title: HiChIP H3K27ac, CD8T, Intron, Cont

description: Library name: Sample20

value: spleen

value: CD8+ T cells

value: pre-activated CD8T, not treated


title: T1R-affected, non-stimulated libray 9

status: Public on Dec 03 2024

type: SRA

city: Montreal

first: Wilian

last: Macedo

state: Quebec

address: 1001 Decarie Blvd

country: Canada

institute: McGill-MUHC

library_source: transcriptomic

data_processing:
Raw fastq files were quality-checked with FastQC v0.11.8 [13], RSeQC v2.6.1 [14] and processed with cutadapt v2.6 [15] to remove leftover adaptors and low-quality bases (≤ 20 Phred score) allowing for a minimum read size of 50bp.
Sequences were aligned to the human reference genome with STAR v2.7.3a, mapped reads projected to transcriptome coordinate. STAR was used with the parameters: “sjdbOverhang = 74”, “twopassMode = Basic”, “quantTranscriptomeBan = IndelSoftclipSingleend”, “outFilterScoreMinOverLread = 0.80” and “outFilterMatchNminOverLread = 0.80”.
BAM files were input to Salmon v1.4.0 to obtain transcript expression estimates. Salmon parameters were “libType = ISR”, “seqBias”, “gcBias” and “discardOrphans”.
Assembly: GRCh38.p13, ENSEMBL release 102
Supplementary files format and content: Tab-delimited text files with raw estimated counts.
Supplementary files format and content: Tab-delimited text files with estimated counts transformed with tximport’s lengthScaledTPM.
Supplementary files format and content: Tab-delimited text files with estimated counts transformed with tximport’s dtuScaledTPM.

molecule: polyA RNA

organism: Homo sapiens

source_name: whole-blood

growth_protocol: Blood samples were obtained and immediately processed for treatment with antigen..

extract_protocol:
Total RNA was extracted using LeukoLOCK leukocytes filters (Ambion) and RNeasy kit (Qiagen), quantified and quality assessed with Agilent 2100 Bioanalyzer (Agilent).
KAPA Stranded mRNA-Seq Kit (Roche, KK8421) and sequenced as 75-bp paired-end reads on Illumina HiSeq 4000 with an expected throughput of 50 million reads per library.

treatment_protocol: Whole blood was divided in two aliquots with one part being stimulated with M. leprae sonicate (20 µg/ml) for approximately 32 hrs or incubated with medium only

tag: cell type

value: whole-blood

tag: treatment

value: RPMI/HEPES

tag: Sex

value: Male

tag: age at_diag

tag: leprosy class

value: BL

tag: multibacilary

tag: lesion (n)


title: T1R-affected, non-stimulated libray 5

value: BB


title: WT-CTCF [CUT&Tag]

city: Beijing

first: Ruifeng

last: Li

address: haidian

country: China

institute: Tsinghua University

library_source: genomic

data_processing:
1) The  CUT&Tag reads were mapped to reference genome by using bowtie2 with the “-p 5 -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant” options, followed by removing low mapped quality reads, mitochondrial reads, duplications. PCR duplicates were removed using picard MarkDuplicates. Macs2 was used for peak calling with the setting of “-f BAM -B --nomodel --keep-dup all”. 2)  CUT&Tag Differential Peak Analysis. The differential peak was analyzed by R package DiffBind73  with the FDR ≤ 0.01 and FC ≥ 1.5. ChIP seeker was used for peak annotation.
Assembly: mm10
Supplementary files format and content: bigwig
Library strategy: CUT&Tag

molecule: genomic DNA

organism: Mus musculus

source_name: spleens and lymph nodes

extract_protocol:
The CUT&Tag experiments were performed as previously described(Vazyme TD903 kit) to generate DNA libraries derived from cells
The CUT&Tag experiments were performed as previously described(Vazyme TD903 kit) to generate DNA libraries derived from cells.

tag: tissue

value: spleens and lymph nodes

value: cd8+ T cell

tag: genotype

value: WT


title: T1R-affected, non-stimulated libray 4


title: WT_Igg [CUT&Tag]


title: 4001-41F

city: Melbourne

first: Mark

middle: D

last: Ziemann

state: VIC

address: 85 Commercial Rd

department: Bioinformatics Working Group

country: Australia

institute: Burnet Institute

data_processing:
Fastq files underwent quality trimming with Skewer v0.2.2 to remove bases from the 3’ ends with Phred quality less than 20.
Reads were the mapped to the human transcriptome (Gencode V37) using Kallisto v0.46.2.
Transcript-level counts were read into R v4.2.1 and were aggregated to the gene level for downstream analysis.
Assembly: Transcriptome Gencode V37
Supplementary files format and content: Gene counts only
Supplementary files format and content: Gene counts in tab separated values format (TSV).

molecule: total RNA

source_name: Fat

extract_protocol:
Tissues were homogenised using a handheld homogeniser, ~20mg of tissue was homogenised in trizol and total RNA was isolated using RNeasy columns (Qiagen, Hilden, Germany), according to manufacturer’s instructions.
Sequencing libraries were generated from 0.5 µg of total RNA using TruSeq Stranded Total RNA preparation kit (Illumina, San Diego, USA) as per manufacturer’s instructions.
Illumina Stranded Total RNA Prep with Ribo-Zero

value: Fat

tag: age

value: F

tag: quickdash


title: T1R-affected, non-stimulated libray 3


title: Liver_LR_8M10T_27ac_2021

city: Houston

first: Amrit

last: Koirala

state: TX

address: 1 Baylor Plaza

country: USA

institute: Baylor College of Medicine

data_processing:
Data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed
Peaks were called using MACS2
bigWig files were generated using deeptools v3.5.2
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Liver

extract_protocol:
Chromatin was cross-linked with formaldehyde, the reaction stopped with glycine, and sonicated with a bioruptor to obtain fragment sizes of 100–300 bp for ChIP-seq. ChIP-validated antibodies used were directed against H3K4me3 (Active Motif #39915), H3K4me1 (Abcam ab8895), H3K27ac (Abcam ab4729), H3K27me3 (Active Motif #61017), and H3K9me3 (Active Motif #61013). Immunoprecipitated DNA was recovered and purified using the QIAquick PCR Purification kit (Qiagen)
QIAseq FX DNA library kit or the QIAseq Ultralow Input Library Kit

value: Liver

tag: strain

value: 10 months

tag: exposure

value: TBT

tag: ID

tag: risk group

value: low risk TBT

tag: batch

tag: chip antibody


title: 4001-41C

source_name: Capsule

value: Capsule


title: Liver_Veh_2M10V_27ac_2021

value: Vehicle


title: Liver_Veh_1M10V_27ac_2021


title: T1R-affected, non-stimulated libray 2

tag: cell type


title: Ankrd KO

city: Hangzhou

first: Tianhui

last: Pan

state: Zhejiang

address: jiefang Road 88

institute: Zhejiang University

description: Library name: M_KO

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were converted to the FASTQ format using Bcl2fastq software
The output CellRanger expression profile matrix was loaded into Seurat (version 4.1.0) for filtering low-quality cells. Cells were projected onto 2D space using tSNE
Hypergeometric testing was used to perform GO and KEGG enrichment analysis on the differential genes
Monocle 2 software was used to model single-cell trajectories and identify branching points, simulating cellular developmental evolution based on gene expression.
Assembly: mm9
Supplementary files format and content: csv files include barcoses  for each Sample
Supplementary files format and content: csv files include  features for each Sample
Supplementary files format and content: mtx files include matrixs for each Sample

source_name: peritoneal F4/80+ cells

extract_protocol:
Single  Cell 3’ v3 Reagent Kit(10× Genomics)
Single  Cell 3’ v3 Reagent Kit(10× Genomics)

treatment_protocol: F4/80+ cells were sorted from the peritoneal lavage fluids of Ankrd22+/+ and Ankrd22-/- mice using FACS for scRNA-Seq.

value: peritoneal F4/80+ cells


title: Liver_TBT_5mo_repressive_2022_input_2022

value: 5 months


title: 4001-41B

source_name: Bone

value: Bone


title: In vivo cardiac fibroblasts from mice treated with AII/phenylephrine - cardiac fibroblasts with loss of TCF21 2 (T4867)

city: Cincinnati

first: Jeffery

last: Molkentin

state: OH

address: 3333 Burnet Ave

department: Molecular Cardiovascular Biology

institute: Cincinnati Children’s Hospital Medical Center

description:
T4867
normalized_counts_allgenes_Tcf21.KO_Control.csv

data_processing:
Read alignment and quantification was performed in Kallisto using standard settings.
Raw counts were normalized using DESeq2
Differential gene expression between conditions was performed using DEseq2
Assembly: GRCm38
Supplementary files format and content: A Comma Seperated Value files containing counts per sample

source_name: Heart

extract_protocol:
MiRNeasy micro kit from Qiagen catalog #217084
SMART-seq V4 Ultra Low input RNA kit

value: Heart

value: Cardiac fibroblast

value: 8-12 weeks old

tag: treatment

value: Tamoxifen and Angiotensin II/phenylephrine


title: Liver_Veh_5mo_repressive_2022_input_2022

tag: Sex

value: Male


title: In vivo cardiac fibroblasts from mice treated with AII/phenylephrine - cardiac fibroblasts with loss of TCF21 1 (T4864)

description:
T4864
normalized_counts_allgenes_Tcf21.KO_Control.csv


title: T1R-affected, non-stimulated libray 1

value: whole-blood

value: RPMI/HEPES

tag: age at_diag

value: BT/BB


title: T1R-free, non-stimulated libray 22

tag: leprosy class


title: v8741B_F

city: Baltimore

first: Keri

last: Martinowich

state: Maryland

address: 855 N Wolfe St Suite 300

institute: Lieber Institute for Brain Development

data_processing:
FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline
Reads were aligned to reference genome GRCh38 (10x Genomics 2020 reference version)
Assembly: GRCh38
Supplementary files format and content: FASTQ and image data files were pre-processed with the 10x SpaceRanger pipeline with Aligned_fiducials.jpg, detected_tissue_image.jpg, scalefactors_json.json, tissue_hires_image.png, tissue_lowres_image.png, tissue_positions_list.csv, barcode, feature, and matrix files for each donor.
Library strategy: Spatial Transcriptomics

source_name: brain (hypothalamus)

extract_protocol:
Hypothalamus was dissected from fresh frozen postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. Tissue was permeabilized and cDNA was synthesized to incorporate positional barcode.
Libraries were prepared using the Visium Spatial Gene Expression slides & kit according to manufacturer's instructions

value: brain (hypothalamus)

value: Female

tag: age (yr)

tag: predominant ancestry

value: caucasian

tag: body mass_index

tag: postmortem interval_(hr)


title: In vivo cardiac fibroblasts from mice treated with AII/phenylephrine - control 3 (T4835)

description:
T4835
normalized_counts_allgenes_Tcf21.KO_Control.csv

tag: tissue

tag: genotype

tag: age


title: Liver_LR_6M5T_27me3_2022

value: Liver

tag: strain

tag: exposure

value: TBT

value: low risk TBT


title: Liver_LR_5M5T_27me3_2022

tag: ID

tag: risk group


title: v8741A_F


title: In vivo cardiac fibroblasts from mice treated with AII/phenylephrine - control 2 (T4780)

description:
T4780
normalized_counts_allgenes_Tcf21.KO_Control.csv


title: T1R-free, non-stimulated libray 21

value: BT

tag: multibacilary

tag: lesion (n)


title: In vivo cardiac fibroblasts from mice treated with AII/phenylephrine - control 1  (T4770)

description:
T4770
normalized_counts_allgenes_Tcf21.KO_Control.csv

tag: cell type

tag: treatment


title: Liver_HR_4M5T_27me3_2022

tag: Sex

value: 5 months

value: high risk TBT

tag: batch

tag: chip antibody


title: v8667A_F

tag: age (yr)

tag: predominant ancestry


title: T1R-free, non-stimulated libray 20

tag: age at_diag

tag: leprosy class


title: Liver_HR_25M5T_27me3_2022

tag: tissue


title: 255_male_CYM

city: Newark

first: Jose

middle: Emiliano

last: Castro Vildosola

state: NJ

address: Stanley S. Bergen Jr. Building

institute: Rutgers University

data_processing:
We used fastqc version v0.12.0 to have check the quality of the files
We used trim galore 06.10  to improve the quality of the files
To align the samples to our reference we created an index using STAR  2.7 and the reference gencode.vM35.transcripts.fa from gencode
Then we used STAR 2.7 to align the samples to the index
Then we used Salmon x86_64 to quantify the samples
Assembly: We used the gencode gencode.vM35.transcripts.fa
Supplementary files format and content: The processed files are in a .tar format that includes the name the length and the abundance of each of the transcripts per sample

source_name: prefrontal cortex

extract_protocol:
Tissue was lysed using the Qiagen TissueLyser method and RNA was extracted using the Qiagen RNeasy Lipid Tissue Mini Kit (cat. No. 74804) per the manufacturer’s instruction. Samples were eluted using nuclease-free water and isolated RNA concentration and quality were assessed using a NanoDrop 2000 spectrophotometer
RNA libraries were prepared and sequencing was performed by the Rutgers University Genomics Center.

treatment_protocol: CYM5541 (CYM) was purchased from Selleck Chemicals (cat. no. S6552).  On the same day as injection, CYM was dissolved in dimethyl sulfoxide (DMSO) to make a final solution of 1.25 mg/mL CYM or CAY in 5% DMSO in corn oil. Mice were treated with 10 mg/kg of CYM, a dose previously used for each drug in the absence of any noted side effects25,26. 5% DMSO in corn oil was used as control vehicle. No obvious signs of distress or immobility were observed. Mice were euthanized three hours following a second daily injection.

