: age at_time_of_surgery

tag: reason for_surgery

value: Benign Uterine

tag: reproductive status

value: Pre

value: D


title: Human_FT_Non-BRCAm_C-23-7


title: Human_FT_Non-BRCAm_C-23-6

value: Post


title: Human_FT_Non-BRCAm_C-23-5

value: Ovarian Cyst


title: Human_FT_BRCA1m_C-23-9

value: Risk Reduction


title: Human_FT_Non-BRCAm_C-23-3


title: SU-DIPG-XVII_vorinostat_SP1_rep2

value: SU-DIPG-XVII


title: Human_FT_Non-BRCAm_C-23-4


title: SU-DIPG-XVII_control_SP1_rep2

value: H3F3A K27M


title: SU-DIPG-XVII_EC-8042_SP1_rep1


title: SU-DIPG-XVII_ATAC_rep1


title: SU-DIPG-IV_ATAC_rep2


title: Human_FT_Non-BRCAm_C-23-18

value: Black

value: Pelvic mass


title: Human_FT_Non-BRCAm_C-23-17


title: Human_FT_Non-BRCAm_C-23-2


title: Human_FT_Non-BRCAm_C-23-13


title: Human_FT_Non-BRCAm_C-23-16


title: Human_FT_BRCA1m_C-23-12


title: Human_FT_Non-BRCAm_C-23-14


title: Human_FT_Non-BRCAm_C-23-15


title: Human_FT_Non-BRCAm_C-23-1


title: Human_FT_BRCA2m_C-21-96

value: Other

value: C


title: SU-DIPG-XVII_EC-8042_rep1


title: Human_FT_BRCA1m_C-21-94


title: Human_FT_BRCA2m_C-23-10


title: Human_FT_BRCA2m_C-21-95


title: Human_FT_BRCA2m_C-23-11


title: Human_FT_BRCA2m_C-21-90


title: Human_FT_BRCA2m_C-21-87


title: Human_FT_BRCA1m_C-21-89


title: Human_FT_BRCA1m_C-21-86


title: Human_FT_BRCA2m_C-21-85


title: Human_FT_BRCA2m_C-21-88


title: Human_FT_BRCA1m_C-21-83


title: Human_FT_BRCA2m_C-21-82


title: Human_FT_BRCA1m_C-21-84


title: Human_FT_Non-BRCAm_C-21-9

value: B


title: Human_FT_BRCA1m_C-21-79


title: Human_FT_BRCA2m_C-21-80


title: Human_FT_Non-BRCAm_C-21-8


title: Human_FT_BRCA1m_C-21-78


title: Human_FT_BRCA1m_C-21-75


title: Human_FT_BRCA2m_C-21-76


title: Human_FT_BRCA2m_C-21-73


title: Human_FT_BRCA1m_C-21-71


title: Human_FT_BRCA1m_C-21-70


title: Human_FT_Non-BRCAm_C-21-7


title: Human_FT_BRCA1m_C-21-72


title: Human_FT_BRCA2m_C-21-69


title: Human_FT_BRCA2m_C-21-68


title: Human_FT_BRCA1m_C-21-93


title: Human_FT_Non-BRCAm_C-21-65


title: Human_FT_Non-BRCAm_C-21-66

value: Cesarean Section


title: Human_FT_Non-BRCAm_C-21-64

value: Fallopian tube

value: Asian


title: Human_FT_BRCA1m_C-21-67

value: White


title: Human_FT_Non-BRCAm_C-21-62

value: Non-BRCAm

value: Tubal Sterilization


title: Human_FT_Non-BRCAm_C-21-61

value: Gender Affirmation

value: Pre


title: Human_FT_Non-BRCAm_C-21-57

value: Benign Uterine


title: Human_FT_Non-BRCAm_C-21-59


title: Human_FT_Non-BRCAm_C-21-58

value: Menorrhagia


title: Human_FT_Non-BRCAm_C-21-6

value: Post


title: Human_FT_Non-BRCAm_C-21-55


title: Human_FT_Non-BRCAm_C-21-52


title: Human_FT_Non-BRCAm_C-21-54

value: Ovarian Cyst


title: Human_FT_Non-BRCAm_C-21-53

value: Ovarian Serous Cystadenoma


title: Human_FT_Non-BRCAm_C-21-50

value: Black


title: Human_FT_Non-BRCAm_C-21-5

value: Endometriosis


title: Human_FT_Non-BRCAm_C-21-44

value: C


title: NC-01

first: Shaotian

last: Fu

address: Minghang

institute: sjtu

description:
Library name: sample 4
10x Genomics

data_processing:
Raw reads from scRNA-seq were processed to generate gene expression matrixes using CeleScope (https://github.com/singleron-RD/CeleScope) v1.9.0 pipeline. Briefly, raw reads were first processed with CeleScope to remove low quality reads with Cutadapt v1.17 (Ref) to trim poly-A tail and adapter sequences. Cell barcode and UMI were extracted. After that, we used STAR v2.6.1a (Ref) to map reads to the reference genome GRCm38 (ensembl version 92 annotation). UMI counts and gene counts of each cell were acquired with featureCounts v2.0.1 (Ref) software, and used to generate expression matrix files for subsequent analysis.
Assembly: mus_musculus_ensembl_92
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Bone marrow

extract_protocol:
We extracted the tibia of the mouse using tweezers and scissors, then flushed the bone marrow tissue out of the tibia into a cell culture dish with a syringe, and dispersed the tissue by gently blowing on it.  and washed with Ca/Mg-free PBS.  To remove the red blood cells, 2 mL GEXSCOPE® red blood cell lysis buﬀer (RCLB, Singleron) was added at 25°C for 10 minutes.  The solution was then centrifuged at 500 × g for 5 min and suspended in PBS.  The blood samples were centrifuged at 400g for 5 min at 4°C, and the supernatant was discarded.  After removed red blood cells, PBMCs were isolated by centrifuged at 400g for 10min at 4°C.  The supernatant was discarded and the PBMCs were resuspended by phosphate buffered saline to obtain a single-cell suspension
Single-cell suspensions (2×105 cells/mL) with PBS (HyClone) were loaded onto microwell chip using the Singleron Matrix® Single Cell Processing System. Barcoding Beads are subsequently collected from the microwell chip, followed by reverse transcription of the mRNA captured by the Barcoding Beads and to obtain cDNA, and PCR amplification. The amplified cDNA is then fragmented and ligated with sequencing adapters. The scRNA-seq libraries were constructed according to the protocol of the GEXSCOPE® Single Cell RNA Library Kits (Singleron) (Ref). Individual libraries were diluted to 4 nM, pooled, and sequenced on Illumina novaseq 6000 with 150 bp paired end reads.

treatment_protocol: Mice were divided into swimming (n=6) and non-swimming (n=6) groups. The swimming group mice starting with 10 minutes of swimming on the first day and gradually increasing to 60 minutes per day within a week. Afterward, they swam for 60 minutes every day, five times a week, for a total of 12 weeks. All swimming training sessions were conducted in the afternoon. The non-swimming group mice did not undergo swimming training.

value: Bone marrow

value: Bone marrow cells

value: Wild type

value: Non-swimming


title: Human_FT_Non-BRCAm_C-21-51

value: Fallopian tube


title: NC-02

description:
Library name: sample 5
10x Genomics


title: Human_FT_Non-BRCAm_C-21-48

value: Non-BRCAm

value: Cesarean Section


title: Human_FT_Non-BRCAm_C-21-43


title: SW-02

description:
Library name: sample 2
10x Genomics

value: Swimming


title: Human_FT_Non-BRCAm_C-21-42

value: Pre


title: Human_FT_Non-BRCAm_C-21-60


title: NC-03

description:
Library name: sample 6
10x Genomics


title: Rice, NET-seq, rep2

first: Yao

last: Yao

state: China

address: Tsinghua university Biotechnology building Haidian  District, Beijing, 100084, China

department: school of life sciences

institute: Tsinghua university

data_processing:
Reads were aligned to the TAIR10 genome using bowtie2 in ChIP-seq analysis
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
STAR software used for alignment in RNA-seq analysis.
HTseq were used for calculate counts  in RNA-seq analysis.
Assembly: TAIR10
Supplementary files format and content: bigwig
Library strategy: NET-seq

molecule: nuclear RNA

organism: Oryza sativa

source_name: seedling

extract_protocol:
RNA-seq: Total RNA was extracted from 14 days old seedlings using the TRIzol and sent to NGS company for library construction and sequencing
ChIP for histone modifications was carried out based on both Caroline Dean and Andrzej T. Wierzbicki’s protocols (Song et al., 2014) . In brief, 2 g of 14 days seedlings were cross-linked with 1% formaldehyde. The cross-linking was stopped by adding 0.125 M glycine and the sample was rinsed five times with ddH2O. Then the plants were frozen with liquid nitrogen, ground into fine powder, and lysed with Honda buffer (containing 0.44 M Sucrose, 12.5% Ficoll, 2.5% Dextran T40, 20 mM Hepes KOH pH 7.4, 10 mM MgCl2, 0.5% Triton X-100, 1 mM PMSF, 1% Plant protease inhibitor cocktail, 5 mM DTT). The homogenate was filtered through Miracloth (Millipore) and then spun at 2000g for 15 min. The nuclear pellet was washed twice with the same buffer mentioned above and resuspended in lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF and 1x protease inhibitor) and sonicated using a Bioruptor Pico with the following settings: 30s on/off intervals, four times for 10 min each. The sample was spun at maximum speed for 10 min. The supernatant was collected and diluted 10-fold with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl). The diluted chromatin solution was incubated with 5 µg of anti-H3K36me1 (ab9048; Abcam), anti-H3K36me2 (ab9049; Abcam) or anti-H3K36me3 (ab9050; Abcam), anti-H3K27me3 (Millipore, 07-449) at 4 °C overnight.The beads were washed with 1 ml of low-salt wash buffer (50 mM Tris–HCl, pH 7.8, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100) once, with 1 ml of high-salt wash buffer (wash buffer with 500 mM NaCl) twice, with 1 ml of LiCl buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA, 0.25 M LiCl, 1% sodium deoxycholate) once and with 1 ml of TE buffer (10 mM Tris–HCl, pH 7.5, 1 mM EDTA) .
ChIP-seq: The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.
NET-seq/NET-seq was performed as described (Zhicheng Dong lab, Nature plants-under revision). In brief, 12 days old seedlings were grounded in liquid nitrogen and resuspended in ice-cold lysis buffer (50mM HEPES [PH 7.5], 150mM NaCl, 1mM EDTA [PH 8], 1% triton X-100, 10% glycerol, 5mM β-mercaptoethanol, 1mM PMSF, 2μg/μl Aprotinin and 2μg/μl Pepstatin A). After that lysis mixture was filtered and centrifuged to discard the supernatant. Nuclear pellet was washed once with HBB (25mM Tris-HCL [PH7.6], 0.44M sucrose, 10mM MgCl2, 0.10% triton-100, 10mM β-mercaptoethanol) and HBC (20mM Tris-HCL [PH7.6], 0.352M sucrose, 8mM MgCl2, 0.08% triton-100, 8mM β-mercaptoethanol and 20% glycerol) buffers, respectively, and resuspended in MNase buffer (20mM Tris-HCL [PH 8], 5mM NaCl, and 2.5mM CaCl2) supplemeneted with 20U of MNase. The reaction mixture was incubated at 37C for 5 minutes and the reaction was later stopped with EDTA. After MNase digestion, sonication was performed with 1s ON/OFF for 10 cycles and centrifuged to obtain the supernatant. Then the supernatant was incubated with antibody (Abcam-Ab817) coated beads for 2 hrs at 4C and the beads containing complex was washed 8 times with NET-2 buffer (50mM Tris-HCL [PH7.4], 150mM NaCl, and 0.05% NP-40). Finally, the beads were resuspended with PNK reaction mixture containing 75 ul PNK buffer, 10ul PNK enzymes (NEB) and 15ul of 10mM ATP and incubated at 37C for 10 minutes on a thermomixture (1400rpm). After that supernatant was removed and beads were washed with NET-2 buffer. The beads were again resuspended in 500ul TRIzol and incubated the mixture for 10 minutes at room temperature. After chloroform purification, RNA was precipitated with 1/10 volume of Ammonium acetate, 3 volume of ethanol and 1ul of GlycoBlue. The precipitated RNA was run on 8% PAGE gel and the gel corresponding to 35-100bp size of RNA was sliced. After RNA recovery from the gel, NEXTflex TM small RNA-Seq Kit V3 was used to construct the libraries. Finally, the libraries were recovered from the 6% PAGE gel corresponding to 140-250 bp size.
ATAC-seq: 1. Excise the tissue (0.1–0.5 g of plant tissue) into a weigh boat on ice until the desired amount has been collected and weighed. 2. Grind the plant tissue to a fine powder in liquid nitrogen using a mortar and pestle. 3. Using a nitrogen-cooled metal lab spoon, quickly transfer the frozen tissue powder to another mortar containing 10 mL ice-cold Nuclei Purification Buffer (NPB). 4. Thoroughly resuspend the powder in NPB by grinding it with a new, clean pestle. 5. Place a 70 μm nylon cell strainer in the center of a long-stemmed funnel and above a 15 mL tube on ice. 6. Use a 10 mL serological pipette to draw up the tissue suspension and filter it through the strainer. Collect the flow-through in the 15 mL tube. 7. Spin down the nuclei at 1,200 g for 10 min at 4 C.  8. Use a 10 mL serological pipet and then a 1 mL pipette tip to carefully remove as much of the supernatant as possible without disturbing the pellet. 9. Gently resuspend the pellet in 1 mL of ice-cold Nuclei Extraction Buffer 2 (NEB2). Transfer this suspension to a new 1.5 mL tube. 10. Spin down the resuspended nuclei at 12,000 g for 10 min at 4 C. 11. Carefully remove the supernatant and resuspend the pellet thoroughly in 300 μL of Nuclei Extraction Buffer 3 (NEB3). 12. Add 300 μL of ice-cold NEB3 to a new 1.5 mL tube. 13. Carefully layer the resuspended pellet from step 11 on top of the fresh NEB3 from step 12. 14. Spin down the two layers at 16,000 g for 10 min at 4 C. 15. Carefully remove the supernatant and resuspend the nuclei pellet in 1 mL of cold NPB. Keep on ice. 16. Spin down the nuclei at 1,500 g for 7 min at 4 C, resolving nuclei in 20ul ddH2O. 17. Tn5 fragmentation using TruePrep® Index Kit V2 for Illumina Vazyme #TD202. 18. PCR  product purification using QIAquick PCR Purification Kit. 19. Index PCR using TruePrep® Index Kit V2 for Illumina Vazyme #TD202. 20 Size selection using SPRI beads left side size selection.

value: seedling

value: WT


title: MSC+PBS 1

city: soochow

first: yuzhu

last: Liu

state: Jiangsu

address: renai road 199

institute: soochow university

description:
Library name: sample7
Ctrl1:fpkm

data_processing:
Samples are sequenced on the platform to get image files, which are transformed by the software of the sequencing platform, and the original data in FASTQ format (Raw Data) is generated.
Sequencing data contains a number of connectors, low-quality Reads, so we use Cutadapt (v1.15) software to filter the sequencing data to get high quality sequence（Clean Data）for further analysis
Assembly: mm10
Supplementary files format and content: tab-delimited test file includes raw counts for each sample
Supplementary files format and content: tsv files include FPKM values for each sample

source_name: bone marrow

growth_protocol: MSCs were cultured in DMEM/F12  with 10% FBS antibiotics in humidified atmosphere with 5％ CO2 at 37℃

extract_protocol:
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.
Total RNA was isolated using the Trizol Reagent (Invitrogen Life Technologies), after which the concentration, quality and integrity were determined using a NanoDrop spectrophotometer (Thermo Scientific). Three micrograms of RNA were used as input material for the RNA sample preparations.

treatment_protocol: Peritoneal interstitial fluid (PF) was collected from control mice, IBD mice (treated with TNBS for 3 days).Mesenchymal stromal cells (MSCs) were co-cultured separately with PF from control mice, PF from TNBS-induced mice, and phosphate-buffered saline (PBS) for 24h.

value: bone marrow

value: mesenchymal stromal cells(SV40)

value: BMMSC

value: MSC+PBS


title: MSC+TNBS-PF 2

description:
Library name: sample5
B_T2:fpkm

value: MSC+TNBS-PF


title: MSC+TNBS-PF 3

description:
Library name: sample6
B_T3:fpkm


title: MSC+PBS 3

description:
Library name: sample9
Ctrl3:fpkm


title: Human_FT_Non-BRCAm_C-21-49

value: White

value: C


title: MSC+TNBS-PF 1

description:
Library name: sample4
B_T1:fpkm


title: Eμ-Myc; PRPS2 KO biol rep 4

city: Cincinnati

first: John

last: Cunningham

state: OH

address: 3125 Eden Ave

department: Cancer & Cell Biology

institute: University of Cincinnati

data_processing:
Differentially expressed genes analysis was performed using Deseq^2 (Illumina); data was plotted using ggplot2 in R (v4.3.3).
Assembly: UCSC mm10
Supplementary files format and content: tab-delineated text file contains the number of reads for each target gene

source_name: primary cells

extract_protocol:
Primary murine B lymphocytes were isolated from spleens of 6w mice. Post-isolation, B lymphocytes were lysed using TRIzol reagent (Invitrogen) and purified via PureLink RNA Mini Kit (Thermo), according to manufacturer's protocol.
RNA libraries for RNA-sequencing were prepared via NEBNext Ultra II Directional RNA Library Prep Kit, according to manufacturer's protocol.