value: prefrontal cortex

tag: genotype

value: CYM


title: Liver_LR_18M5T_27me3_2022

tag: strain

tag: age


title: 257_male_CYM


title: T1R-free, non-stimulated libray 18

value: BL


title: T1R-free, non-stimulated libray 19

value: BB


title: Liver_HR_17M5T_27me3_2022

value: Male

tag: exposure

tag: ID


title: v6588B_F

tag: body mass_index

tag: postmortem interval_(hr)


title: v6588A_F


title: Liver_LR_16M5T_27me3_2022

tag: risk group


title: v6197A_M


title: 247_male_CYM

tag: treatment


title: T1R-free, non-stimulated libray 17

tag: cell type

value: whole-blood

tag: Sex

tag: multibacilary

tag: lesion (n)


title: Liver_HR_15M5T_27me3_2022

tag: batch

tag: chip antibody


title: 245_male_CYM


title: v1735A_M

tag: age (yr)

tag: predominant ancestry


title: v5993A_F

tag: tissue


title: Liver_HR_13M5T_27me3_2022

tag: strain


title: Liver_HR_12M5T_27me3_2022

tag: age


title: T1R-free, non-stimulated libray 13

value: RPMI/HEPES

tag: age at_diag

tag: leprosy class


title: 239_male_veh

tag: genotype

value: Vehicle


title: T1R-free, non-stimulated libray 16


title: erythroid cells, V600E_ATACseq, D10, rep2

first: Yuelin

last: Deng

state: Beijing

address: Beijing, China

institute: Peking University

data_processing:
The adaptors were removed from the raw ATAC-seq paired data using trim_galore software with default parameters. Trimmed cleaned reads were aligned to human reference genome hg19 using Bowtie2 (version 2.3.4.1) S14 with default parameters and converted to bam files using samtoolsS7. ATAC-seq peaks were identified using MACS2S15 with the following parameters: “-q 0.05 --nomodel --shift -100 --extsize 200”. The signal enrichment plot around the TSS of all protein coding genes was generated using deeptools. The example tracks were visualized using IGV softwareS16. The motifs of ATAC-seq peaks were enriched using Homer softwareS17.
Assembly: hg19
Supplementary files format and content: BW files include cleaned reads for each Sample.

source_name: erythroid cells differentiated from UCB-CD34+

extract_protocol:
10-day differentiated erythroid cells from UCB-CD34+ were electroporated using Lonza P3 primary cell kit (V4XP-3024) and lysed after 48 hours of culture or treatment in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 8 mM MgCl2 and NP-40) on ice for 5 min to extract nuclei. The cells were centrifuged at 500 g for 5 min to remove the supernatant. The nuclei were incubated with the Tn5 transposome and corresponding buffer at 37°C for 30 min (Vazyme, TD501).
The stop buffer was added to the reaction to terminate the tagmentation. DNA Clean Beads were used to purify DNA. A subsequent PCR step was used to add an additional index to the fragments. Two biological replicates per sample were sequenced using a Novaseq 6000 (PE150, Illumina) by Novogene (Beijing).

value: BRAFV600E overexpression


title: 235_male_veh


title: 241_male_veh


title: 253_male_CYM


title: erythroid cells, V600E_ATACseq, D10, rep1

value: erythroid cells differentiated from UCB-CD34+


title: T1R-free, non-stimulated libray 11


title: v1225A_M

value: brain (hypothalamus)

value: caucasian

tag: body mass_index

tag: postmortem interval_(hr)


title: T1R-free, non-stimulated libray 12

tag: treatment


title: 251_male_CYM


title: erythroid cells, G_ATACseq, D10, rep2

tag: cell type

value: empty vector overexpression, treat with GDC-0879 small molecule


title: T1R-free, non-stimulated libray 15

tag: Sex


title: T1R-free, non-stimulated libray 10

value: BT/BB

tag: multibacilary


title: Liver_LR_11M5T_27me3_2022

value: Liver

tag: exposure

value: TBT

tag: ID

tag: risk group

value: low risk TBT


title: v5459A_M

tag: age (yr)


title: Liver_Veh_6M5V_27me3_2022

value: 5 months

tag: batch

tag: chip antibody


title: Liver_LR_14M5T_27me3_2022

tag: tissue

tag: strain


title: erythroid cells, G_ATACseq, D10, rep1


title: 226_female_CYM

value: prefrontal cortex

value: CYM


title: T1R-free, non-stimulated libray 9

tag: age at_diag

value: BB

tag: lesion (n)


title: T1R-free, non-stimulated libray 14

value: Male

tag: leprosy class

value: BT


title: erythroid cells, C_ATACseq, D10, rep2

value: empty vector overexpression, treat with DMSO


title: Liver_Veh_5M5V_27me3_2022

tag: age

value: Vehicle


title: 225_male_veh

tag: genotype


title: 224_female_CYM

tag: treatment


title: Liver_Veh_4M5V_27me3_2022


title: T1R-free, non-stimulated libray 7

tag: cell type

value: whole-blood

value: RPMI/HEPES


title: Liver_LR_6M5T_9me3_2022

tag: Sex


title: hNSC RNA CIRPSR_KO_ctrl rep6

city: Neuherberg

first: Juliane

last: Winkelmann

address: Ingolstaedter Landstr. 1

department: Institute of Neurogenomics

country: Germany

institute: Helmholtz-Zentrum München

data_processing:
reads were trimmed for adaptors and filtered for quality using Trimmomatic v0.39
reads were mapped with STAR v2.7.0a to the hg19 genome assembly
Assembly: hg19
Supplementary files format and content: tab-delimited txt file contains raw counts for each sample

source_name: hNSC

growth_protocol: Human Neural Stem Cells (hNSC) from Gibco™ (N7800-100) were cultured in StemPro® NSC SFM in dishes were coated with Geltrex

extract_protocol:
Cells were harvested 48 h after infection. RNA was extracted using the RNeasy Mini Kit (Qiagen)
The libraries were prepared using the TruSeq stranded mRNA Sample Preparation kit (Illumina), and sequenced in paired-end mode (2x100 bases) on the Novaseq6000 sequencer (Illumina) with a depth of  ≥ 10 Million reads per sample

treatment_protocol: hNSC were infected with lentivirus encoding CRISPR-activation or CRISPR/Cas9 machinery, with guides targeting either MEIS1 or MEIS2, or non-targeting control guides.

tag: cell line

value: hNSC

value: human neural stem cell


title: T1R-free, non-stimulated libray 6

tag: multibacilary


title: hNSC RNA CRISPR_KO_MEIS2 rep6


title: 227_male_veh


title: 221_male_veh


title: Liver_LR_5M5T_9me3_2022

tag: exposure

tag: ID


title: Liver_HR_10M5T_27me3_2022

tag: risk group

value: high risk TBT


title: T1R-free, non-stimulated libray 5


title: erythroid cells, C_ATACseq, D10, rep1

value: erythroid cells differentiated from UCB-CD34+


title: 220_female_CYM


title: 218_female_CYM


title: Liver_HR_4M5T_9me3_2022

value: Liver

tag: batch


title: hNSC RNA CRISPRa_ctrl rep6


title: T1R-free, non-stimulated libray 4

value: BT/BB


title: hNSC RNA CRISPR_KO_MEIS1 rep6


title: hNSC RNA CRISPRa_MEIS2 rep6


title: Liver_LR_18M5T_9me3_2022

value: TBT

value: low risk TBT

tag: chip antibody


title: Liver_HR_25M5T_9me3_2022

tag: tissue

value: 5 months


title: T1R-free, non-stimulated libray 2


title: 214_female_CYM

value: prefrontal cortex

value: CYM


title: 216_female_CYM


title: T1R-free, non-stimulated libray 3

value: Male

value: BB


title: T1R-free, non-stimulated libray 8


title: Liver_HR_17M5T_9me3_2022

tag: strain


title: hNSC RNA CRISPRa_MEIS1 rep6


title: 206_female_veh


title: T1R-free, non-stimulated libray 1

tag: age at_diag


title: hNSC RNA CIRPSR_KO_ctrl rep5


title: Liver_LR_16M5T_9me3_2022


title: hNSC RNA CRISPR_KO_MEIS1 rep5


title: 192_female_veh


title: Liver_HR_15M5T_9me3_2022


title: 186_female_veh


title: hNSC RNA CRISPRa_ctrl rep5


title: Liver_HR_13M5T_9me3_2022


title: 182_female_veh


title: hNSC RNA CRISPRa_MEIS2 rep5


title: 190_female_veh


title: Liver_HR_12M5T_9me3_2022


title: Liver_LR_11M5T_9me3_2022


title: hNSC RNA CRISPRa_MEIS1 rep5


title: In vivo cardiac fibroblasts from hearts with no injury - cardiac fibroblasts with loss of TCF21 3

description:
A4440
normalized_counts_allgenes_ALLconditions_Tcf21_KO_Control.csv

value: Heart

value: Cardiac fibroblast

value: 8-12 weeks old

value: Tamoxifen


title: hNSC RNA CIRPSR_KO_ctrl rep4

value: hNSC


title: hNSC RNA CRISPR_KO_MEIS2 rep4

value: human neural stem cell


title: Liver_Veh_6M5V_9me3_2022

value: Vehicle


title: In vivo cardiac fibroblasts from hearts with no injury - cardiac fibroblasts with loss of TCF21 2

description:
A4393
normalized_counts_allgenes_ALLconditions_Tcf21_KO_Control.csv


title: hNSC RNA CRISPR_KO_MEIS1 rep4


title: hNSC RNA CRISPRa_ctrl rep4


title: 204_female_veh


title: In vivo cardiac fibroblasts from hearts with no injury - control 3

description:
A4377
normalized_counts_allgenes_ALLconditions_Tcf21_KO_Control.csv


title: hNSC RNA CRISPR_KO_MEIS2 rep5


title: hNSC RNA CRISPRa_MEIS2 rep4


title: Liver_LR_14M5T_9me3_2022


title: Liver_TBT_5mo_4me1_2021_input_2021


title: Liver_HR_10M5T_9me3_2022

value: high risk TBT


title: Liver_TBT_5mo_4me3_2021_input_2021

value: Liver


title: Liver_TBT_5mo_27ac_2021_input_2021


title: In vivo cardiac fibroblasts from mice treated with angiotensin II/phenylephrine - TCF21 overexpressor 2

description:
B4486
normalized_counts_allgenes_ALLconditions_OverExpressorsvsControl.csv

value: Tamoxifen and Angiotensin II/phenylephrine


title: hNSC RNA CIRPSR_KO_ctrl rep3


title: hNSC RNA CRISPRa_MEIS1 rep4


title: Liver_Veh_5M5V_9me3_2022


title: In vivo cardiac fibroblasts from hearts with no injury - control 2

description:
A4376
normalized_counts_allgenes_ALLconditions_Tcf21_KO_Control.csv


title: BIG104A72

city: London

first: Victor

last: Tybulewicz

address: 1 Midland Road

country: United Kingdom

institute: Francis Crick Institute

data_processing:
Read trimming and adaptor removal with Trimmomatic (v 0.36)
Read alignment with STAR ( v 2.5.2a) and gene quantification with RSEM( v 1.2.31)
Differential expression analysis DESeq2
Assembly: GRCm38 Ensembl release 86
Supplementary files format and content: table of normalized counts per gene per sample obtained from DESeq

source_name: CD4+ T cell (isolated from lymph nodes)

growth_protocol: Naïve CD4+ T cells were activated on plate-bound anti-CD3e (145-2C11) and anti-CD28 (37.51) antibodies

extract_protocol:
Cells were lysed using QIAzol lysis kit (Qiagen) and RNA was extracted using RNAeasy mini kit (Qiagen) according to the manufacturer's instructions
cDNA library synthesis using KAPA mRNA HyperPrep Kit (Illumina) and libraries were sequenced on the Illumina HiSeq 4000 following manufacturer's protocols.
, single end, 75bp read length, 25million reads

treatment_protocol: We combined a loxP-flanked and a deleted allele of Wnk1 (Wnk1fl and Wnk1-) with a tamoxifen-inducible Cre recombinase expressed from the ROSA26 locus (ROSA26CreERT2, RCE) to generate Wnk1fl/+/RCE and Wnk1fl/-/RCE female mice. Female RAG1-/- recipient mice were irradiated with 1 dose of 5 Gy from a 37Cs source. Bone marrow cells were transferred intravenously into irradiated recipient mice which were maintained on 0.02% enrofloxacin (Baytril, Bayer Healthcare) for 4 weeks. The hematopoietic compartment was allowed to reconstitute for at least 8 weeks after bone marrow transfer. Chimeric mice were injected intraperitoneally with 2 mg tamoxifen in 100mL of corn oil on 3 consecutive days. Mice were sacrificed 7 days after initial tamoxifen injection and cervical, axial, brachial, inguinal, and mesenteric lymph nodes were harvested. Lymph nodes were dissociated into single cells and CD4+ T cell were enriched by negative depletion using magnetic-activated cell sorting. Samples were depleted for CD8+CD11b+CD11c+B220+GR1+ cells. Live naïve CD4+ T cells were then isolated using fluorescence-activated cell sorting. Samples were negatively depleted for dead (amine-reactive-dyehi) CD25+CD44+ cells and positively enriched for CD4+CDCD62L+ cells. Naïve CD4+ T cells were then resuspended in T cell media (RPMI-1640, 100 mM non-essential amino acids, 20 mM HEPES, 10% FCS, 100 U/mL Penicillin, 100 mg/mL Streptomycin, 2 mM L-glutamine, 100 mM 2-mercaptoethanol) at 106 cells/ml. Cells were then activated on plate-bound anti-CD3e (145-2C11) and anti-CD28 (37.51) for 0 (unactivated), 1, 3, 6, 12, or 24 hr (500,000 cells/(24-well plate) well). Antibodies were immobilized on 24-well cell culture plates by incubating 0.25ml of 4mg/ml anti-CD3e and 4mg/ml anti-CD28 overnight at 4°C.