value: spleen

value: B lymphocytes

value: E mu-Myc; PRPS2 KO


title: MSC+PBS 2

description:
Library name: sample8
Ctrl2:fpkm


title: SW-03

description:
Library name: sample 3
10x Genomics

value: Bone marrow

value: Bone marrow cells

value: Wild type


title: Human_FT_Non-BRCAm_C-21-39

value: Fallopian tube

value: Non-BRCAm

value: Menorrhagia


title: SW-01

description:
Library name: sample 1
10x Genomics

value: Swimming


title: Human_FT_Non-BRCAm_C-21-46

value: Black

value: Cesarean Section

value: Pre


title: Eμ-Myc; PRPS2 KO biol rep 3


title: Human_FT_Non-BRCAm_C-21-41

value: Benign Uterine


title: Human_FT_Non-BRCAm_C-21-38


title: MSC+ctrl-PF 2

description:
Library name: sample2
B_C2:fpkm

value: bone marrow

value: mesenchymal stromal cells(SV40)

value: BMMSC

value: MSC+ctrl-PF


title: Eμ-Myc biol rep 3

value: spleen

value: B lymphocytes

value: E mu-Myc


title: Eμ-Myc biol rep 4


title: Rice, NET-seq, rep1

value: seedling

value: WT


title: Human_FT_Non-BRCAm_C-21-4

value: Fallopian tube

value: White

value: Adnexal Mass

value: Post

value: B


title: Human_FT_Non-BRCAm_C-21-37

value: Non-BRCAm

value: Black

value: Cesarean Section

value: C


title: MSC+ctrl-PF 1

description:
Library name: sample1
B_C1:fpkm

value: bone marrow

value: mesenchymal stromal cells(SV40)


title: Eμ-Myc biol rep 1


title: Eμ-Myc biol rep 2


title: MSC+ctrl-PF 3

description:
Library name: sample3
B_C3:fpkm

value: BMMSC

value: MSC+ctrl-PF


title: WT biol rep 4

value: spleen

value: B lymphocytes


title: Human_FT_BRCA1m_C-21-35

value: Risk Reduction

value: Pre


title: WT biol rep 2

value: WT


title: Foxd1_sort_E185_T1_rep4

first: Xiaobing

last: Shi

address: 333 Bostwick Ave. NE

description: Library name: Sample 8

data_processing:
Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq
Fastq files were mapped to mm10 mouse genome by HISAT2
Gene reads count tables were generated by HTSeq
CPM (counts per million) and fold change values were calculated edgeR
Assembly: mm10
Supplementary files format and content: text files includes raw reads count

source_name: kidney

extract_protocol:
RNA are extracted by RNeasy Mini Kit
KAPA Stranded mRNA-Seq Kit and SMART-Seq v4 Ultra Low Input RNA Kit

value: kidney


title: Human_FT_BRCA2m_C-21-34

value: Fallopian tube

value: White


title: WT biol rep 1


title: Human_FT_BRCA1m_C-21-33

value: Post


title: WT biol rep 3


title: Foxd1_sort_E185_T1_rep2

description: Library name: Sample 6


title: Eμ-Myc; PRPS2 KO biol rep 2

value: E mu-Myc; PRPS2 KO


title: Human_FT_BRCA1m_C-21-32


title: Foxd1_sort_E185_T1_rep1

description: Library name: Sample 5


title: 5637GRC2.R2.P15

city: Yuseong-gu

first: Seung Woo

last: Baek

state: Daejeon

address: Gwahak-ro 125

country: South Korea

institute: Korea Research Institute Biology & Biotechnology

description: replicate 2

data_processing:
Reference genome indexing and read mapping of samples were performed using STAR software (ver. 2.6.1a).
FeatureCounsts (ver. 1.6.2) was used to calculate genereated binary alignment map (BAM) files.
The read counts per million fragments mapped (CPM) of each samples were used to estimate the expression level of each gene.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include CPM values for each Sample

growth_protocol: 5637 and Phase3, phase7, phase 15, gemcitabine-resistant 5637 bladder cancer cells were cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin-streptomycin antibiotics solution. All of the cells were maintained at 37˚C with 5% CO2.

extract_protocol:
RNA samples for sequencing were isolated using the Qiagen RNeasy Mini Kit (Qiagen, Hilden, Germany) according to the manufacturer’s protocol. Total RNA isolation was performed in a reverse transcription reaction with poly(dT) primers using PrimeScriptTM reverse transcriptase (TAKARA, Shiga, Japan) according to the manufacturer’s protocol. The library’s quality and quantity were measured by a Nanodrop spectrophotometer (ND-1000; Thermo Scientific, Waltham, MA, USA).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: phenotype

tag: phase

value: Bladder cancer


title: 5637GRC2.R3.P15

description: replicate 3


title: 5637GRC2.R1.P15

description: replicate 1


title: Eμ-Myc; PRPS2 KO biol rep 1


title: Human_FT_BRCA2m_C-21-31

value: B


title: 5637GRC2.R4.P7

description: replicate 4


title: Foxd1_sort_E185_WT_rep4

description: Library name: Sample 4


title: Human_FT_BRCA1m_C-21-30


title: 5637GRC2.R3.P7

description: replicate 3


title: 5637GRC2.R3.P3

description: replicate 3


title: 5637GRC2.R1.P7

description: replicate 1


title: Foxd1_sort_E185_T1_rep3

description: Library name: Sample 7


title: 5637GRC2.R2.P7

description: replicate 2


title: Human_FT_BRCA1m_C-21-29


title: 5637GRC2.R4.P15

description: replicate 4


title: 5637GRC2.R2.P3

description: replicate 2


title: Foxd1_sort_E185_WT_rep2

description: Library name: Sample 2


title: Human_FT_BRCA2m_C-21-28

value: Black


title: 5637GRC2.R1.P3

description: replicate 1


title: Foxd1_sort_E185_WT_rep1

description: Library name: Sample 1


title: 5637.R2.P0 GRC2

description: replicate 2


title: Human_FT_BRCA1m_C-21-25


title: 5637.R4.P0 GRC2

description: replicate 4


title: Foxd1_sort_E185_WT_rep3

description: Library name: Sample 3


title: 5637.R3.P0 GRC2

description: replicate 3


title: 5637.R1.P0 GRC2

description: replicate 1


title: 5637GRC1.R2.P15

description: replicate 2


title: 5637GRC1.R4.P15

description: replicate 4


title: 5637GRC1.R3.P15

description: replicate 3


title: IL1r_Het_Naive

city: Zürich

first: Manfred

last: Kopf

address: Otto-Stern-Weg 7

department: Biologie

country: Switzerland

institute: ETH Zürich

description:
Library name: IL1r_Het_Naive
10x Genomics

data_processing:
Single cell gene expression data were pre-processed with a standard Cell Ranger v7.0.0 (10x Genomics) pipeline with parameters expectedCells=10000 and includeIntrons=TRUE, aligning reads to the GRCm39 mouse reference transcriptome (Ensembl release 106).
Assembly: GRCm39
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz).
Supplementary files format and content: Tab-separated file containing barcode information, sample and clusters identifier of the combined dataset (annotation.tsv).

source_name: Kidney

extract_protocol:
Kidneys were transferred into RNAlater solution (Sigma Aldrich, R0901) and kept at 4 overnight. The next day, the RNAlater solution was removed, and the tissues were snap frozen in liquid nitrogen until processing. Processing of the tissue was done at the day of sequencing. In short, tissues were thawed, then cut into small pieces using a surgical blade. Next, the tissues were lysed using a Dounce homogenizer with Nuclei EZ lysis buffer (Sigma Aldrich NUC-101). The tissues were ground with a loose pestle 12-15 times, then another 12-15 times with a tight pestle. Homogenized tissue was incubated 5 minutes on ice, filtered using a 40um sieve and washed with Nuclei EZ lysis buffer. Nuclei were then pelleted at 500g for 5 minutes and washed once with 1%BSA containing RNAse inhibitor (New England BioLabs, 0.2U/ul). Nuclei were briefly vortexed and strained through a 30um strainer. The quality of the nuclei was assessed under the microscope.
Library preparation and RNA sequencing was performed by using Drop-seq platform from 10X Genomics. 10000 cells per sample were loaded in to the 10X Chromium controller and library preparation was performed according to the manufacturer’s indications

treatment_protocol: Mice were infected intravenuously with 10^5 CFU Candida albicans, 8 hours prior to harvesting of the kidney.

value: Kidney


title: IL1r_KO_infected

description:
Library name: IL1r_KO_infected
10x Genomics

value: Candida albicans


title: Human_FT_BRCA1m_C-21-22


title: Human_FT_BRCA2m_C-21-20


title: Human_FT_Non-BRCAm_C-21-18

value: Non-BRCAm

value: Ovarian Cyst


title: Human_FT_BRCA2m_C-21-26


title: 5637GRC1.R1.P15

description: replicate 1


title: IL1r_KO_Naive

description:
Library name: IL1r_KO_Naive
10x Genomics


title: 5637GRC1.R2.P7

description: replicate 2


title: FL_CTL_3

city: Suita

first: Masaki

last: Nomura

state: Osaka

address: 2-2, Yamadaoka

department: Department of Cancer Pathology

institute: Graduate School of Medicine, The University of Osaka

data_processing:
The adapter sequences were removed from the FASTQs using Trimmomatic (0.39).
The cleaned FASTQs were aligned using Bowtie2 (2.4.4) to the mouse reference genome mm10.
The duplicated reads were removed using picard (2.26.2) MarkDuplicates.
The bigWig files were generated using bamCoverage (3.5.1).
Peaks were called using MACS2 (2.2.7.1) with the significance cut-off q-value <0.05.
Assembly: mm10
Supplementary files format and content: bigWig, narrowPeak

source_name: Fetal liver

extract_protocol:
FACS-sorted Lin-c-Kit+ E14.5 fetal liver HSPCs (150,000 cells per sample) were processed by a transposition reaction and purification followed the manual of ATAC-seq kit from Active motif (#13150)
ATAC libraries were prepared for sequencing using standard Illumina protocols

value: Fetal liver

tag: strain

value: Lineage- c-Kit+ fetal liver cells

value: CD45.2(+) Brd9fl/fl

tag: developmental stage


title: FL_Brd9KO_3

value: CD45.2(+) Vav1-iCre Brd9fl/fl


title: IL1r_Het_infected

description:
Library name: IL1r_Het_infected
10x Genomics


title: Human_FT_Non-BRCAm_C-21-16

value: Asian

value: Cervical Dysplasia


title: Human_FT_Non-BRCAm_C-21-17

value: Fallopian tube

value: Pre


title: 5637GRC1.R3.P7

description: replicate 3


title: FL_CTL_1


title: 5637GRC1.R4.P3

description: replicate 4


title: 5637GRC1.R2.P3

description: replicate 2


title: 5637GRC1.R3.P3

description: replicate 3


title: 5637GRC1.R1.P7

description: replicate 1


title: FL_Brd9KO_2


title: Human_FT_Non-BRCAm_C-21-14

value: Post


title: 5637GRC1.R4.P7

description: replicate 4


title: 5637GRC1.R1.P3

description: replicate 1


title: 5637.R4.P0 GRC1

description: replicate 4


title: test_4

data_processing:
The FASTQ-sequenced reads were mapped to the mm10 genome using Hisat2.
Gene counts calculated by FeatureCounts were normalized and differentially expressed genes were identified with Adjusted p value < 0.05 by DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample.
Supplementary files format and content: tab-delimited text file includes results of differentially expressed gene analysis.

extract_protocol:
MACS-selected Lin- E14.5 fetal liver cells were proceeded to RNA extraction using RNeasy columns (Qiagen).
RNA libraries were prepared using TruSeq Stranded mRNA Library Prep Kit.

value: Lineage- fetal liver cells


title: 5637.R3.P0 GRC1

description: replicate 3

value: Bladder cancer


title: 5637.R1.P0 GRC1

description: replicate 1


title: Human_FT_Non-BRCAm_C-21-11

value: White

value: Benign Uterine

value: B


title: efs, KO4, H3K36me3-2-ChIP

data_processing:
Reads were aligned to the TAIR10 genome using bowtie2 in ChIP-seq analysis
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Assembly: TAIR10
Supplementary files format and content: bigwig

extract_protocol:
ChIP for histone modifications was carried out based on both Caroline Dean and Andrzej T. Wierzbicki’s protocols (Song et al., 2014) . In brief, 2 g of 14 days seedlings were cross-linked with 1% formaldehyde. The cross-linking was stopped by adding 0.125 M glycine and the sample was rinsed five times with ddH2O. Then the plants were frozen with liquid nitrogen, ground into fine powder, and lysed with Honda buffer (containing 0.44 M Sucrose, 12.5% Ficoll, 2.5% Dextran T40, 20 mM Hepes KOH pH 7.4, 10 mM MgCl2, 0.5% Triton X-100, 1 mM PMSF, 1% Plant protease inhibitor cocktail, 5 mM DTT). The homogenate was filtered through Miracloth (Millipore) and then spun at 2000g for 15 min. The nuclear pellet was washed twice with the same buffer mentioned above and resuspended in lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF and 1x protease inhibitor) and sonicated using a Bioruptor Pico with the following settings: 30s on/off intervals, four times for 10 min each. The sample was spun at maximum speed for 10 min. The supernatant was collected and diluted 10-fold with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl). The diluted chromatin solution was incubated with 5 µg of anti-H3K36me1 (ab9048; Abcam), anti-H3K36me2 (ab9049; Abcam) or anti-H3K36me3 (ab9050; Abcam), anti-H3K27me3 (Millipore, 07-449) at 4 °C overnight.The beads were washed with 1 ml of low-salt wash buffer (50 mM Tris–HCl, pH 7.8, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100) once, with 1 ml of high-salt wash buffer (wash buffer with 500 mM NaCl) twice, with 1 ml of LiCl buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA, 0.25 M LiCl, 1% sodium deoxycholate) once and with 1 ml of TE buffer (10 mM Tris–HCl, pH 7.5, 1 mM EDTA) .
ChIP-seq: The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.
NET-seq/NET-seq was performed as described (Zhicheng Dong lab, Nature plants-under revision). In brief, 12 days old seedlings were grounded in liquid nitrogen and resuspended in ice-cold lysis buffer (50mM HEPES [PH 7.5], 150mM NaCl, 1mM EDTA [PH 8], 1% triton X-100, 10% glycerol, 5mM β-mercaptoethanol, 1mM PMSF, 2μg/μl Aprotinin and 2μg/μl Pepstatin A). After that lysis mixture was filtered and centrifuged to discard the supernatant. Nuclear pellet was washed once with HBB (25mM Tris-HCL [PH7.6], 0.44M sucrose, 10mM MgCl2, 0.10% triton-100, 10mM β-mercaptoethanol) and HBC (20mM Tris-HCL [PH7.6], 0.352M sucrose, 8mM MgCl2, 0.08% triton-100, 8mM β-mercaptoethanol and 20% glycerol) buffers, respectively, and resuspended in MNase buffer (20mM Tris-HCL [PH 8], 5mM NaCl, and 2.5mM CaCl2) supplemeneted with 20U of MNase. The reaction mixture was incubated at 37C for 5 minutes and the reaction was later stopped with EDTA. After MNase digestion, sonication was performed with 1s ON/OFF for 10 cycles and centrifuged to obtain the supernatant. Then the supernatant was incubated with antibody (Abcam-Ab817) coated beads for 2 hrs at 4C and the beads containing complex was washed 8 times with NET-2 buffer (50mM Tris-HCL [PH7.4], 150mM NaCl, and 0.05% NP-40). Finally, the beads were resuspended with PNK reaction mixture containing 75 ul PNK buffer, 10ul PNK enzymes (NEB) and 15ul of 10mM ATP and incubated at 37C for 10 minutes on a thermomixture (1400rpm). After that supernatant was removed and beads were washed with NET-2 buffer. The beads were again resuspended in 500ul TRIzol and incubated the mixture for 10 minutes at room temperature. After chloroform purification, RNA was precipitated with 1/10 volume of Ammonium acetate, 3 volume of ethanol and 1ul of GlycoBlue. The precipitated RNA was run on 8% PAGE gel and the gel corresponding to 35-100bp size of RNA was sliced. After RNA recovery from the gel, NEXTflex TM small RNA-Seq Kit V3 was used to construct the libraries. Finally, the libraries were recovered from the 6% PAGE gel corresponding to 140-250 bp size.