value: stimulated with anti-CD3e (145-2C11) and anti-CD28 (37.51)

tag: activation/stimulation time

value: CD4+ T cell


title: In vivo cardiac fibroblasts from hearts with no injury - control 1

description:
A4375
normalized_counts_allgenes_ALLconditions_Tcf21_KO_Control.csv


title: Liver_TBT_5mo_active_2018_input_2018

value: 5 months

value: TBT


title: BIG104A71


title: In vivo cardiac fibroblasts from mice treated with angiotensin II/phenylephrine - control 3

description:
B4563
normalized_counts_allgenes_ALLconditions_OverExpressorsvsControl.csv

value: Pdgfra-creERT


title: hNSC RNA CRISPR_KO_MEIS2 rep3


title: In vivo cardiac fibroblasts from mice treated with angiotensin II/phenylephrine - TCF21 overexpressor 1

description:
B4568
normalized_counts_allgenes_ALLconditions_OverExpressorsvsControl.csv


title: In vivo cardiac fibroblasts from hearts with no injury - cardiac fibroblasts with loss of TCF21 1

description:
A4392
normalized_counts_allgenes_ALLconditions_Tcf21_KO_Control.csv


title: BIG104A70


title: Liver_TBT_5mo_active_2022_input_2022

value: Male


title: hNSC RNA CRISPR_KO_MEIS1 rep3


title: Liver_Veh_5mo_4me3_2021_input_2021


title: In vivo cardiac fibroblasts from mice treated with angiotensin II/phenylephrine - control 2

description:
B4561
normalized_counts_allgenes_ALLconditions_OverExpressorsvsControl.csv


title: hNSC RNA CRISPRa_ctrl rep3


title: BIG104A69


title: Liver_Veh_5mo_4me1_2021_input_2021


title: In vivo cardiac fibroblasts from mice treated with angiotensin II/phenylephrine - control 1

description:
B4559
normalized_counts_allgenes_ALLconditions_OverExpressorsvsControl.csv


title: BIG104A68


title: hNSC RNA CRISPRa_MEIS2 rep3


title: Tcf21-MCM/fl myocardial infarction; scRNA-seq

description: 10x genomics

data_processing:
Raw sequencing reads were processed on Cell ranger 5.0.1 from 10X Genomics. Reads were demultiplexed and aligned to the mm10 mouse genome.
Assembly: mm10
Supplementary files format and content: tab seperated value files and matrix files

extract_protocol:
Single cells were obtained by flow cytometry of live nucleated cells from cardiac tissue digests.
Single-cell droplet libraries were generated according to manufacturers’ instructions (Chromium Next GEM Single Cell 3’ Reagent Kits v3.1 (Dual index), PN-1000268, 10X Genomics; user guide CG000315). Samples had a greater than 70% viability. About 16,000 cells were loaded to recover 10,000 cells. Briefly, gel emulsion beads (GEM) were generated by combining gel beads, master mix containing the cells and partitioning oil and loaded onto a Chromium Next GEM Chip G at a low dilution. Poly-adenylated mRNA from the cell lysate contained in every GEM was reverse transcribed to cDNA adding an Illumina R1 primer sequence, unique molecular identifier (UMI) and the 10X barcode. The barcoded first-strand cDNA was then purified with MyoOne Silane DynaBeads (20000048, 10x Genomics) and amplified using 14 PCR cycles. The full-length barcoded cDNA was then enzymatically fragmented and size selected using SPRIselect (B23317, Beckman Coulter) and adaptor ligated. The cDNA was then amplified for library construction adding an Illumina R2 primer sequence, paired-end constructs with the P5 and P7 sequences used for Illumina amplification and sample indexes were added.

value: Interstitial cells

value: Tamoxifen and myocardial infarction


title: Liver_Veh_5mo_27ac_2021_input_2021


title: BIG104A67


title: hNSC RNA CRISPRa_MEIS1 rep3


title: Tcf21-MCM myocardial infarction; scRNA-seq

description: 10x genomics

value: Heart


title: hNSC RNA CIRPSR_KO_ctrl rep2


title: BIG104A66


title: Liver_Veh_5mo_active_2018_input_2018


title: BIG104A65


title: Liver_HR_17M5T_4me3_2022


title: hNSC RNA CRISPR_KO_MEIS1 rep2


title: hNSC RNA CRISPR_KO_MEIS2 rep2


title: Tcf21-MCM/fl baseline; scRNA-seq

description: 10x genomics


title: Tcf21-MCM baseline; scRNA-seq

description: 10x genomics


title: ATAC_nave-KO_rep2

first: Chen

last: Dong

address: Haidian District

department: Institute for Immunology and School of Medicine

data_processing:
1) ATAC-seq Peak Calling.The ATAC-seq reads were mapped to reference genome by using bowtie2 with the “-p 5 -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant” options, followed by removing low mapped quality reads, mitochondrial reads, duplications. Macs272 was used for peak calling with the setting of “-f BAM -B --nomodel --keep-dup all”. 2) ATAC-seq Differential Peak Analysis. The differential peak was analyzed by R package DiffBind73  with the FDR ≤ 0.01 and FC ≥ 1.5. 3) Motif Enrichment for ATAC-seq Peaks. Homer74 script findMotifsGenome was used to enrich motifs for ATAC-seq peaks with the “mm10 -p 30 -preparse -size -300,100 -len 8,10,12” options. Q-value ≤ 0.1 and p-value ≤ 0.01 were used as cutoff for significant enrichment.
Assembly: mm10
Supplementary files format and content: bigwig

extract_protocol:
ATAC-seq DNA library was constructed using TruePrep DNA Library Prep Kit V2 for Illumina and TruePrep Index Kit V2 for Illumina.
Briefly, 15,000~50,000 sorted cells were resuspended in 35μL lysis buffer (10mM Tris-HCl, 10mM NaCl, 3mM MgCl2, 0.1% IGEPAL CA-630) and incubated on ice for 10 min with 3 times vortex. DNA fragmentation was conducted by adding 10μL 5 X TTBL, 5μL TTE Mix and shaking at 37℃ for 30 min. Fragmented DNA was purified using 1.8 X AMPure beads, barcoded with dual indexes and PCR amplified. Size selection and purification of DNA fragments were done using AMPure beads. Size distribution and molarity of the sequencing library were determined by Qubit (Thermo Fisher Scientific). Sequencing was performed using Illumina X-ten by Novogene. Every sample has two replicates.

value: spleens and lymph nodes

value: cd8+ T cell

value: TRIM28 knockout


title: BIG104A63


title: Liver_HR_15M5T_4me3_2021


title: Liver_HR_25M5T_4me3_2022


title: hNSC RNA CRISPRa_MEIS2 rep2

value: hNSC

value: human neural stem cell


title: Liver_HR_13M5T_4me3_2022

value: high risk TBT


title: BIG104A64


title: BIG104A62


title: ATAC_nave-KO_rep1


title: Liver_HR_10M5T_4me3_2022

value: Liver


title: ATAC_naive_WT_rep1

value: WT


title: BIG104A60

value: stimulated with anti-CD3e (145-2C11) and anti-CD28 (37.51)


title: ATAC_activated_KO_rep2


title: Liver_HR_12M5T_4me3_2022


title: ATAC_naive_WT_rep2


title: hNSC RNA CRISPRa_MEIS1 rep2


title: hNSC RNA CIRPSR_KO_ctrl rep1


title: BIG104A58

value: CD4+ T cell


title: Liver_HR_4M5T_4me3_2021

value: 5 months


title: hNSC RNA CRISPRa_ctrl rep2


title: Liver_HR_1M5T_4me3_2018

value: TBT


title: BIG104A57


title: Liver_LR_6M5T_4me3_2021

value: low risk TBT


title: BIG104A59


title: BIG104A61


title: Liver_LR_5M5T_4me3_2021

value: Male


title: hNSC RNA CRISPRa_ctrl rep1


title: hNSC RNA CRISPR_KO_MEIS2 rep1


title: ATAC_activated_KO_rep1


title: Liver_LR_4M5T_4me3_2018


title: hNSC RNA CRISPR_KO_MEIS1 rep1


title: ATAC_activated_WT_rep1


title: ATAC_Activated_rep2


title: BIG104A55


title: BIG104A56


title: ATAC_Activated_rep1


title: hNSC RNA CRISPRa_MEIS2 rep1


title: hNSC RNA CRISPRa_MEIS1 rep1


title: BIG104A53


title: Liver_LR_16M5T_4me3_2021


title: BIG104A54


title: Liver_LR_18M5T_4me3_2022


title: CD34 cells, V600E_RNAseq, D6, rep2

data_processing:
PKUHPC(High-Performance Computing Platform of the Center for Life Sciences (Peking University))
Trimmed sequence reads were mapped to hg19 using Bowtie2. Read count extraction and normalization were performed using PKUHPC (High-Performance Computing Platform of the Center for Life Sciences (Peking University)).
Assembly: hg19
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: CD34+ cells

extract_protocol:
RNA was extracted with TRIzol following the manual of RNA isolater Total RNA Extraction Reagent (Vazyme Biotech, Cat.# R401-01)
Total RNA quality was assessed using Agilent 2100 bioanalyzer and then 1 μg of total RNA was quantified using the Qubit High-sensitivity kit (Life Technologies, Q32852), and the RNA-seq library was constructed by NEBNext UltraTM RNA Library Prep Kit for Illumina (NEB, E7530L).

value: CD34+ cells

value: BRAFV600E overexpression


title: ATAC_activated_WT_rep2


title: ATAC_Naive_rep2


title: ATAC_Naive_rep1


title: CD34 cells, GDC_RNAseq, D6, rep2

value: treat with GDC-0879 small molecule


title: CD34 cells, V600E_RNAseq, D6, rep1


title: Liver_LR_14M5T_4me3_2022


title: BIG104A52


title: diabetic skin, replicate 1

city: Los Angeles

first: Riki

last: Kawaguchi

state: CA

address: 760 Westwood Plaza, Room 37-420

department: Department of Psychiatry and Neurology Department of Psychiatry

institute: University of California, Los Angeles

description: diabetic skin, replicate 1

data_processing:
Cell Ranger from 10x Genomics was used for alignment and quantification
Assembly: mm10
Supplementary files format and content: Barcodes, features, and count matrix, in the forms of tab-separated values and market exchange format, in a zipped file for each sample

source_name: skin

extract_protocol:
Cells are sorted live immune and non-immune cells from the skin and nerve of  diabetic and control mice.
The scRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3' Reagent Kit v3.1 following the manufacturer's instructions (10X Genomics).

value: skin

value: Cd45+ immune cells

value: High Fat High Fructose Diet


title: BIG104A50


title: Liver_LR_11M5T_4me3_2022


title: Liver_LR_5M5T_4me3_2018


title: BIG104A49


title: CD34 cells, CTRL_RNAseq, D6, rep1

value: control


title: Liver_LR_6M5T_4me3_2018


title: CD34 cells, CTRL_RNAseq, D6, rep2


title: diabetic skin, replicate 2

description: diabetic skin, replicate 2


title: CD34 cells, GDC_RNAseq, D6, rep1


title: Liver_LR_3M5T_4me3_2018


title: BIG104A48


title: CD34 cells, WT_ATACseq, D6, rep2

library_source: other

data_processing:
The adaptors were removed from the raw ATAC-seq paired data using trim_galore software with default parameters. Trimmed cleaned reads were aligned to human reference genome hg19 using Bowtie2 (version 2.3.4.1)S14 with default parameters and converted to bam files using samtoolsS7. ATAC-seq peaks were identified using MACS2S15 with the following parameters: “-q 0.05 --nomodel --shift -100 --extsize 200”. The signal enrichment plot around the TSS of all protein coding genes was generated using deeptools. The example tracks were visualized using IGV softwareS16. The motifs of ATAC-seq peaks were enriched using Homer softwareS17.
Assembly: hg19
Supplementary files format and content: BW files include cleaned reads for each Sample

molecule: other

extract_protocol:
1x103 infected or treated day 5 matained CD34+ cells were lysed in lysis buffer (10 mM Tris-HCl (pH 7.4), 10 mM NaCl, 3 8 mM MgCl2 and NP-40) on ice for 5 min to extract nuclei. The cells were centrifuged at 500 g for 5 min to remove the supernatant. The nuclei were incubated with the Tn5 transposome and corresponding buffer at 37°C for 30 min (Vazyme, TD501).
The stop buffer was added to the reaction to terminate the tagmentation. DNA Clean Beads were used to purify DNA. A subsequent PCR step was used to add an additional index to the fragments. Two biological replicates per sample were sequenced using a Novaseq 6000 (PE150, Illumina) by Novogene (Beijing).