value: seedling


title: 5637.R2.P0 GRC1

description: replicate 2


title: efs, KO4, H3K36me3-1-ChIP


title: test_3


title: Human_FT_Non-BRCAm_C-21-10

value: Non-BRCAm


title: test_2


title: test_1


title: efs, KO4, 1-10-Input


title: efs, KO3, H3K36me3-1-ChIP


title: SU-DIPG-XVII_control_Input

value: SU-DIPG-XVII

value: H3F3A K27M

value: DMSO


title: Human_FT_Non-BRCAm_C-21-13


title: efs, KO3, 1-10-Input


title: efs, KO4, H3-ChIP


title: control_3

value: Fetal liver

value: CD45.2(+) Brd9fl/fl


title: efs, KO3, H3-ChIP


title: control_2


title: efs, KO3, H3K36me3-2-ChIP


title: Human_FT_Non-BRCAm_C-21-1

value: Black

value: Ovarian Serous Cystadenoma


title: control_1


title: Col-0, H3K36me3-2-ChIP


title: SU-DIPG-XVII_combine-ATAC-rep2

value: H3F3A K32M


title: SU-DIPG-XVII_vorinostat_ATAC_rep2

value: H3F3A K30M

value: vorinostat


title: Col-0, H3-ChIP


title: Col-0, 1-10-Input


title: SU-DIPG-XVII_combine-ATAC-rep1

value: H3F3A K31M


title: Col-0, H3K36me3-1-ChIP


title: Brd9_KO-FL-LK [scRNA-seq]

description: 10x Genomics

data_processing:
Gene counts were generated by running cellranger count (7.2.0) with mm10-2020A as the transcriptome dataset.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

extract_protocol:
Lineage-c-Kit+ E14.5 fetal liver HSPCs were collected in PBS with 0.04% BSA and maintained on ice. The number of viable cells was counted before use in experiments.
Libraries were prepared according to the manufacturer’s protocol using the 10x Genomics Chromium Next GEM Single Cell 3’ Kit v3.1 and Dual Index Kit.

value: Lineage- c-Kit+ fetal liver cells

value: CD45.2(+) Vav1-iCre Brd9fl/fl


title: merge_NET, C1

data_processing:
Reads were aligned to the TAIR10 genome using bowtie2 in ChIP-seq analysis
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
Assembly: TAIR10
Supplementary files format and content: bigwig
Library strategy: NET-seq


title: SU-DIPG-XVII_vorinostat_ATAC_rep1

value: H3F3A K29M


title: WT-FL-LK [scRNA-seq]

description: 10x Genomics


title: SU-DIPG-XVII_control_ATAC_rep2

value: H3F3A K28M


title: merge_NET, C2

value: seedling


title: efs, H3ac_2


title: efs, H3K27ac_2


title: efs, H3ac_1


title: efs, H3


title: efs, H3K27ac_1


title: efs, acmo2, K36me3_2


title: BWpool3-FB

city: Buffalo

first: Mark

middle: D

last: Long

state: NY

address: Elm & Carlton Streets

department: Bioinformatics & Biostatistics

institute: Roswell Park Comprehensive Cancer Center

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)
BWpool3_barcodes.tsv.gz
BWpool3_features.tsv.gz
BWpool3_matrix.mtx.gz

library_source: other

data_processing:
Raw sequence data demultiplexing, barcode processing, alignment (GRCh38) and filtering for true cells were performed using the Cell Ranger Single-Cell Software Suite (v6.0.0)
Sample demultiplexing from hashtag feature barcoding (TotalSeq-C antibodies, BioLegend), subsequent filtering for high quality cells, and downstream analyses were performed using Seurat (v4)
Assembly: GRCh38
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz, filtered_contig_annotations.csv

molecule: protein

source_name: PBMC

extract_protocol:
Single live CD45+ CD3+ cells were enriched from cryopreserved PBMC samples obtained pre-treatment and on-treatment at 4, 8, 12, 24, and 32 weeks by flow cytometry sorting using a BD FACSAria II (BD Biosciences).
Cells were counted, hashed with TotalSeq-C0251, TotalSeq-C0252, TotalSeq-C0253 and TotalSeq-C0254 anti-human antibodies, BioLegend) and pooled in 2 separate batches across 3 GEMs (batch 1 = BWpool1 & BWpool2 containing PreTx/TotalSeq-C0251, OnTx.4wk/TotalSeq-C0252,  OnTx.8wk/TotalSeq-C0253,  OnTx.12wk/TotalSeq-C0254; batch2 = BWpool3 containing  OnTx.24wk/TotalSeq-C0251, OnTx.32wk/TotalSeq-C0252).
scRNA/VDJ-seq (5'GEX, VDJ, HTO):
The pooled cells were then counted again and immediately loaded onto the chromium chip G using the standard protocol for the Chromium single-cell 5’ kit v2 (10x Genomics, Inc).
Following the final bead purification, all three libraries were pooled as 80% mRNA library, 10% ADT library and 10% HTO library before sequencing.

value: PBMC

value: CD45+CD3+ cells

tag: library type

value: HTO

tag: antibodies/tags


title: Six2_sort_E185_T1_rep3

tag: tissue

value: kidney

tag: development stage


title: SU-DIPG-XVII_control_ATAC_rep1

tag: cell line

value: SU-DIPG-XVII

value: H3F3A K27M

value: DMSO


title: Six2_sort_E185_WT_rep3


title: Six2_sort_E185_T1_rep2


title: Six2_sort_E185_WT_rep1


title: efs, acmo1, K36me3_2


title: efs, acmo1, K36me3_1


title: BWpool1-FB

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)
BWpool1_barcodes.tsv.gz
BWpool1_features.tsv.gz
BWpool1_matrix.mtx.gz

tag: cell type

value: PreTx--/TotalSeq-C0251 ; OnTx.4wk_1--/TotalSeq-C0252 ; OnTx.8wk--/TotalSeq-C0253 ; OnTx.12wk--/TotalSeq-C0254


title: efs, acmo2, K36me3_1


title: efs, 5d, H3K36me3, 2


title: efs, 5d, H3K36me3, 1


title: BWpool3-VDJ

description:
VDJ library
VDJ

molecule: other

value: VDJ


title: efs, 5d, H3


title: Six2_sort_E185_WT_rep2

tag: genotype


title: BWpool2-FB

description:
Cell Hashing library
Hashtag-derived oligonucleotide (HTO)
BWpool2_barcodes.tsv.gz
BWpool2_features.tsv.gz
BWpool2_matrix.mtx.gz


title: Six2_sort_E185_T1_rep1


title: BWpool2-VDJ

description:
VDJ library
VDJ


title: BWpool1-VDJ

description:
VDJ library
VDJ


title: Six2_sort_E145_WT_rep1


title: Six2_sort_E145_WT_rep3


title: Col0, H3ac_2


title: BWpool1-GEX

description:
5' mRNA library
5'RNA


title: Six2_sort_E145_T1_rep2


title: Col0, H3


title: Col0, H3K27ac_2


title: Col05d, H3K36me3, 1


title: Six2_sort_E145_WT_rep2


title: Col0, 5d, H3


title: Six2_sort_E145_T1_rep1


title: Col0, acmo2, K36me3_2


title: Col0, H3K27ac_1


title: Col0, acmo2, K36me3_1


title: H69AR without Supinoxin Replicate 3

city: West Lafayette

first: Elizabeth

middle: J

last: Tran

state: IN

address: 175 S. University Street

department: Biochemistry

institute: Purdue University

data_processing:
The libraries were sequenced using Illumina NovaSeq PE150 cassettes for paired-end sequencing with a 150-bp read length.
Data quality control was conducted using the TrimGalore toolkit (version 0.4.4) (RRID:SCR_011847), with a minimum Phred score of 30 and a minimum read length of 50 bp.
The quality trimmed reads were aligned to the human reference genome (GRCh38) obtained from the Ensembl database.
The RNA-seq protocol included quality control and trimmin (fastp), alignment (STAR), and quantification (FeatureCounts).
Differential expression analysis was performed using both DESeq2 and edgeR methods.
Assembly: GRCh38
Supplementary files format and content: Excel file with raw counts for each sample

growth_protocol: H69AR cells were maintained in RPMI-1640 supplemented with 20% fetal bovine serum (FBS) with antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA extraction was performed using TRIzol Reagent (Thermo 15596026)
Library construction and RNA sequencing were performed by Novogene Co., Ltd., Beijing, China.

treatment_protocol: H69AR confluent cells were treated with 70 nM of Supinoxin.

value: Epithelial cell

value: WT without Supinoxin

tag: treatment

value: No drug treatment


title: Col0, H3ac_1


title: BWpool3-GEX

description:
5' mRNA library
5'RNA


title: Col0, acmo1, K36me3_2


title: Col0, 5d, H3K36me3, 2


title: BWpool2-GEX

description:
5' mRNA library
5'RNA


title: Six2_sort_E145_T1_rep3


title: H69AR without Supinoxin Replicate 2


title: efssdg26, H3K36me3, rep1

data_processing:
Reads were aligned to the TAIR10 genome using bowtie2 in ChIP-seq analysis
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
STAR software used for alignment in RNA-seq analysis.
HTseq were used for calculate counts  in RNA-seq analysis.
Assembly: TAIR10
Supplementary files format and content: bigwig

value: sdg26 efs

value: H3K36me3; ab9050; Abcam


title: Six2_E185_WT_rep2


title: efssdg26, H3K36me3, rep2


title: efssdg26, H3

value: H3; ab1791, Abcam


title: H69AR without Supinoxin Replicate 1


title: Six2_E185_WT_rep1


title: efssdg25, H3K36me3, rep2

value: sdg25 efs


title: efssdg25, H3K36me3, rep1

value: seedling


title: H69AR with Supinoxin Replicate 1

value: WT with Supinoxin

value: Supinoxin drug treatment


title: H69AR with Supinoxin Replicate 3


title: efssdg4, H3K36me3, rep1

value: sdg4 efs


title: Six2_E185_T3_rep2

value: kidney


title: efssdg25, RNAseq, rep2


title: efssdg25, RNAseq, rep1


title: Six2_E185_T1_rep2


title: SU-DIPG-XVII_combine_rep1

data_processing:
Library construction and sequencing were carried out by Novogene.
RNA-seq reads were aligned to mouse genome build mm10 or human genome assembly hg38 using Hisat2 V2.1.0.
Expression levels for all RefSeq transcripts were quantified to fragment per kilobase million (FPKM) using StringTie v2.1.1.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each sample

value: SU-DIPG-XVII


title: efssdg25, H3


title: sdg4, RNAseq, rep2


title: Six2_E185_T1_rep1


title: Six2_E185_T3_rep1


title: efssdg4, H3


title: SU-DIPG-XVII_vorinostat_rep1

value: H3F3A K27M

value: vorinostat


title: SU-DIPG-XVII_vorinostat_rep2


title: Foxd1_E185_WT_rep3


title: H69AR with Supinoxin Replicate 2


title: efssdg4, RNAseq, rep1


title: SU-DIPG-XVII_combine_rep2


title: efssdg4, H3K36me3, rep2


title: Foxd1_E185_WT_rep2


title: efssdg4, RNAseq, rep2


title: efssdg26, RNAseq, rep1


title: sdg4, RNAseq, rep1


title: efssdg26, RNAseq, rep2


title: efs, ATAC, rep2

value: efs


title: efs, ATAC, rep1


title: Foxd1_E185_WT_rep1


title: SU-DIPG-XVII_control_rep2

value: DMSO


title: Col0, ATAC, rep1


title: efs, Ser2p, rep1


title: Col0, Ser2p, rep2


title: Col0, ATAC, rep2


title: efs, Ser2p, rep2


title: efssdg4, Ser2p, rep1


title: Foxd1_E185_T1_rep1


title: SU-DIPG-IV_vorinostat_rep1

value: SU-DIPG-IV

value: HIST1H3B K27M


title: SU-DIPG-XVII_control_rep1


title: Col0, Ser2p, rep1


title: SU-DIPG-IV_combine_rep2


title: efssdg2526, Ser2p, rep1

value: efs sdg25 sdg26


title: testes-KI-KI-rep2

city: Nanjing

first: Feng

last: Li

address: Longmian Avenue 101

institute: Nanjing Medical University

data_processing:
Illumina NovaSeq platform
reads were filtered by fastp (version 0.18.0)
StringTie v1.3.1
RNAs differential expression analysis was performed by DESeq2 software
Assembly: mm39
Supplementary files format and content: excel files include FPKM values for each sample

source_name: Testes

growth_protocol: testes were isolated from sacrificed mouse

extract_protocol:
Total cellular RNA was extracted using a TRIzol reagent (Takara).
Sequencing libraries were generated using VAHTS mRNA-seq v2 Library Prep Kit for Illumina following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

value: Testes

tag: age

value: KI-KI


title: Foxd1_E185_T1_rep2


title: SU-DIPG-IV_control_rep2


title: testes-KI-KI-rep3


title: efssdg4, Ser2p, rep2


title: sdg4, Ser2p, rep1


title: SU-DIPG-IV_vorinostat_rep2


title: sdg4, Ser2p, rep2


title: SU-DIPG-IV_combine_rep1


title: Foxd1_E185_T1_rep3


title: efs, Ser5p, rep2


title: OI-V tibia scRNA-seq

city: Shenzhen

first: Zhijia

last: Tan

address: 1st Haiyuan Road, Futian district

department: Orthopaedic and Traumatology

institute: The University of Hong Kong-Shenzhen Hospital

description: 10X Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: tibia

extract_protocol:
Tibia was dissected from Prx1-Cre;Ifitm5 flox c.-14C>T mouse at P6 stage. Skeletal cells were isolated according to the described protocol.
Single cells were encapsulated for library preparation and sequencing using the Chromium single cell platform (10X Genomics Inc)according to the manufacturer’s protocol. Library size and concentration were determined by Qubit, quantitative PCR, and Bioanalyzer assays.

value: tibia

value: osteoblast, chondrocytes

value: Prx1-Cre; Ifitm5 flox c.-14C>T


title: testes-KI-KI-rep1


title: Col0, acmo1, K36me3_1

value: seedling


title: efssdg2526, Ser2p, rep2

data_processing:
Reads were aligned to the TAIR10 genome using bowtie2 in ChIP-seq analysis
Read coverage normalized to 1x sequencing depth (also known as Reads Per Genomic Content (RPGC))
STAR software used for alignment in RNA-seq analysis.
HTseq were used for calculate counts  in RNA-seq analysis.
Assembly: TAIR10
Supplementary files format and content: bigwig
Library strategy: NET-seq


title: efs, Ser5p, rep1


title: testes-WT-KI-rep3

value: WT-KI


title: testes-WT-KI-rep2


title: Col0, H3K4me1, rep2

value: H3K4me1; ab8895, Abcam


title: Col0, H3K27me3, rep1

value: H3K27me3; Millipore, 07-449


title: testes-WT-WT-rep2

value: WT-WT


title: testes-WT-KI-rep1


title: testes-WT-WT-rep1


title: Col0, H3K27me3, rep2


title: atxr2, H3K36me3, rep2

value: H3K36me3; ab9050; Abcam


title: sdg8, H3K27me3, rep1


title: Col0, H3K4me2, rep1

value: H3K4me2; Millipore, 07-030


title: sdg4, H3

value: H3; ab1791, Abcam


title: sdg26, H3


title: sdg8, H3K27me3, rep2


title: Y11_γδT17 IL-7 IL-1b IL-23 DMSO

city: Mainz

first: Matthias

last: Klein

address: Langenbeckstrasse 1

department: Inst. for Immunology

institute: University Medical Center Mainz

data_processing:
Sequence reads were trimmed for adapter sequences and further processed using the software CLC Genomics workbench (v22.0.1 with CLC's default settings for RNA-Seq analysis). Reads were aligned to GRCm38 genome. Tables with expression values TPM, RPKM and total counts are available in the processed data files.
Assembly: GRCm38
Supplementary files format and content: txt

source_name: Lymph nodes

growth_protocol: CD27−γδ T cells were expanded in vitro as previously described (McKenzie et al., 2017). This protocol was adapted to have pure CD27−γδ T cells asγδT17 by sorting out expanded CD27-γδTCR+, γδT17 cells. CD27+ γδ T cells were separated and maintained by 20 ng ml–1 IL-7 as γδIFN culture. Sorted γδT17 cells were expanded for three days by 20 ng ml–1IL-7. Then, the cells were harvested and plated at 1 × 106 cells ml–1 in 96-well U-bottom plates to be stimulated with indicated cytokines (5 ng ml–1murine IL-1β/IL-23).

extract_protocol:
total RNA was extracted using Rneasy plus micro kit (Qiagen). 100 ng of total RNA (RIN>9) was used for library preparation
RNA quality was assessed on a Bioanalyzer 2100 using a RNA 6000 Nano chip (both from Agilent, Santa Clara, CA). 100 ng of total RNA (integrity > 9) was used to generate barcoded mRNA-seq cDNA libraries using the NEBNext® Poly(A) mRNA Magnetic Isolation Module and NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (both from NEB, Ipswich, MA) with a final amplification of 13 PCR cycles. RNA was quantified using the Qubit HS assay kit (Thermo Fisher) and the library size distribution was determined using the Bioanalyzer HS DNA assay (Agilent). Those premade libraries were sent to Novogene (Cambridge, UK) and were sequenced on a Illumina NovaSeq 6000 instrument aiming for a minimum of 50 million PE150 reads per sample.

treatment_protocol: After expanding, as mentioned in the growth protocol, γδT17 cells were treated with indicated cytokines in the presence or absence of indicated SorA (dissolved in DMSO).