value: BRAFWT overexpression


title: diabetic nerve, replicate 2

description: diabetic nerve, replicate 2

source_name: sciatic nerve

value: sciatic nerve


title: diabetic nerve, replicate 1

description: diabetic nerve, replicate 1


title: control skin, replicate 2

description: control skin, replicate 2

value: Control Diet


title: BIG104A47


title: CD34 cells, WT_ATACseq, D6, rep1


title: CD34 cells, V600E_ATACseq, D6, rep2


title: Liver_Veh_9M5V_4me3_2021

value: Liver

value: Vehicle


title: Liver_Veh_5M5V_4me3_2021


title: BIG104A46

value: stimulated with anti-CD3e (145-2C11) and anti-CD28 (37.51)

value: CD4+ T cell


title: BIG104A51


title: control nerve, replicate 2

description: control nerve, replicate 2

value: WT


title: CD34 cells, V600E_ATACseq, D6, rep1


title: Liver_Veh_4M5V_4me3_2021

value: 5 months


title: BIG104A45


title: control skin, replicate 1

description: control skin, replicate 1


title: CD34 cells, GDC_ATACseq, D6, rep2


title: Liver_LR_2M5T_4me3_2018

value: Male

value: TBT

value: low risk TBT


title: control nerve, replicate 1

description: control nerve, replicate 1


title: Liver_Veh_6M5V_4me3_2018


title: scRNA-seq of tumor-bearing muse brain: M002

city: Birmingham

first: Jianmei

middle: Wu

last: Leavenworth

state: AL

address: 1670 University Boulevard

department: Neurosurgery

institute: UAB

data_processing:
The barcoded processing, gene counting were made using the Cell Ranger Count v7.1.0(https://cloud.10xgenomics.com/cloud-analysis)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: glioma tumor-bearing brain

extract_protocol:
glioma tumor-bearing brain tissue  was digested into a single cell suspension and single cells were sorted using fluorescence-activated cell sorting (FACS) using CD45- and CD45+ fractions.
Library was constructed using manufacturer's protocol (single cell 3' v3 protocol, 10X genomics)

value: glioma tumor-bearing brain

value: M002 oncolytic herpes simplex virus (oHSV)


title: Liver_Veh_5M5V_4me3_2018


title: CD34 cells, CTRL_ATACseq, D6, rep2

value: CD34+ cells


title: BIG104A42


title: BIG104A43


title: CD34 cells, GDC_ATACseq, D6, rep1

value: treat with GDC-0879 small molecule


title: Retina, Normoxia

city: Basel

first: Duygu

last: Karademir Sigurdsson

address: Klybeckstrasse 200

country: Switzerland

institute: Institute of Molecular and Clinical Ophthalmology Basel

description:
10X Genomics
seurat_object.rds

data_processing:
Demultiplexing was performed with cellranger mkfastq (v3)
cellranger count (v3) was used for alignment to reference genome and generating feature counts for single barcodes.
cellranger aggr (v3) was used to combine samples in the same matrix.
Seurat v3.2 was used for downstream normalization, scaling, dimensionality reduction, and clustering. Harmony was used for batch correction.
Assembly: GRCm38.p5 Release_91-2018-02-26
Supplementary files format and content: Final analysis as a Seurat object. Normoxic samples have the barcode suffix "_1", and hypoxic samples have the barcode suffix "_2".

source_name: Retina

extract_protocol:
Retinas were isolated with the Winkler method, and the vitreous was cleared in ice-cold 1X PBS. The retinas were then digested with the Worthington Tissue Dissociation kit to generate single-cell suspensions. These suspensions were fixed in methanol prior to sequencing and kept at -80°C. The samples were rehydrated immediately before loading onto a 10X Genomics chip to generate cell-bead suspensions (v3 chemistry).
Library construction was performed according to 10X Genomics standard protocols.
Single Cell 3' v3 chemistry

treatment_protocol: Mice were exposed to 7% oxygen for 6 hours to induce hypoxic conditions in the retina.

value: Retina

value: normoxic


title: BIG104A41


title: BIG104A40


title: Retina, Hypoxia

description:
10X Genomics
seurat_object.rds

value: 7% oxygen, 6 hours


title: CD34 cells, CTRL_ATACseq, D6, rep1

value: control


title: Liver_Veh_3M5V_4me3_2018

value: Liver


title: ChIP-WT_CTCF-rep2

data_processing:
1) The ChIP-seq reads were mapped to reference genome by using bowtie2 with the “-p 5 -t -q -N 1 -L 25 -X 2000 --no-mixed --no-discordant” options, followed by removing low mapped quality reads, mitochondrial reads, duplications. PCR duplicates were removed using picard MarkDuplicates. Macs272 was used for peak calling with the setting of “-f BAM -B --nomodel --keep-dup all”. 2) ChIP-seq and CUT&Tag Differential Peak Analysis. The differential peak was analyzed by R package DiffBind73  with the FDR ≤ 0.01 and FC ≥ 1.5.
Assembly: mm10
Supplementary files format and content: bigwig

source_name: spleens and lymph nodes

extract_protocol:
ChIP assay was performed using Active Motif’s ChIP assay kit (53035) according to manufacturer’s instructions with slight modifications
Briefly, a total of 1 x 107 cells were harvested and cross-linked with paraformaldehyde. Then cells were lysed and digested with shearing enzyme followed by sonication. Anti-TRIM28 antibody (Active Motif, 61173), Anti-CTCF (CST, 3418), Anti-SMC1 (Bethyl Laboratories, A300-055A), and Anti-H3k27ac (Active motif, 39133) was added to supernatant followed by Dynabeads Protein A (LifeTechnologies) pulling down target fragment. The precipitated DNA was then washed, eluted, de-crosslinked and purified for realtime qPCR analysis or sent to BGI Genomics for cDNA library preparation and sequencing. Every sample has two replicates.

value: spleens and lymph nodes

value: CTCF

value: cd8+ T cell


title: BIG104A39

value: stimulated with anti-CD3e (145-2C11) and anti-CD28 (37.51)

value: CD4+ T cell


title: Liver_Veh_2M5V_4me3_2018

value: Male

value: 5 months

value: Vehicle


title: ChIP-KO_CTCF-rep2

value: TRIM28 knockout


title: BIG104A44


title: H3K27me3_RKO_Input

city: Grand Rapids

first: Scott

last: Rothbart

state: MI

address: 333 Bostwick Avenue NE

institute: Van Andel Research Institute

data_processing:
ChIP sequencing reads were 3’ trimmed and filtered for quality and adapter content using TrimGalore (v0.6.0) with “trim_galore --quality 25 –fastqc --paried” and the quality was assessed by FastQC (v0.11.8). Reads were aligned to human assembly hg38 with bowtie2 (v2.3.5) using “bowtie2 -I 0 -X 1000 --end-to-end --sensitive” and were deduplicated using removeDups from samblaster (v.0.1.24). SAM files were converted to BAM files, sorted, and indexed using samtools (v1.9). MACS2 and siQ-ChIP were used independently for peak calling and signal normalization. MACS2 peaks were called using “macs2 callpeak -f BAMPE --broad -B” for H3K9me3 and H3K27me3 ChIP-seq, and using “macs2 callpeak -f BAMPE -B” for UHRF1 and H3K18ub ChIP-seq, with Input as the control. For siQ-ChIP normalization, aligned SAM files were then processed for pair-end reads with high mapping quality (MAQ > 20), correct pair orientation (Sam Flags = 99, 163), and fragment length as described for siQ-ChIP (https://github.com/BradleyDickson/siQ-ChIP) using “awk -v MAQ=20 '$5>=MAQ && $2==99 || $5>=MAQ && $2==163 {print $3"\t"$4"\t"$4+$9-1}' sample.sam | awk '$2<=$3 {print $1"\t"$2"\t"$3"\t"$3-$2}' | sort -k1,1 -k2,2n > sample.bed”. Param.in files were prepared for each sample with all required parameters and measurements required for siQ-ChIP normalization. IP tracks (bigwig files) (with H3K9me3, H3K18ub, UHRF1, and H3K27me3 efficiency values) were generated with the execution of “./getsiq.sh > errorfile” with the EXPlayout file (NOTE: params.in and EXPlayout files are provided with the GEO accession).
Assembly: hg38
Supplementary files format and content: bigwig
Supplementary files format and content: narrowPeak
Supplementary files format and content: broadPeak
Supplementary files format and content: siQ-ChIP EXPlayout
Supplementary files format and content: siQ-ChIP parameters

source_name: RKO

growth_protocol: RKO cells were cultured on gelatin-coated dishes in RPMI 1640 medium with L-glutamine (Gibco), supplied with 1X penicillin/streptomycin (Invitrogen), 0.1 mM non-essential amino acids (GIBCO), 1 mM Sodium Pyruvate (GIBCO), and 10% Fetal Bovine Serum (Millipore Sigma) at 5% CO2 and 37°C. Cells were passaged every 2−3 days by removal of medium, wash in PBS, dissociation by 1X trypsin, resuspension in medium, and pelleting by centrifugation, followed by resuspension, and plating at a density of approximately 1 million cells/10 cm dish.

extract_protocol:
Chromatin preparation: After the indicated treatments, RKO cells were crosslinked with 1% formaldehyde. The chromatin preparation for H3K9me3, UHRF1, and H3K27me3 ChIP were performed using sonication-based chromatin shearing as follows: About 10 million cells were resuspended in cell lysis buffer and nuclei were isolated and chromatin was fragmented with a Covaris E220 Evolution Focused-Ultrasonicator for 12 min with default settings. The chromatin preparation for H3K18ub ChIP was performed using MNase digestion as follows: About 10 million cells were resuspended in cell lysis buffer and nuclei were isolated and fragmented by 50U MNase (NEB). The digested chromatin was further solubilized with Covaris E220 Evolution Focused-Ultrasonicator for 1 min with default settings. IP: 5 ul H3K9me3 antibody (Active Motif,Cat#39161) and 5 ug of soluble chromatin, 2.5 ul UHRF1 antibody (Bioworld,Cat# BS7227) and 10 ug soluble chromatin, 5 ul H3K18ub antibody (Cell Signaling, Cat#37771) and 20 ug soluble chromatin, and 5 ul H3K27me3 antibody (Cell Signaling,Cat#9733) and 5 ug soluble chromatin were incubated at 4°C for 18 hours. Samples were immunoprecipitated with 30 ul Dynabeads Protein A magnetic beads (Thermo Fisher Scientific) at 4°C for 2 hours followed by washes. IP chromatin was eluted and the eluted chromatin was subject to reverse crosslink and DNA purification before sequencing.
Libraries for Input and IP samples were prepared by the Van Andel Genomics Core from 10 ng of input material and all available IP material using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems, Wilmington, MA USA). Prior to PCR amplification, end repaired and A-tailed DNA fragments were ligated to uniquely barcoded dual indexes (IDT, Coralville, IA USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.), QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA), and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). 50 bp, paired-end sequencing was performed on an Illumina NovaSeq6000 sequencer using an S2, 100 bp sequencing kit (Illumina Inc., San Diego, CA, USA) to a minimum read depth of 50M read pairs per IP library and 100M read pairs per Input library. Base calling was done by Illumina RTA3 and the output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).

treatment_protocol: RKO cells were introduced with doxycycline (Dox)-inducible shRNA targeting UHRF1 (tet-on shUHRF1). UHRF1 knockdown (KD) was performed by 4-day treatment with 20ng/mL Dox before cell collection. DNMT1 inhibition was performed by 2-day treatment with 1uM GSK862 before cell collection. Equivalent amount of DMSO was added to un-treated cell as DMSO control.

value: RKO

tag: antibody

value: Cell Signaling,Cat#9733

value: DMSO


title: BIG104A38


title: Liver_Veh_1M5V_4me3_2018

data_processing:
Data quality was assessed using FastQC and low quality basepairs were removed using TrimGalore
ChIP-Seq reads were mapped to the mouse genome build UCSC mm10 using bowtie2 and duplicate reads were removed
Peaks were called using MACS2
bigWig files were generated using deeptools v3.5.2
Assembly: mm10
Supplementary files format and content: bigWig

source_name: Liver

extract_protocol:
Chromatin was cross-linked with formaldehyde, the reaction stopped with glycine, and sonicated with a bioruptor to obtain fragment sizes of 100–300 bp for ChIP-seq. ChIP-validated antibodies used were directed against H3K4me3 (Active Motif #39915), H3K4me1 (Abcam ab8895), H3K27ac (Abcam ab4729), H3K27me3 (Active Motif #61017), and H3K9me3 (Active Motif #61013). Immunoprecipitated DNA was recovered and purified using the QIAquick PCR Purification kit (Qiagen)
QIAseq FX DNA library kit or the QIAseq Ultralow Input Library Kit

tag: age


title: H3K27me3_RKO_UHRF1 KD+DNMT1i_rep2

value: DNMT1 inhibitor_GSK3484862 + shUHRF1


title: Liver_LR_6M5T_4me1_2021

value: TBT

value: low risk TBT


title: KO_input

tag: genotype


title: BIG104A37

tag: treatment


title: scRNA-seq of tumor-bearing muse brain: saline

value: glioma tumor-bearing brain

value: saline control


title: Liver_Veh_4M5V_4me3_2018

value: Liver


title: H3K27me3_RKO_UHRF1 KD_rep2


title: WT_input

value: spleens and lymph nodes

tag: cell type

value: WT


title: BIG104A36

value: stimulated with anti-CD3e (145-2C11) and anti-CD28 (37.51)


title: H3K27me3_RKO_UHRF1 KD_rep1


title: KO_H3K27ac

value: cd8+ T cell


title: Liver_LR_16M5T_4me1_2021

tag: Sex

value: Male


title: H3K27me3_RKO_DNMT1i_rep2

tag: cell line

value: DNMT1 inhibitor_GSK3484862


title: BIG104A34

value: CD4+ T cell


title: Liver_HR_4M5T_4me1_2021

value: 5 months

value: high risk TBT


title: Liver_HR_15M5T_4me1_2021


title: BIG104A35


title: Input


title: BIG104A33


title: Liver_HR_25M5T_4me1_2022


title: H3K27me3_RKO_DMSO control_rep2

value: RKO

value: Cell Signaling,Cat#9733


title: BIG104A32


title: H3K27me3_RKO_UHRF1 KD+DNMT1i_rep1

value: DNMT1 inhibitor_GSK3484862 + shUHRF1


title: Liver_LR_5M5T_4me1_2021

value: TBT


title: rnaseq_antiil2_rep2

data_processing:
1) Raw data processing. Raw sequencing reads were first adapter-trimmed by Trim Galore v0.4.4 with the “--paired” option, and aligned to mm10 reference genome with HISAT2 (version 2.2.1) with “-X 600 --rg-id --rg --known-splicesite-infile --novel-splicesite-outfile -p 25 --reorder” options. StringTie (v2.1.4) was used for transcript quantification with GENCODE vM12 annotation and “-e -B -p 10 -G -o” options. “prepDE.py” script was used to extract the read count information directly from the gtf files generated by StringTie with “-i -g -t” options. The reads count per gene was regarded as the gene expression. 2) Differential Genes Analysis. The gene expression matrix was normalized and analyzed by DESeq2 as the software recommended.
Assembly: mm10
Supplementary files format and content: CSV  file includes normalized counts for each Sample

extract_protocol:
Total RNA from CD8+ T cells was extracted by TRIzol (Invitrogen) according to manufacturer’s instruction.
total RNA was sent to BGI Genomics for cDNA library preparation and sequencing. Every sample has two replicates.


title: BIG104A31


title: H3K18ub_RKO_Input

value: Cell Signaling, Cat#37771

value: DMSO


title: Liver_LR_14M5T_4me1_2022

value: low risk TBT


title: Liver_HR_13M5T_4me1_2022

value: Liver


title: H3K18ub_RKO_UHRF1 KD+DNMT1i_rep2


title: BIG104A30


title: WT_H3k27ac

value: spleens and lymph nodes


title: H3K18ub_RKO_UHRF1 KD+DNMT1i_rep1


title: Liver_LR_18M5T_4me1_2022


title: Liver_LR_11M5T_4me1_2022


title: BIG104A28


title: H3K27me3_RKO_DNMT1i_rep1


title: rnaseq_wt_rep1

value: WT


title: Activated_rnaseq_ko_rep2

value: TRIM28 knockout


title: trim28

value: cd8+ T cell


title: H3K18ub_RKO_UHRF1 KD_rep2


title: Liver_HR_10M5T_4me1_2022

value: Male


title: Activated_rnaseq_ko_rep1


title: Liver_LR_6M5T_4me1_2018


title: BIG104A26

value: stimulated with anti-CD3e (145-2C11) and anti-CD28 (37.51)


title: H3K27me3_RKO_DMSO control_rep1


title: rnaseq_antiil2_rep1


title: Activated_rnaseq_wt_rep2


title: H3K18ub_RKO_DNMT1i_rep1

value: DNMT1 inhibitor_GSK3484862


title: H3K18ub_RKO_DNMT1i_rep2


title: BIG104A25

value: CD4+ T cell


title: Liver_HR_4M5T_4me1_2018

value: 5 months

value: high risk TBT


title: Liver_LR_5M5T_4me1_2018


title: Activated_rnaseq_wt_rep1


title: rnaseq_wt_rep2


title: BIG104A24


title: BIG104A29


title: H3K18ub_RKO_DMSO control_rep2

value: RKO


title: EW-22/TR/shControl Dox +, 1 biological Rep, 96h

type: RNA

city: Heidelberg

first: Thomas

middle: Georg Philipp

last: Grunewald

address: Im Neuenheimer Feld 280

department: Division of Translational Pediatric Sarcoma Research

institute: German Cancer Research Center (DKFZ)

description: Gene expression data

hyb_protocol: Following fragmentation, 10 μg of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Clariom D™ Arrays. Microarrays were washed and stained with Affymetrix GeneChip® 3000 Fluidics Station.

scan_protocol: Microarrays were scanned with Affymetrix GeneChip® 3000 Scanner.

data_processing:
The data were analyzed with RMA using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
processed data value: RMA signal intensity

label: Biotin

source_name: shRNA Control

label_protocol: Biotinylated cRNA were prepared using Affymetrix GeneChip® WT PLUS Reagent Kit according to its manufacture's instruction from 6 μg total RNA.

growth_protocol: 100.000-200.000 cells were cultured in T-25 flasks for 96h.

extract_protocol: RNA was extracted with RNA isolation kits from Macherey-Nagel.

treatment_protocol: Cells were treated with/without doxycycline (0.1 μg/ml) for 96h with a refreshment after 48h.

tag: disease state

value: Ewing Sarcoma


title: Liver_LR_3M5T_4me1_2018

tag: exposure

value: TBT


title: EW-22/TR/shControl Dox -, 1 biological Rep, 96h

description: Gene expression data


title: BIG104A23


title: BIG104A22


title: Liver_LR_2M5T_4me1_2018

tag: ID


title: H3K18ub_RKO_DMSO control_rep1

value: Cell Signaling, Cat#37771


title: UHRF1_RKO_Input

value: Bioworld,Cat# BS7227

value: DMSO


title: H3K18ub_RKO_UHRF1 KD_rep1


title: EW-22/TR/shGLRX3_2 Dox +, 1 biological Rep, 96h

description: Gene expression data

source_name: shRNA against GLRX3 5UTR, CDS region


title: BIG104A27


title: Liver_HR_1M5T_4me1_2018

value: Liver

tag: risk group


title: BIG104A21


title: UHRF1_RKO_UHRF1 KD+DNMT1i_rep2

value: DNMT1 inhibitor_GSK3484862 + shUHRF1


title: Liver_Veh_9M5V_4me1_2021

value: Vehicle

tag: batch


title: BIG104A20


title: UHRF1_RKO_UHRF1 KD+DNMT1i_rep1


title: EW-22/TR/shGLRX3_2 Dox -, 1 biological Rep, 96h

description: Gene expression data


title: BIG104A19


title: EW-22/TR/shGLRX3_1 Dox +, 1 biological Rep, 96h

description: Gene expression data


title: Liver_Veh_4M5V_4me1_2021

tag: chip antibody


title: EW-22/TR/shGLRX3_1 Dox -, 1 biological Rep, 96h

description: Gene expression data


title: UHRF1_RKO_UHRF1 KD_rep2


title: Liver_Veh_5M5V_4me1_2021

tag: tissue


title: A-673/TR/shGLRX3_2 Dox +, 1 biological Rep, 96h

description: Gene expression data


title: Liver_Veh_6M5V_4me1_2018

tag: strain


title: BIG104A18


title: Liver_Veh_5M5V_4me1_2018


title: A-673/TR/shGLRX3_2 Dox -, 1 biological Rep, 96h

description: Gene expression data


title: BIG104A17


title: UHRF1_RKO_DNMT1i_rep2


title: A-673/TR/shGLRX3_1 Dox +, 1 biological Rep, 96h

description: Gene expression data


title: UHRF1_RKO_UHRF1 KD_rep1


title: BIG104A16


title: Liver_Veh_4M5V_4me1_2018


title: UHRF1_RKO_DNMT1i_rep1


title: BIG104A15


title: Liver_Veh_3M5V_4me1_2018


title: A-673/TR/shGLRX3_1 Dox -, 1 biological Rep, 96h

description: Gene expression data


title: BIG104A14


title: BIG104A13


title: Liver_Veh_1M5V_4me1_2018


title: Z-3-HAC_shoot_17h_2

city: Ghent

first: Willem

last: Desmedt

address: Valentin Vaerwyckweg 1

department: Plants and Crops

country: Belgium

institute: Ghent University

data_processing:
Trimming and adapter removal (Trimmomatic v 0.39; settings: 5 bp sliding window, trim if Phred < 20, discard if < 40 bp after trimming)
Alignment to rice genome (Rsubread v 2.6.4)
Read counting (Rsubread v 2.6.4)
Differential expression analysis (DESeq2 v 1.74.1)
Assembly: Os-Nipponbare-Reference-IRGSP-1.0
Supplementary files format and content: Count table, untransformed (in .csv format)

organism: Oryza sativa

source_name: Shoots, whole

growth_protocol: As described in https://doi.org/10.1111/nph.18152

extract_protocol:
Flash freezing + grinding in liquid nitrogen-cooled pestle and mortar + Qiagen RNEasy Plant Mini kit
Lexogen QuantSeq 3’ mRNA-Seq Library Prep Kit FWD

treatment_protocol: As described in https://doi.org/10.1104/pp.15.00107

value: Shoots, whole

tag: Stage

value: 3 weeks after germination

tag: cultivar

value: Kitaake

tag: time


title: Liver_LR_6M5T_27ac_2021

value: Male

tag: age

value: low risk TBT


title: BIG104A12

value: unstimulated

tag: activation/stimulation time

value: CD4+ T cell

tag: genotype


title: H3K9me3_RKO_UHRF1 KD+DNMT1i_rep2

tag: antibody

value: Active Motif,Cat#39161

tag: treatment


title: Z-3-HAC_shoot_17h_1


title: BIG104A11

tag: cell type


title: H3K9me3_RKO_UHRF1 KD+DNMT1i_rep1

tag: cell line

value: RKO


title: Liver_LR_5M5T_27ac_2021

tag: Sex

value: 5 months

tag: exposure


title: Mock_shoot_17h_3

value: Mock


title: Liver_HR_4M5T_27ac_2021

value: TBT

tag: ID

tag: risk group

value: high risk TBT


title: Mock_shoot_17h_2


title: UHRF1_RKO_DMSO control_rep2

value: Bioworld,Cat# BS7227

value: DMSO


title: BIG104A9


title: H3K9me3_RKO_UHRF1 KD_rep2


title: H3K9me3_RKO_UHRF1 KD_rep1


title: Mock_shoot_17h_1


title: BIG104A10


title: BIG104A8


title: Z-3-HAC_shoot_17h_3


title: Liver_Veh_2M5V_4me1_2018

value: Liver

tag: batch

tag: chip antibody


title: BIG104A7

tag: strain


title: Z-3-HAC_shoot_1h_3

tag: tissue

tag: Stage


title: Liver_LR_16M5T_27ac_2021


title: Liver_HR_15M5T_27ac_2021


title: UHRF1_RKO_DMSO control_rep1


title: H3K9me3_RKO_DNMT1i_rep2

value: DNMT1 inhibitor_GSK3484862


title: H3K9me3_RKO_DNMT1i_rep1


title: Liver_HR_25M5T_27ac_2022


title: H3K9me3_RKO_Input


title: BIG104A6


title: Z-3-HAC_shoot_1h_1

value: Shoots, whole

tag: cultivar

tag: time


title: H3K9me3_RKO_DMSO control_rep1


title: Liver_HR_17M5T_27ac_2022

tag: age


title: Mock_shoot_1h_2

value: 3 weeks after germination


title: H3K9me3_RKO_DMSO control_rep2


title: BIG104A5

tag: activation/stimulation time

tag: genotype


title: RNA-seq_RKO_UHRF1_KD+DNMT1i_rep3

description:
RNA-seq_Dox+GSK_3
cpm_counts_genenames.txt
raw_counts.tsv
de_res.Dox.GSK_vs_Veh.tsv
de_res.Dox.GSK_vs_GSK.tsv

data_processing:
Raw 50 bp paired-end reads were trimmed with TrimGalore! followed by quality control analysis with FastQC. Trimmed reads were aligned to GRCh38.p12 and indexed to GENCODE v29 via STAR (v2.5.3a) aligner with flags ‘-twopassMode Basic\ -quantMode GeneCounts’ for feature counting. ReadsPerGene output count files were constructed into a raw read count matrix in R. Low count genes were filtered (1 count in at least one sample) prior to edgeR (v3.36.0) count normalization. Differential expression analysis was conducted using DESeq2(1.40.1). Genes were considered differentially expressed if |Log2FC| > 1 and FDR < 0.01.
Assembly: hg38
Supplementary files format and content: tab-delimited text file includes raw counts and CPM normalzied counts for each sample
Supplementary files format and content: tsv file includes DESeq2 analyses of differential expression results between treatment groups

extract_protocol:
TRIzol Reagent (Invitrogen) was added directly to adhered cells, collected, and stored at -80°C. After thawing, total RNA was extracted following the manufacturer’s protocol, and RNA was resuspended in DEPC Nuclease-Free water.
Libraries were prepared by the Van Andel Institute Genomics Core (RRID:SCR_022913) from 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. Prior to PCR amplification, cDNA fragments were ligated to IDT for Illumina TruSeq UD Indexed adapters (Illumina Inc, San Diego CA, USA). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies, Inc.) and QuantiFluor® dsDNA System (Promega Corp., Madison, WI, USA).  Individually indexed libraries were pooled and 50 bp, paired end sequencing was performed on an Illumina NovaSeq6000 sequencer to an average depth of 50M raw paired-reads per transcriptome. Base calling was done by Illumina RTA3 and output of NCS was demultiplexed and converted to FastQ format with Illumina Bcl2fastq (v1.9.0).