value: Lymph nodes

value: gamma delta

value: WT

value: IL-7 IL-1b IL-23 DMSO


title: atxr2, H3K36me3, rep1


title: Y10_γδT17 IL-7 DMSO

value: IL-7 DMSO


title: Y12_γδT17 IL-7 IL-1b IL-23 SorA

value: IL-7 IL-1b IL-23 SorA


title: sdg25, H3K36me3, rep2


title: sdg26, H3K36me3, rep1


title: testes-WT-WT-rep3

value: Testes


title: atxr2, H3


title: SU-DIPG-IV_control_rep1

extract_protocol:
RNA was harvested using, 1 mg of total RNA was used for construction of sequencing libraries.
RNA libraries were prepared for sequencing using  oligo -dT beads

value: SU-DIPG-IV

value: HIST1H3B K27M

value: DMSO


title: sdg26, H3K36me3, rep2

value: seedling


title: Y9_γδT17 IL-7 IL-1b IL-23 SorA


title: Col0, Ser5p, rep2


title: Col0, Ser5p, rep1


title: Col0, H3K4me1, rep1

value: H3K4me1; ab8895, Abcam


title: Col0, H3K4me2, rep2


title: sdg25, H3K36me3, rep1


title: sdg4, H3K36me3, rep2


title: sdg25, H3


title: Y8_γδT17 IL-7 IL-1b IL-23 DMSO


title: sdg8, H3, pollen

source_name: pollen

value: pollen


title: sdg4, H3K36me3, rep1


title: Col-0, H3, pollen


title: Y5_γδT17 IL-7 IL-1b IL-23 DMSO


title: Y1_γδT17 IL-7 DMSO


title: sdg8, H3K36me1, rep2

value: H3K36me1; ab9048; Abcam


title: Y2_γδT17 IL-7 IL-1b IL-23 DMSO


title: Col-0, H3K36me1, rep2


title: Y3_γδT17 IL-7 IL-1b IL-23 SorA


title: Col-0, H3, CL

source_name: Cauline leaf

value: Cauline leaf


title: Col-0, H3K36me2, rep1

value: H3K36me2; ab9049, Abcam


title: sdg8, H3, CL

value: H3; ab1791, Abcam


title: sdg8, H3K36me2, rep1


title: sdg8, H3K36me2, rep2


title: Col-0, H3, germination

source_name: germination

value: germination


title: Y7_γδT17 IL-7 DMSO

value: Lymph nodes

value: gamma delta


title: sdg8, H3K36me3, rep2, germination

value: H3K36me3; ab9050; Abcam


title: Y4_γδT17 IL-7 DMSO

value: WT

value: IL-7 DMSO


title: Col-0, H3K36me2, rep2


title: Col-0, H3K36me1, rep1


title: brain, Tbx1+/- rep4, vitamin b12

city: Naples

first: Gabriella

last: Lania

address: Via Pietro Castellino

country: Italy

institute: IGB-CNR

data_processing:
Sequence reads were trimmed using bbduk softwareto remove adapter sequences, poly-A tails and low-quality end bases (regions with average quality below 6)
Alignment was performed with STAR] on the reference provided by UCSC Genome Browser
The expression levels of genes were determined with htseq-count using the Gencode/Ensembl gene model
Differential expression analysis was performed using edgeR [5], a statistical package based on generalized linear models, suitable for multifactorial experiments.
Assembly: mm10
Supplementary files format and content: tab delimited text file includes raw count for each sample

source_name: brain hemisphere

growth_protocol: Adult Tbx1+/- and wt mice  4 weeks old

extract_protocol:
Qiagen RNeasy micro/mini plus Kit for RNA isolation and provide 10 μl of RNA at the exact concentration of 50 ng/μL
Quantseq 3′-biased protocol

treatment_protocol: intraperitoneal injection of vB12 dissolved in PBS 20 mg/kg (stored away from light) or with PBS, twice a week for 4 weeks

value: brain hemisphere

value: vitamin B12


title: Y6_γδT17 IL-7 IL-1b IL-23 SorA

value: IL-7 IL-1b IL-23 SorA


title: sdg8, H3, germination

extract_protocol:
RNA-seq: Total RNA was extracted from 14 days old seedlings using the TRIzol and sent to NGS company for library construction and sequencing
ChIP for histone modifications was carried out based on both Caroline Dean and Andrzej T. Wierzbicki’s protocols (Song et al., 2014) . In brief, 2 g of 14 days seedlings were cross-linked with 1% formaldehyde. The cross-linking was stopped by adding 0.125 M glycine and the sample was rinsed five times with ddH2O. Then the plants were frozen with liquid nitrogen, ground into fine powder, and lysed with Honda buffer (containing 0.44 M Sucrose, 12.5% Ficoll, 2.5% Dextran T40, 20 mM Hepes KOH pH 7.4, 10 mM MgCl2, 0.5% Triton X-100, 1 mM PMSF, 1% Plant protease inhibitor cocktail, 5 mM DTT). The homogenate was filtered through Miracloth (Millipore) and then spun at 2000g for 15 min. The nuclear pellet was washed twice with the same buffer mentioned above and resuspended in lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF and 1x protease inhibitor) and sonicated using a Bioruptor Pico with the following settings: 30s on/off intervals, four times for 10 min each. The sample was spun at maximum speed for 10 min. The supernatant was collected and diluted 10-fold with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl). The diluted chromatin solution was incubated with 5 µg of anti-H3K36me1 (ab9048; Abcam), anti-H3K36me2 (ab9049; Abcam) or anti-H3K36me3 (ab9050; Abcam), anti-H3K27me3 (Millipore, 07-449) at 4 °C overnight.The beads were washed with 1 ml of low-salt wash buffer (50 mM Tris–HCl, pH 7.8, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100) once, with 1 ml of high-salt wash buffer (wash buffer with 500 mM NaCl) twice, with 1 ml of LiCl buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA, 0.25 M LiCl, 1% sodium deoxycholate) once and with 1 ml of TE buffer (10 mM Tris–HCl, pH 7.5, 1 mM EDTA) .
ChIP-seq: The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.
NET-seq/NET-seq was performed as described (Zhicheng Dong lab, Nature plants-under revision). In brief, 12 days old seedlings were grounded in liquid nitrogen and resuspended in ice-cold lysis buffer (50mM HEPES [PH 7.5], 150mM NaCl, 1mM EDTA [PH 8], 1% triton X-100, 10% glycerol, 5mM β-mercaptoethanol, 1mM PMSF, 2μg/μl Aprotinin and 2μg/μl Pepstatin A). After that lysis mixture was filtered and centrifuged to discard the supernatant. Nuclear pellet was washed once with HBB (25mM Tris-HCL [PH7.6], 0.44M sucrose, 10mM MgCl2, 0.10% triton-100, 10mM β-mercaptoethanol) and HBC (20mM Tris-HCL [PH7.6], 0.352M sucrose, 8mM MgCl2, 0.08% triton-100, 8mM β-mercaptoethanol and 20% glycerol) buffers, respectively, and resuspended in MNase buffer (20mM Tris-HCL [PH 8], 5mM NaCl, and 2.5mM CaCl2) supplemeneted with 20U of MNase. The reaction mixture was incubated at 37C for 5 minutes and the reaction was later stopped with EDTA. After MNase digestion, sonication was performed with 1s ON/OFF for 10 cycles and centrifuged to obtain the supernatant. Then the supernatant was incubated with antibody (Abcam-Ab817) coated beads for 2 hrs at 4C and the beads containing complex was washed 8 times with NET-2 buffer (50mM Tris-HCL [PH7.4], 150mM NaCl, and 0.05% NP-40). Finally, the beads were resuspended with PNK reaction mixture containing 75 ul PNK buffer, 10ul PNK enzymes (NEB) and 15ul of 10mM ATP and incubated at 37C for 10 minutes on a thermomixture (1400rpm). After that supernatant was removed and beads were washed with NET-2 buffer. The beads were again resuspended in 500ul TRIzol and incubated the mixture for 10 minutes at room temperature. After chloroform purification, RNA was precipitated with 1/10 volume of Ammonium acetate, 3 volume of ethanol and 1ul of GlycoBlue. The precipitated RNA was run on 8% PAGE gel and the gel corresponding to 35-100bp size of RNA was sliced. After RNA recovery from the gel, NEXTflex TM small RNA-Seq Kit V3 was used to construct the libraries. Finally, the libraries were recovered from the 6% PAGE gel corresponding to 140-250 bp size.
ATAC-seq: 1. Excise the tissue (0.1–0.5 g of plant tissue) into a weigh boat on ice until the desired amount has been collected and weighed. 2. Grind the plant tissue to a fine powder in liquid nitrogen using a mortar and pestle. 3. Using a nitrogen-cooled metal lab spoon, quickly transfer the frozen tissue powder to another mortar containing 10 mL ice-cold Nuclei Purification Buffer (NPB). 4. Thoroughly resuspend the powder in NPB by grinding it with a new, clean pestle. 5. Place a 70 μm nylon cell strainer in the center of a long-stemmed funnel and above a 15 mL tube on ice. 6. Use a 10 mL serological pipette to draw up the tissue suspension and filter it through the strainer. Collect the flow-through in the 15 mL tube. 7. Spin down the nuclei at 1,200 g for 10 min at 4 C.  8. Use a 10 mL serological pipet and then a 1 mL pipette tip to carefully remove as much of the supernatant as possible without disturbing the pellet. 9. Gently resuspend the pellet in 1 mL of ice-cold Nuclei Extraction Buffer 2 (NEB2). Transfer this suspension to a new 1.5 mL tube. 10. Spin down the resuspended nuclei at 12,000 g for 10 min at 4 C. 11. Carefully remove the supernatant and resuspend the pellet thoroughly in 300 μL of Nuclei Extraction Buffer 3 (NEB3). 12. Add 300 μL of ice-cold NEB3 to a new 1.5 mL tube. 13. Carefully layer the resuspended pellet from step 11 on top of the fresh NEB3 from step 12. 14. Spin down the two layers at 16,000 g for 10 min at 4 C. 15. Carefully remove the supernatant and resuspend the nuclei pellet in 1 mL of cold NPB. Keep on ice. 16. Spin down the nuclei at 1,500 g for 7 min at 4 C, resolving nuclei in 20ul ddH2O. 17. Tn5 fragmentation using TruePrep® Index Kit V2 for Illumina Vazyme #TD202. 18. PCR  product purification using QIAquick PCR Purification Kit. 19. Index PCR using TruePrep® Index Kit V2 for Illumina Vazyme #TD202. 20 Size selection using SPRI beads left side size selection.