tag: treatment

value: shUHRF1_doxycycline+DNMT1 inhibitor


title: BIG104A4

tag: cell type


title: RNA-seq_RKO_UHRF1_KD+DNMT1i_rep1

description:
RNA-seq_Dox+GSK_1
cpm_counts_genenames.txt
raw_counts.tsv
de_res.Dox.GSK_vs_Veh.tsv
de_res.Dox.GSK_vs_GSK.tsv

tag: cell line


title: BIG104A3


title: RNA-seq_RKO_UHRF1_KD+DNMT1i_rep2

description:
RNA-seq_Dox+GSK_2
cpm_counts_genenames.txt
raw_counts.tsv
de_res.Dox.GSK_vs_Veh.tsv
de_res.Dox.GSK_vs_GSK.tsv


title: Z-3-HAC_root_17h_3

source_name: Roots, whole

value: Roots, whole

value: Kitaake


title: Z-3-HAC_shoot_1h_2


title: Mock_shoot_1h_1


title: Liver_LR_14M5T_27ac_2022

tag: Sex

value: Male

value: low risk TBT


title: BIG104A2

value: unstimulated

value: CD4+ T cell


title: 1.00 μM Triacsin C, MM.1S GFP(+) Luc(+), 24 hours, Biol Rep 3

city: Burlington

first: Princess

last: Rodriguez

state: Vermont

address: 89 Beaumont Avenue

department: Microbiology and Molecular Genetics

institute: University of Vermont

data_processing:
RNA sequence data was analyzed using the nf-core/rnaseq pipeline v3.9 using the Nextflow workflow manager v22.10.2
Raw reads were subjected to quality checking and reporting (FastQC v0.11.9/ MultiQC v1.13; and low quality sequence (Phred score <20)  using Trim Galore v 0.6.7 were removed
Reads were aligned to the Homo sapiens hg38 reference genome using STAR v2.7.10a and SAMtools v1.15.1.
Read counts were quantified using SALMON v1.5.2, and DESeq2 v1.28.0 was used to identify differentially expressed genes (log2FC |1|, padj < 0.05) and identified via the Wald test and adjusted for multiple testing using the Benjamini and Hochberg method
Assembly: Homo sapiens hg38
Supplementary files format and content: merged tab-delimited Salmon quantified gene abundance per sample

source_name: MM.1S GFP (+) Luciferace (+)

growth_protocol: MM.1S GFP(+) Luciferase (+) were maintained in RPMI-1640 (Gibco) + 10% Fetal Bovine Serum (FBS, VWR) and 1% Antibiotic/Antimycotic (ThermoFisher Scientific) under humid conditions with 5% CO2 at 37 Celcius in tissue-culture treated

extract_protocol:
RNA was isolated using the Qiagen RNeasy Plus Mini Kit (Qiagen) according to the manufacturer’s protocol.
Sequence libraries were prepared with SMARTer® Stranded Total RNA-Seq Kit v2 (Takara Bio) library prep on 6 ng of total RNA

treatment_protocol: MM.1S GFP(+) Luciferase (+) cells were treated with either vehicle (dimethyl sulfoxide) or 1.00 μM triacsin C (Cayman Chemicals) for 24 hours in RPMI-1640 + 10% FBS + 1% Antibiotic/Antimycotic under humid conditions with 5% CO2 at 37 C

value: MM.1S GFP (+) Luciferace (+)

value: Multiple Myeloma

value: KRAS Gly12Ala, TRAF3 Val536_Asn545del

value: 1.00 μM Triacsin C

value: 24 hours

value: Female


title: Liver_LR_11M5T_27ac_2022

value: Liver

value: 5 months

tag: exposure

value: TBT


title: Z-3-HAC_root_17h_2

value: 3 weeks after germination


title: Mock_shoot_1h_3

value: Shoots, whole

value: Mock


title: Liver_HR_12M5T_27ac_2022

tag: ID

value: high risk TBT


title: BIG104A1


title: Liver_LR_18M5T_27ac_2022

value: Male

tag: risk group


title: RNA-seq_RKO_DNMT1i_rep2

description:
RNA-seq_GSK_2
cpm_counts_genenames.txt
raw_counts.tsv
de_res.GSK_vs_Veh.tsv
de_res.Dox.GSK_vs_GSK.tsv

value: RKO

value: 1uM DNMT1 inhibitor_GSK3484862


title: 1.00 μM Triacsin C, MM.1S GFP(+) Luc(+), 24 hours, Biol Rep 2


title: Liver_LR_6M5T_27ac_2018

value: low risk TBT

tag: batch


title: Z-3-HAC_root_17h_1

value: Roots, whole

value: Kitaake


title: Mock_root_17h_3


title: Liver_HR_13M5T_27ac_2022

tag: chip antibody


title: RNA-seq_RKO_UHRF1_KD_rep3

description:
RNA-seq_Dox_3
cpm_counts_genenames.txt
raw_counts.tsv
de_res.Dox_vs_Veh.tsv


title: 1.00 μM Triacsin C, MM.1S GFP(+) Luc(+), 24 hours, Biol Rep 1

value: MM.1S GFP (+) Luciferace (+)

value: Multiple Myeloma

value: KRAS Gly12Ala, TRAF3 Val536_Asn545del


title: Liver_LR_5M5T_27ac_2018

tag: strain


title: Vehicle (DMSO), MM.1S GFP(+) Luc(+), 24 hours, Biol Rep 3

value: Vehicle (DMSO)

value: 24 hours

value: Female


title: Mock_root_17h_2

tag: tissue


title: RNA-seq_RKO_DNMT1i_rep3

description:
RNA-seq_GSK_3
cpm_counts_genenames.txt
raw_counts.tsv
de_res.GSK_vs_Veh.tsv
de_res.Dox.GSK_vs_GSK.tsv

value: 1uM DNMT1 inhibitor_GSK3484863


title: Liver_HR_4M5T_27ac_2018

value: Liver

value: 5 months

value: TBT


title: Vehicle (DMSO), MM.1S GFP(+) Luc(+), 24 hours, Biol Rep 2


title: RNA-seq_RKO_UHRF1_KD_rep1

description:
RNA-seq_Dox_1
cpm_counts_genenames.txt
raw_counts.tsv
de_res.Dox_vs_Veh.tsv


title: Liver_LR_3M5T_27ac_2018


title: RNA-seq_RKO_DMSO control_rep3

description:
RNA-seq_Veh_3
cpm_counts_genenames.txt
raw_counts.tsv

value: DMSO


title: Vehicle (DMSO), MM.1S GFP(+) Luc(+), 24 hours, Biol Rep 1


title: Mock_root_17h_1

tag: Stage

value: 3 weeks after germination

value: Mock


title: Liver_HR_10M5T_27ac_2022

value: Male

value: high risk TBT


title: Liver_LR_2M5T_27ac_2018

value: low risk TBT


title: Liver_HR_1M5T_27ac_2018


title: RNA-seq_RKO_DMSO control_rep2

description:
RNA-seq_Veh_2
cpm_counts_genenames.txt
raw_counts.tsv

value: RKO


title: Z-3-HAC_root_1h_2

value: Roots, whole

tag: cultivar

value: Kitaake


title: RNA-seq_RKO_UHRF1_KD_rep2

description:
RNA-seq_Dox_2
cpm_counts_genenames.txt
raw_counts.tsv
de_res.Dox_vs_Veh.tsv


title: Liver_Veh_9M5V_27ac_2021

value: Vehicle


title: RNA-seq_RKO_DNMT1i_rep1

description:
RNA-seq_GSK_1
cpm_counts_genenames.txt
raw_counts.tsv
de_res.GSK_vs_Veh.tsv
de_res.Dox.GSK_vs_GSK.tsv

value: 1uM DNMT1 inhibitor_GSK3484862


title: Z-3-HAC_root_1h_1

tag: time


title: RNA-seq_RKO_DMSO control_rep1

description:
RNA-seq_Veh_1
cpm_counts_genenames.txt
raw_counts.tsv


title: Mock_root_1h_3


title: x1225C_M

hyb_protocol: The next day, the slides were washed twice in 1X PBS-T followed by an incubated wash in post hybridization wash buffer (Xenium Post Hybridization Wash Buffer, Part No. 2000395, 10X Genomics). Three washes of 1X PBS-T were completed before addition of ligation mix to each slide.Slides were then incubated at 37℃ for 2 hours . After ligation, the slides were washed three times in 1X PBS-T, and then incubated in an amplification master mix at 30℃ for 2 hours. After amplification, slides were washed three times in TE buffer followed by three washes in 1X PBS and then incubated in diluted reducing reagent B for 10 minutes at room temperature. Slides were then washed in 70% ethanol followed by two washes of 100% ethanol. Autofluorescence solution was then added to each slide and incubated in the dark for 10 minutes at room temperature. Slides were then rinsed three times with 100% ethanol before drying on a 37℃ preheated thermocycler for 5 minutes. Additional washes were performed before adding Xenium Nuclei Staining Buffer, which incubated for 1 minute in the dark at room temperature. Slides were then washed three times in 1X PBS-T and stored at 4℃ prior to being loaded on the Xenium analyzer at the Johns Hopkins Single Cell & Transcriptomics Core (SCTC). The solutions needed to run the Xenium analyzer were prepared according to the manufacturer's instructions. Region selection was guided by our team with instrument operation performed by the SCTC Core.

scan_protocol: The Xenium instrument was used for automated imaging and onboard processing of the data.

data_processing:
Original Xenium outputs per above were generated with different versions of the Xeniumranger software / Xenium instrument firmware. In order to mitigate these discrepancies, we re-ran Xeniumranger resegment version 1.7 on all samples with resegment-nuclei set to TRUE. (Incidentally, the results only changed if this setting was enabled, despite neither version being initially processed with version 1.7). All subsequent processing was performed per code in the github repository at https://github.com/LieberInstitute/spatial_HYP .
In the raw data, transcripts are microscope-detected instances of specific sequential fluorescent outputs in a given pixel location, corresponding to serial target-specific tags on a hybridization probe. Nuclei and cell segmentation boundaries are polygonal coordinates of the segmented nuclei and cells as defined by Xeniumranger 1.7.

source_name: Hypothalamus

label_protocol: For probe hybridization, ligation, and amplification, the 10X Genomics protocol: Xenium In Situ Gene Expression was followed (CG000582, Rev E). The probe hybridization solution was then prepared. We used a combination of the off-the shelf “human brain,” probe panel designed by 10X Genomics (Xenium Human Brain Gene Expression Panel, Part No.1000599) and our custom probe panel (10X Genomics; Xenium Custom Gene Expression Panel, Part No. 1000561). Details of the custom probe panel design are described in the manuscript. Probe mix was applied to each slide, a cassette lid was applied to each slide cassette and the slides were incubated at 50℃ overnight.

growth_protocol: Hypothalamus was dissected from frozen (-80C), unfixed postmortem human tissue. 10 micron coronal sections were obtained by cryosectioning. RNAscope was performed on tissue sections to confirm VMH (NR5A1 positive) and ARC (NPY positive); tissue blocks containing these hypothalamic areas were then sectioned to collect 10 micron coronal sections onto microscopy slides for Xenium.

extract_protocol: enium slides were fixed and permeabilized according to 10X Genomics’ Xenium In Situ for Fresh Frozen Tissues – Fixation & Permeabilization Protocol (CG000581, Rev C).

tag: postmortem interval (hours)

tag: age (years)

tag: body mass index

tag: xenium run (2 slides per run)


title: Liver_Veh_5M5V_27ac_2021

tag: age


title: Met_3

first: Chad

last: Creighton

address: One Baylor Plaza, Mail Stop: BCM305

department: Biostatistics, Ducan Cancer Center

description: MDA-MB-231 cells treated with metformin, biological replicate 3

data_processing:
Sequenced reads in FASTQ files were mapped to hg19 whole genome using STAR, and Fragments Per Kilobase of transcript per Million mapped reads (FPKM) were calculated using Cufflinks.
Assembly: hg19
Supplementary files format and content: tab-delimited text files include UCSC transcript id and their FPKM values along with confidence intervals for each sample.

growth_protocol: MDA-MB-231 cell line was from the American Type Culture Collection (ATCC).

extract_protocol:
Total RNA was extracted using RNeasy Kit (Qiagen) by the manufacture’s instruction. RNA purity and concentration were measured using Nanodrop.
Preparation of RNA library and transcriptome sequencing was conducted by Novogene Corporation Inc. (Sacramento, CA USA). The datasets were processed and analyzed using Illumina NovaSeq 6000 Sequencing System.

treatment_protocol: Cells were treated with metformin (5mM) or vehicle control.

tag: cell line

tag: treatment

value: metformin


title: Liver_Veh_4M5V_27ac_2021

first: Amrit

last: Koirala

address: 1 Baylor Plaza

tag: Sex

tag: exposure


title: Mock_root_1h_2


title: Met_2

description: MDA-MB-231 cells treated with metformin, biological replicate 2


title: x1225B_M


title: Mock_root_1h_1


title: x6588C_F

value: Female


title: Met_1

description: MDA-MB-231 cells treated with metformin, biological replicate 1


title: Z-3-HAC_root_1h_3


title: x8741D_F


title: KO_rep2

first: Ruifeng

last: Li

address: haidian

institute: Tsinghua University

data_processing:
We performed read mapping and filtering of the Hi-C data following previous methods. All Hi-C sequencing reads were mapped to the mouse reference genome (mm10) using HiC-Pro (v2.11.4). We used the iterative correction and eigenvector decomposition (ICE) method to normalize raw interaction matrices.
Assembly: mm10
Supplementary files format and content: .hic files

extract_protocol:
The Hi-C experiment was performed following the in situ Hi-C protocol
a total of 1 x 106 cells were isolated and crosslinked with 1% formaldehyde for 10 min at room temperature, and next, 2.5 M glycine solution was added at a final concentration of 0.2 M. Then, the cells were collected, flash-frozen in liquid nitrogen and stored at -80°C. The fixed cells were then lysed on ice-cold Hi-C lysis buffer for 30 minutes on ice, followed by Mbo I (NEB, R0147) digestion overnight. The next day, treat sample at 62 ° C for 10 min to inactivate Mbo I, and then biotin-14-dATP (Life Technologies, 19524-016) was added to label the digested ends. Then, add ligation master mix (NEB, B0202 & M0202) and connect overnight. On the third day, use Covaris LE220 (Covaris) to break the end-ligated DNA fragments to a suitable length, followed by size selection with AMPure XP beads (Beckman Coulter, A63881). Dynabeads MyOne Streptavidin T1 beads (Life Technologies, 65602) pull down the biotin-labeled fragments, and these fragments are the fragments that truly represent chromatin interactions.

value: spleens and lymph nodes

tag: cell type

value: cd8+ T cell

tag: genotype

value: TRIM28 knockout


title: x8741C_F


title: Liver_Veh_6M5V_27ac_2018

value: Liver

value: 5 months

tag: ID

tag: risk group

tag: batch

tag: chip antibody


title: x1735C_M


title: Liver_Veh_5M5V_27ac_2018

tag: tissue

tag: strain


title: WT_rep2

value: WT


title: KO_rep1


title: x1735B_M

tag: postmortem interval (hours)


title: x5993C_F

tag: age (years)


title: Con_2

description: MDA-MB-231 cells treated with control, biological replicate 2

value: control


title: Con_1

description: MDA-MB-231 cells treated with control, biological replicate 1


title: Con_3

description: MDA-MB-231 cells treated with control, biological replicate 3


title: Liver_Veh_4M5V_27ac_2018

value: Male


title: x5993B_F

tag: body mass index


title: Liver_Veh_3M5V_27ac_2018


title: vegetative cells, sad1.2 csi1Δ, biological replicate 3

city: Salamanca

first: Alberto

last: Pineda-Santaella

address: Pintor Fernando Gallego

country: Spain

institute: IBFG

description: growth in rich medium at 30ºC

data_processing:
BGI platform quality control-filtered (score >= 37) sequences reads were mapped to the Schizosaccharomyces pombe (strain 972 h-) reference genome (assembly ASM294v2.47 from Pombase) using HISAT2.
Feature reads counts were obtained with htseq-count using the genome annotation file for the corresponding assembly from Pombase.
Generated SAM/BAM files were used to perform the differential gene expression analysis with DESeq2.
Plots were done with R and Rstudio.
Assembly: Schizosaccharomyces pombe, strain 972 h-, assembly ASM294v2.47
Supplementary files format and content: tab-delimited text file contains normalized abundance measurements

organism: Schizosaccharomyces pombe

source_name: vegetative haploid cells

growth_protocol: An asynchronic culture of 30 mL of exponentially-growing cells at an O.D. of 0.5.

extract_protocol:
The crashed pellet is deep-frozen again and submitted to RNA extraction protocol from the Rneasy Kit (QIAGEN, Cat. No. / ID: 74104), obtaining a sample of total RNA in 50 μL of Rnase-free water.
5 ug of this total RNA sample was enriched in mRNA through oligo dT selection and the library was prepared and sequenced as paired-end via DNB technology by the BGI platform.

treatment_protocol: The culture is spinned down and washed twice with equal volume of miliQ water and the pellet is deep-frozen in liquid nitrogen. The frozen pellet is covered by liquid nitrogen in a pestle and gently fragmented and crushed with a mortar down to dust.

value: vegetative haploid cells

value: sad1.2 csi1{delta}


title: Liver_Veh_2M5V_27ac_2018

institute: Baylor College of Medicine


title: naive_rep2

city: Beijing


title: x6197B_M

first: Keri

last: Martinowich

address: 855 N Wolfe St Suite 300

tag: xenium run (2 slides per run)


title: vegetative cells, sad1.2 csi1Δ, biological replicate 2

description: growth in rich medium at 30ºC


title: Liver_Veh_1M5V_27ac_2018

tag: age


title: naive_rep1


title: WT_rep1


title: x8667B_F


title: vegetative cells, sad1.2 csi1Δ, biological replicate 1

description: growth in rich medium at 30ºC


title: ChIP-WT-Igg-1

tag: cell line

value: Igg


title: x5459C_M


title: vegetative cells, wt control, biological replicate 3

description: growth in rich medium at 30ºC

value: wt


title: ChIP-WT-CTCF-rep1

value: CTCF


title: vegetative cells, wt control, biological replicate 2

description: growth in rich medium at 30ºC


title: ChIP-KO-Igg-1


title: x5459B_M


title: vegetative cells, wt control, biological replicate 1

description: growth in rich medium at 30ºC


title: dmWT_UV0hr_rep2_A3

city: Pullman

first: John

middle: J.

last: Wyrick

state: WA

address: Biotechnology Life Sciences 241

department: School of Molecular Biosciences

institute: Washington State University

description: Replicate 2

data_processing:
Base calling by Torrent_Suite 5.0.4
Fastq files were separated into individual libraries using A1-A6 barcodes, and the barcode sequences were trimmed, as well as the 3' nucleotide of the sequencing read, using a custom perl script
Fastq files were aligned to the Drosophila genome (dm6) using bowtie2-2.2.6 software to generate SAM files
SAM files were converted to BAM files using samtools
BAM files were converted to BED files using BEDTOOLS2 bamtoBed
Damage coordinates were mapped using custom perl script
Only reads mapping to dipyrimidine sequences (i.e., TT, TC, CT, CC), corresponding to CPD lesions were retained in BED file using custom perl script.
BED files were converted to WIG file using COUNT function of IGVTools
Assembly: dm6
Supplementary files format and content: WIG files containing counts of DNA CPD lesion reads filtered for only dipyrimidine mapping sequences. A sequencing read count was assigned half-integer positions calculated as the average position of the lesion-containing dipyrimidine sequence (i.e., for a CPD lesion occurring at a dipyrimidine at positions 10 and 11, a read count would be assigned to position 10.5). For no UV (untreated samples), just a txt file with dinucleotide counts are provided
Library strategy: CPD-seq

organism: Drosophila melanogaster

source_name: Drosophila S2 cells

growth_protocol: Drosophila S2 cells were grown at 28°C in  Schneider’s Drosophila medium  supplemented with 10% heat-inactivated fetal bovine serum , 100 U/ml of penicillin, 100 g/ml of streptomycin, and 0.25 g/ml of amphotericin B.

extract_protocol:
Genomic DNA was isolated from the cell pellets using GenElute Mammalian genomic DNA miniprep kits (G1N70, Sigma-Aldrich)
CPD-seq procedure is adopted from the published emRiboSeq method (Nature Protocols 2015 10, 1433–1444). Briefly, DNA fragments were first ligated to a double-stranded adaptor DNA trP1, and free 3'-OHs were blocked by terminal transferase and dideoxy-ATP.  CPD lesions were  cleaved with T4 endonuclease V and apurinic/apyrimidinic (AP) endonuclease, APE 1, to generage new 3'-OHs. DNA was then ligated to adaptor  A. Up to 3 different barcoded A adaptors (A1: AAGAGGAT; A2: TTCGTGAT; A3: CCTGAGAT) were used to generate libraries for different experiments. DNA was purified with Streptavidin beads and amplified for up to 6 cycles in a PCR reaction with primers complimentary to A and trP1, and the resulting DNA libraries were used for DNA sequencing.

treatment_protocol: Upon ~80% confluence the culture medium was removed, washed once with 1X phosphate buffered saline (PBS) and layered with 2ml of sterile PBS. The cells were exposed to 100 J/m2 UVC. Following irradiation, PBS was removed, and cells were harvested with vigorous pipetting and pelleted for the “UV cellular” sample. For "UV naked DNA", isolated genomic DNA from unirradiated cells was spotted on clean cover glass and exposed to 80 J/m2 UVC.

value: Drosophila S2 cells

tag: treatment

value: UV irradiated 100 J/m2


title: Naive_Astrocytes_CLEC16A_KO_library

city: Boston

first: Zhaorong

address: 60 Fenwood Road

institute: Dana Farber Cancer Institute

description:
Library name: Naive_Astrocytes_CLEC16A_KO
Astrocytes Isolated by FACS sorting from Naive CLEC16A condition knockout mice

data_processing:
scRNA-Seq data was demultiplexed and quantified using the Cellranger multi function (GRCm38 reference genome), generating a count matrix for each scRNA-Seq sample; cells with more than 500 genes detected and less than 25% mitochondrial contents were retained for analysis.
Assembly: GRCm38
Supplementary files format and content: RDS format of Seurat Objects, which contains the metadata information and the count matrix for all the libraries

source_name: CNS

extract_protocol:
For single cell RNA-sequencing, CNS cells from n=3 Control EAE and n=3 CLEC16AGFAP EAE (Day 23) were hashed before FACS sorting using multiplex 3’ Cell Plex Set Kit A (#100261, 10x Genomics).  After sorting and washing,  astrocytes from 6 samples were pooled and loaded into one well of a 10X Chromium Next GEM Chip G (10X Genomics).
Single-cell libraries were further generated using the Single Cell 3’ Reagent Kit v3.1 chemistry (10x Genomics) using Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 (PN-1000128) according to the manufacturer’s protocol. The generated scRNA-seq libraries were sequenced by NOVA-Seq S1 at the Broad Institute.

value: CNS

value: Astrocytes

value: CLEC16A Knockout


title: ChIP-KO-CTCF-rep1

value: spleens and lymph nodes

value: cd8+ T cell


title: dmWT_NoUV_rep2_A2


title: Tfh cells, control 2

status: Public on Dec 02 2024

city: Suzhou

first: Lyu

last: Fulian

address: Renai Street

institute: Soochow University

data_processing:
The Fastp software was used to remove reads that contained adaptor contamination, low-quality bases, and undetermined bases with default parameters. Differentially expressed genes (DEGs) were selected with a fold change (FC) > 1.5 and p-value < 0.05 using the R package edgeR. Enrichment analysis for the functions of the DEGs was conducted using GSEApy (version 0.10.2) in Python3.
Assembly: mm8
Supplementary files format and content: gene_fpkm.txt

source_name: spleen

extract_protocol:
Mouse naïve CD4+ T cells were polarized under Tfh conditions in the presence or absence of DMF for 3 days.
Total RNAs were extracted and then subjected to RNA-seq on the Illumina HiSeq2000 in LC Bio.

value: spleen

value: Mouse primary cells


title: dmWT_UV0hr_A1

description: Replicate 1

value: WT


title: Tfh cells, DMF 1

value: DMF-treated


title: Tfh cells, DMF 2


title: EAE_Astrocytes_CLEC16A_KO_library

description:
Library name: EAE_Astrocytes_CLEC16A_KO
Astrocytes Isolated by FACS sorting from EAE induced CLEC16A condition knockout mice


title: Tfh cells, control 1


title: PHILO, Arabidopsis, H3K9ac, 20K, rep2

city: Piscataway

first: Mark

last: Zander

address: 190 Frelinghuysen Rd

institute: Rutgers State University of New Jersey

data_processing:
ChIP-seq reads were aligned to the TAIR10 (Arabidopsis thaliana).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and IgG samples as controls.
Assembly: TAIR10 (Arabidopsis thaliana)
Supplementary files format and content: bigwig
Supplementary files format and content: domain.csv

organism: Arabidopsis thaliana

source_name: 10-day-old whole seedling

growth_protocol: Ten-day-old Col-0 Arabidopsis seedlings, grown under a 16 h light/8 h dark cycle were used for PHILO ChIP-seq analysis.

extract_protocol:
Tissues were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'->5' exo-) (New England Biolabs)), adapter ligation (1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).

treatment_protocol: No treatment

value: whole seedling

value: 10 days

value: anti-H3K9ac (39137, Active Motif)

tag: ecotype


title: dmWT_nakedDNA_A1

description: Replicate 1

source_name: Genomic DNA derived from Drosophila S2 cells

value: UV irradiated 80 J/m2


title: CUT&Tag, Arabidopsis, H3K9ac, rep2

data_processing:
ChIP-seq reads were aligned to the TAIR10 (Arabidopsis thaliana).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and IgG samples as controls.
Assembly: TAIR10 (Arabidopsis thaliana)
Supplementary files format and content: bigwig
Supplementary files format and content: domain.csv
Library strategy: CUT&Tag


title: PHILO, Arabidopsis, H3K9ac, 100K, rep2


title: PHILO, Arabidopsis, H3K9ac, 100K, rep1


title: PHILO, Arabidopsis, H3K9ac, Sonic_0.001g, rep2


title: PHILO, Arabidopsis, H3K9ac, 500K, rep1


title: PHILO, Arabidopsis, H3K9ac, eChIP rep1


title: PHILO, Arabidopsis, H3K9ac, eChIP rep2


title: PHILO, Arabidopsis, H3K9ac, Sonic_0.001g, rep1


title: PHILO, Arabidopsis, H3K9ac, 500K, rep2


title: PHILO, Arabidopsis, H3K9ac, 14cyc, rep2


title: PHILO, Arabidopsis, H3K9ac, 10cyc, rep2


title: PHILO, Arabidopsis, H3K9ac, 12cyc, rep1


title: PHILO, Arabidopsis, H3K9ac, 10cyc, rep1


title: CUT&Tag, Arabidopsis, H3K9ac, rep1


title: PHILO, Arabidopsis, H3K9ac, 12cyc, rep2


title: PHILO, Arabidopsis, H3K9ac, 5M, rep2


title: PHILO, Arabidopsis, H3K9ac, 10M, rep2


title: PHILO, Arabidopsis, H3K9ac, 2M, rep2


title: PHILO, Arabidopsis, H3K9ac, 5M, rep1


title: PHILO, Arabidopsis, H3K9ac, 14cyc, rep1


title: PHILO, Arabidopsis, H3K9ac, 10M, rep1


title: PHILO, Arabidopsis, H3K9ac, 1M, rep2


title: PHILO, Arabidopsis, H3K9ac, 20K, rep1


title: PHILO, Arabidopsis, H3K9ac, 0.5M, rep1


title: PHILO, Arabidopsis, H3K9ac, 0.5M, rep2


title: PHILO, Arabidopsis, H3K9ac, 1M, rep1


title: PHILO, Arabidopsis, IgG, MNase, rep2

data_processing:
ChIP-seq reads were aligned to the TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa) using Bowtie2 (version 2.4.1).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and IgG samples as controls.
Assembly: TAIR10 (Arabidopsis thaliana), SLM_r2.0.pmol (Solanum lycopersicum), cs10 (Cannabis sativa)
Supplementary files format and content: bigwig, domain.csv

growth_protocol: Ten-day-old Col-0 Arabidopsis seedlings, two-week-old Micro-Tom tomato (Solanum lycopsericum) seedlings, and two-week-old Otto II Boax hemp (Cannabis sativa)seedlings grown under a 16 h light/8 h dark cycle were used for PHILO ChIP-seq analysis.

extract_protocol:
Tissues were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'5' exo-) (New England Biolabs)), adapter ligation(1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).