title: sdg8, H3K36me3, rep1, germination


title: brain, Tbx1+/- rep5, vitamin b12


title: Col-0, H3K36me3, rep2, germination


title: brain, Tbx1+/- rep3, vitamin b12


title: sdg8, H3K36me3, rep2, CL


title: Col-0, H3K36me3, rep1, germination


title: sdg8, H3K36me1, rep1


title: sdg8, H3K36me3, rep1, CL


title: Col-0, H3K36me3, rep2, CL


title: brain, Tbx1+/- rep1, vitamin b12


title: Col-0, H3K36me3, rep2, pollen


title: brain, Tbx1+/- rep 4, PBS

value: PBS


title: Col-0, H3K36me3, rep1, CL


title: brain, Tbx1+/- rep2, vitamin b12


title: sdg8, H3K36me3, rep1, pollen


title: brain, Tbx1+/- rep 3, PBS


title: sdg8, H3K36me3, rep2, pollen


title: 17097_STZDFO_M3B2_rat_116_S17

city: Saint Paul

first: Jared

last: Fine

state: MN

address: 295 Phalen Blvd

institute: HealthPartners

data_processing:
Sequencing reads were mapped to the rat reference genome (rattus_norvegicus/Rnor_6.0) using Hisat2.
Differentially expressed genes were determined using edgeR software package with an Absolute fold-change cutoff set at >2 and FDR < 0.05
Assembly: rattus_norvegicus
Supplementary files format and content: 9FineRawcounts.txt

organism: Rattus norvegicus

source_name: hippocampus

extract_protocol:
RNA was harvested using the RNeasy mini plus kit (Qiagen).
Illumina TruSeq libraryprep kit

treatment_protocol: Rats were treated with intranasal insulin or deferoxamine

value: hippocampus

value: neural

value: ICV STZ (surgical)

value: IN DFO


title: Col-0, H3K36me3, rep1, pollen

city: Beijing

value: pollen


title: sdg8, RNAseq, rep2

extract_protocol:
RNA-seq: Total RNA was extracted from 14 days old seedlings using the TRIzol and sent to NGS company for library construction and sequencing
ChIP for histone modifications was carried out based on both Caroline Dean and Andrzej T. Wierzbicki’s protocols (Song et al., 2014) . In brief, 2 g of 14 days seedlings were cross-linked with 1% formaldehyde. The cross-linking was stopped by adding 0.125 M glycine and the sample was rinsed five times with ddH2O. Then the plants were frozen with liquid nitrogen, ground into fine powder, and lysed with Honda buffer (containing 0.44 M Sucrose, 12.5% Ficoll, 2.5% Dextran T40, 20 mM Hepes KOH pH 7.4, 10 mM MgCl2, 0.5% Triton X-100, 1 mM PMSF, 1% Plant protease inhibitor cocktail, 5 mM DTT). The homogenate was filtered through Miracloth (Millipore) and then spun at 2000g for 15 min. The nuclear pellet was washed twice with the same buffer mentioned above and resuspended in lysis buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS, 1 mM PMSF and 1x protease inhibitor) and sonicated using a Bioruptor Pico with the following settings: 30s on/off intervals, four times for 10 min each. The sample was spun at maximum speed for 10 min. The supernatant was collected and diluted 10-fold with ChIP dilution buffer (1.1% Triton X-100, 1.2 mM EDTA, 16.7 mM Tris-HCl, pH 8.0, 167 mM NaCl). The diluted chromatin solution was incubated with 5 µg of anti-H3K36me1 (ab9048; Abcam), anti-H3K36me2 (ab9049; Abcam) or anti-H3K36me3 (ab9050; Abcam), anti-H3K27me3 (Millipore, 07-449) at 4 °C overnight.The beads were washed with 1 ml of low-salt wash buffer (50 mM Tris–HCl, pH 7.8, 150 mM NaCl, 1 mM EDTA, 0.1% SDS, 1% Triton X-100) once, with 1 ml of high-salt wash buffer (wash buffer with 500 mM NaCl) twice, with 1 ml of LiCl buffer (10 mM Tris–HCl, pH 7.8, 1 mM EDTA, 0.25 M LiCl, 1% sodium deoxycholate) once and with 1 ml of TE buffer (10 mM Tris–HCl, pH 7.5, 1 mM EDTA) .
ChIP-seq: The first adapter was ligated to the 3’ end of the ssDNA using Adaptase (Swift Biosciences) via a highly efficient, proprietary reaction that only tails 3’ ends of ssDNA and ligates the first truncated adapter to 3’ ends simultaneously. This method avoids the bias inherent in random primer-based methods, as it ligates adapters in a sequence-independent manner. The extension step was performed using the primer paired to the first adapter, followed by a ligation reaction to add the second truncated adapter to the 5’ ends. An indexing PCR step was performed to add the indexed sequence, and the library was amplified.

value: seedling


title: brain, Tbx1+/- rep 2, PBS


title: 17097_STZDFO_M3B1_rat_95_S16


title: brain, Tbx1+/- rep 5, PBS


title: Col-0, RNAseq, rep1


title: brain, WT rep 4, PBS


title: sdg8, H3


title: Col-0, H3


title: brain, Tbx1+/- rep 1, PBS


title: brain, WT rep 3, PBS


title: sdg8, H3K36me3, rep1

value: anti-H3K36me3 (ab9050; Abcam)


title: Col-0, H3K36me3, rep2


title: Col-0, H3K36me3, rep1


title: brain, WT rep 5, PBS


title: sdg8, RNAseq, rep1


title: Col-0, RNAseq, rep2


title: 17097_STZSal_M3B2_rat_127_S20

value: IN saline


title: 17097_STZSal_M3B1_rat_91_S19


title: 17097_STZSal_M3B1_rat_101_S18


title: sdg8, H3K36me3, rep2


title: 17097_Sham_M3B1_rat_90_S13

value: wild type


title: brain, WT rep 2, PBS


title: IL1R_KO3_brain_candida_8h

description: Library name: IL1R_KO3_brain_candida_8h

data_processing:
Sequenced libraries were aligned with STAR to the mouse reference genome GRCm38.p6 (release M23) and FeatureCounts was used to count mapped reads per gene.
Assembly: mm10
Supplementary files format and content: tab-delimited text file including gene name and raw counts per sample

source_name: Brain

extract_protocol:
Total RNA was isolated from whole mouse brain (Il1r-/- and Il1r+/- mice, 8h after infection with 105 CFU C. albicans) using RNeasy plus micro kit (Qiagen) according to the manufacturer’s protocol.
Libraries were prepared using SMART-Seq RNA Stranded sample kit (Takara Bio) and sequenced by NovaSeq X Plus (Illumina). Sequencing was done using paired-end 150bp reads with a final sequencing depth of 25M paired-end reads per sample on average.

treatment_protocol: Il1r-/- and Il1r+/- mice were infected intraveneusly with 10^5CFU Candida albicans, 8 hours prior to harvesting of the brains.

value: Brain

value: Candida albicans


title: 17097_Sham_M3B1_rat_100_S12