treatment_protocol: no treatment

value: IgG (#015-000-003, Jackson ImmunoResearch)


title: PHILO, Arabidopsis, H3K9ac, 2M, rep1


title: PHILO, Arabidopsis, IgG, MNase, rep1


title: PHILO, Arabidopsis, H3K9ac, MNase_0.005g, rep1


title: PHILO, Arabidopsis, H3K9ac, MNase_Single_seedling_0.1g, rep2


title: PHILO, Arabidopsis, H3K9ac, MNase_0.1g, rep2


title: PHILO, Arabidopsis, H3K9ac, MNase_0.005g, rep2


title: PHILO, Arabidopsis, H3K9ac, MNase_Single_seedling_0.1g, rep1


title: PHILO, Arabidopsis, H3K9ac, sonic_0.1g, rep1


title: PHILO, Arabidopsis, H3K9ac, MNase_0.1g, rep1


title: PHILO, Arabidopsis, H3K9ac, sonic_0.1g, rep2


title: PHILO, Col-0, IgG, ctrl, rep3

data_processing:
ChIP-seq reads were aligned to the TAIR10 genome using Bowtie2 (version 2.4.1).
To generate ChIP-seq coverage plots, bamCoverage (binSize 5) from deepTools (version 3.5.2) was used.
Histone marks domains were identified with epic2 (version 0.0.52) using default parameters and Col-0 IgG samples as controls.
MYC2 DNA binding peaks were identified with MACS2 (version 2.2.7.1) by comparing two biological replicates of untreated (ctrl) and 2 h JA-treated myc2 MYC2:MYC2-FLAG seedlings.
Assembly: TAIR10
Supplementary files format and content: bigwig, narrowPeak, domain.csv

growth_protocol: Arabidopsis seedlings were grown for 10 days under long day conditions.

extract_protocol:
Seedlings were crosslinked with 1% formaldehyde solution for 2 x 10 min. After quenching, samples were shock-frozen, ground and chromatin was subsequently extracted. Chromatin was sonicated with a Diagenode Bioruptor.
Libraries were prepared as follows. End repair (5 μl of End Repair Reaction Buffer + 2.5 μl of End Repair Enzyme Mix from the NEBNext End Repair Module (New England Biolabs)), A-tailing (2.5 µl NEBnext dA-Tailing Reaction Buffer + 1.5 µl Klenow Fragment (3'5' exo-) (New England Biolabs)), adapter ligation(1 µl TruSeq DNA Unique Dual Indexes (UDIs) v2 (Illumina), 2.5 µl T4 DNA Ligase Reaction Buffer + 1.25 µl T4 DNA Ligase (New England Biolabs)), and PCR enrichment (12.5 µl NEBNext High-Fidelity 2X PCR Master Mix (New England Biolabs).

treatment_protocol: Seedlings were either untreated or treated for the indicated hours with gaseous MeJA.

value: 10-day-old whole seedling

value: control


title: PHILO, jazD, H3K9ac, WD, rep3

value: jazD

value: 2h JA withdrawal


title: Set2, Col-0, ctrl, rep1

data_processing:
RNA-seq reads were aligned to the TAIR10 genome using STAR software (version 2.7.5a).
Transcripts were quantified for each sample with RSEM (version 1.3.3).
Differentially expressed genes between ctrl and 2h JA samples in each of the two sets (Set1: two biologcal repliactes, Set2: three biological replicates) were identified with edgeR (version 3.36.0).
Assembly: TAIR10
Supplementary files format and content: genes.results files including TPM and FPKM values for each sample.
Supplementary files format and content: edgeR analysis output as tab-delimited text files

growth_protocol: Arabidopsis seedlings were grown for 10 days under long day conditions

extract_protocol:
Total RNA of Col-0 seedlings was extracted using RNeasy Plant Mini Kit (Qiagen).
cDNA library preparation was carried out with a TruSeq Stranded mRNA Library Prep kit (Illumina) following the manufacturer’s protocol.

treatment_protocol: Seedlings were either untreated or treated for the indicated hours with gaseous MeJA


title: Set2, Col-0, ctrl, rep2


title: Set2, Col-0, 2hJA, rep1

value: 2 h JA


title: PHILO, jazD, H3K9ac, 2hJA, rep3

value: 2h JA


title: Set1, Col-0, 2hJA, rep1


title: Set2, Col-0, 2hJA, rep2


title: PHILO, jazD, H3K9ac, WD, rep2


title: Set1, Col-0, ctrl, rep1


title: PHILO, jazD, H3K9ac, 2hJA, rep2


title: PHILO, jazD, H3K9ac, WD, rep1


title: Set2, Col-0, ctrl, rep3


title: Set1, Col-0, 2hJA, rep2


title: PHILO, Col-0, IgG, ctrl, rep1


title: PHILO, jazD, H3K9ac, 2hJA, rep1


title: PHILO, jazD, H3K9ac, 1hJA, rep2

value: 1h JA


title: PHILO, jazD, H3K9ac, 1hJA, rep1


title: PHILO, jazD, H3K9ac, ctrl, rep2


title: PHILO, jazD, H3K9ac, ctrl, rep3


title: PHILO, jazD, H3K9ac, 1hJA, rep3


title: Set2, Col-0, 2hJA, rep3


title: PHILO, jazD, H3K9ac, ctrl, rep1


title: PHILO, tpltpr1tpr4, H3K9ac, WD, rep3


title: Set1, Col-0, ctrl, rep2


title: PHILO, tpltpr1tpr4, H3K9ac, WD, rep1


title: PHILO, Col-0, IgG, ctrl, rep2


title: PHILO, tpltpr1tpr4, H3K9ac, 2hJA, rep3


title: PHILO, tpltpr1tpr4, H3K9ac, 2hJA, rep1


title: PHILO, tpltpr1tpr4, H3K9ac, ctrl, rep2


title: PHILO, tpltpr1tpr4, H3K9ac, 1hJA, rep1


title: PHILO, tpltpr1tpr4, H3K9ac, 1hJA, rep2


title: PHILO, tpltpr1tpr4, H3K9ac, ctrl, rep3


title: PHILO, tpltpr1tpr4, H3K9ac, 1hJA, rep3


title: PHILO, hda6, H3K9ac, 2hJA, rep2


title: PHILO, tpltpr1tpr4, H3K9ac, ctrl, rep1


title: PHILO, hda6, H3K9ac, 2hJA, rep3


title: PHILO, hda6, H3K9ac, 2hJA, rep1


title: PHILO, hda6, H3K9ac, 1hJA, rep2


title: PHILO, hda6, H3K9ac, 1hJA, rep3


title: PHILO, hda6, H3K9ac, WD, rep2


title: PHILO, hda6, H3K9ac, ctrl, rep1


title: PHILO, tpltpr1tpr4, H3K9ac, WD, rep2


title: PHILO, hda6, H3K9ac, ctrl, rep3


title: PHILO, ninja, H3K9ac, WD, rep2

value: ninja


title: PHILO, ninja, H3K9ac, WD, rep1


title: PHILO, ninja, H3K9ac, 2hJA, rep3


title: PHILO, ninja, H3K9ac, WD, rep3


title: PHILO, hda6, H3K9ac, 1hJA, rep1


title: PHILO, ninja, H3K9ac, 2hJA, rep2


title: PHILO, ninja, H3K9ac, 1hJA, rep3


title: PHILO, ninja, H3K9ac, 2hJA, rep1


title: PHILO, ninja, H3K9ac, 1hJA, rep2


title: PHILO, ninja, H3K9ac, 1hJA, rep1


title: PHILO, hda6, H3K9ac, WD, rep1


title: PHILO, hda6, H3K9ac, WD, rep3


title: PHILO, ninja, H3K9ac, ctrl, rep3


title: PHILO, ninja, H3K9ac, ctrl, rep2


title: PHILO, hac1, H3K9ac, 2hJA, rep3


title: PHILO, hac1, H3K9ac, 2hJA, rep1


title: PHILO, hac1, H3K9ac, 1hJA, rep3


title: PHILO, hac1, H3K9ac, 2hJA, rep2


title: PHILO, hac1, H3K9ac, WD, rep3


title: PHILO, hac1, H3K9ac, WD, rep1


title: PHILO, tpltpr1tpr4, H3K9ac, 2hJA, rep2


title: PHILO, hda6, H3K9ac, ctrl, rep2


title: PHILO, hac1, H3K9ac, 1hJA, rep1


title: PHILO, hac1, H3K9ac, ctrl, rep3


title: PHILO, hac1, H3K9ac, 1hJA, rep2


title: PHILO, hac1, H3K9ac, ctrl, rep1


title: PHILO, hac1, H3K9ac, ctrl, rep2


title: PHILO, med25, H3K9ac, WD, rep1


title: PHILO, med25, H3K9ac, WD, rep3


title: PHILO, med25, H3K9ac, 2hJA, rep3


title: PHILO, med25, H3K9ac, 1hJA, rep3


title: PHILO, med25, H3K9ac, 2hJA, rep2


title: PHILO, med25, H3K9ac, ctrl, rep1


title: PHILO, myc234, H3K9ac, WD, rep3


title: PHILO, med25, H3K9ac, ctrl, rep2


title: PHILO, med25, H3K9ac, 1hJA, rep1


title: PHILO, hac1, H3K9ac, WD, rep2


title: PHILO, ninja, H3K9ac, ctrl, rep1


title: PHILO, myc234, H3K9ac, WD, rep1


title: PHILO, med25, H3K9ac, ctrl, rep3


title: PHILO, myc234, H3K9ac, 1hJA, rep2


title: PHILO, myc234, H3K9ac, WD, rep2


title: PHILO, med25, H3K9ac, WD, rep2


title: PHILO, myc234, H3K9ac, 1hJA, rep3


title: PHILO, myc234, H3K9ac, ctrl, rep3


title: PHILO, myc2, H3K9ac, WD, rep1


title: PHILO, myc2, H3K9ac, 2hJA, rep3


title: PHILO, myc234, H3K9ac, 1hJA, rep1


title: PHILO, myc234, H3K9ac, 2hJA, rep3


title: PHILO, myc234, H3K9ac, ctrl, rep1


title: PHILO, med25, H3K9ac, 2hJA, rep1


title: PHILO, myc2, H3K9ac, 2hJA, rep2


title: PHILO, myc2, H3K9ac, 2hJA, rep1


title: PHILO, myc2, H3K9ac, WD, rep2


title: PHILO, med25, H3K9ac, 1hJA, rep2


title: PHILO, myc234, H3K9ac, ctrl, rep2


title: PHILO, myc2, H3K9ac, ctrl, rep3


title: PHILO, myc2, H3K9ac, 1hJA, rep1


title: PHILO, myc234, H3K9ac, 2hJA, rep1


title: PHILO, myc2, H3K9ac, 1hJA, rep3


title: PHILO, myc234, H3K9ac, 2hJA, rep2


title: PHILO, myc2, H3K9ac, ctrl, rep2


title: PHILO, myc2, H3K9ac, WD, rep3


title: PHILO, Col-0, H3K9ac, WD, rep2


title: PHILO, myc2, H3K9ac, 1hJA, rep2


title: PHILO, Col-0, H3K9ac, 2hJA, rep3


title: PHILO, myc2, H3K9ac, ctrl, rep1


title: PHILO, Col-0, H3K9ac, WD, rep1


title: PHILO, Col-0, H3K9ac, WD, rep3


title: PHILO, Col-0, H3K9ac, 2hJA, rep2


title: PHILO, Col-0, H3K9ac, 2hJA, rep1


title: PHILO, Col-0, H3K9ac, 1hJA, rep2


title: PHILO, Col-0, H3K9ac, 1hJA, rep1


title: PHILO, Col-0, H3K9ac, 1hJA, rep3


title: PHILO, TC, Col-0, Pol II, 2hJA, rep2

value: anti-RNA polymerase II 8WG16 (Pol II) (#664906, Biolegend)


title: PHILO, Col-0, H3K9ac, ctrl, rep2


title: PHILO, Col-0, H3K9ac, ctrl, rep1


title: PHILO, Col-0, H3K9ac, ctrl, rep3


title: PHILO, TC, Col-0, Pol II, 2hJA, rep3


title: PHILO, TC, Col-0, Pol II, ctrl, rep2


title: PHILO, TC, Col-0, Pol II, 2hJA, rep1


title: PHILO, TC, Col-0, H3K4me3, 2hJA, rep2

value: anti-H3K4me3 (#04-475, Millipore Sigma)


title: PHILO, TC, Col-0, H3K4me3, 2hJA, rep3


title: PHILO, TC, Col-0, Pol II, ctrl, rep3


title: PHILO, TC, Col-0, Pol II, ctrl, rep1


title: PHILO, TC, Col-0, H3K4me3, 2hJA, rep1


title: PHILO, TC, Col-0, IgG, ctrl, rep3


title: PHILO, TC, Col-0, H3K4me3, ctrl, rep2


title: PHILO, TC, Col-0, IgG, ctrl, rep2


title: PHILO, TC, Col-0, H3K4me3, ctrl, rep1


title: PHILO, TC, Col-0, H3K4me3, ctrl, rep3


title: PHILO, TC, Col-0, IgG, ctrl, rep1


title: PHILO, TC, Col-0, H3K9ac, WD, rep2


title: PHILO, TC, Col-0, H3K9ac, WD, rep1


title: PHILO, TC, Col-0, H3K9ac, WD, rep3


title: PHILO, TC, Col-0, H3K9ac, 1hJA, rep3


title: PHILO, TC, Col-0, H3K9ac, 2hJA, rep1


title: PHILO, TC, Col-0, H3K9ac, 0.5hJA, rep3

value: 0.5h JA


title: PHILO, TC, Col-0, H3K9ac, 1hJA, rep2


title: PHILO, TC, Col-0, H3K9ac, 1hJA, rep1


title: PHILO, TC, Col-0, H3K9ac, 0.25hJA, rep3


title: PHILO, TC, Col-0, H3K9ac, ctrl, rep2


title: PHILO, TC, Col-0, H3K9ac, 0.25hJA, rep2


title: PHILO, TC, Col-0, H3K9ac, 0.25hJA, rep1


title: PHILO, TC, Col-0, H3K9ac, 0.5hJA, rep1


title: PHILO, TC, Col-0, H3K9ac, ctrl, rep1


title: PHILO, Col-0, H3K36me3, rep1

value: anti-H3K36me3 (#61021, Active Motif)

value: untreated


title: PHILO, Col-0, H3K27me3, rep3

value: anti-H3K27me3 (#39155, Active Motif)


title: PHILO, Col-0, H3K36me3, rep2


title: PHILO, Col-0, H3K36me3, rep3


title: PHILO, Col-0, H3K27me3, rep1


title: PHILO, Col-0, H3K4me3, rep1