title: Patient 19, end of treatment

description:
Library name: P19_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AE


title: Patient 17, end of treatment

status: Public on Jan 03 2025

type: SRA

city: Houston

first: Zheng

last: Yin

state: TX

address: 6565 Fannin St, MC: F6-300

department: Systems Medicine and Bioengineering

country: USA

institute: Houston Methodist Cancer Center

description:
Library name: P17_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AC

library_source: transcriptomic

data_processing:
confirming the quality of the data using FastQC
using STAR 2.7.9a to map the raw data to reference human genome version GRCH38 and generated BAM files
using SubRead.featurecounts V2.0.3 was applied to the BAM files to estimate the abundance of genes within each sample
Using R package DESeq to identify differentially expressed genes in EOT vs. BL conditions
Using ConsensusPathDB v050621 to carry out overrepresentation analysis and identify canonical pathways enriched with EOT up- and down-regulated genes, respectively
Assembly: human genome version GRCH38
Supplementary files format and content: Excel workbook containing raw counts for 44,759 transcripts in 32 samples

molecule: total RNA

organism: Homo sapiens

source_name: breast

extract_protocol:
Total RNA was extracted from frozen biopsies according to the manufacturer's protocol using the RNeasy® Lipid Tissue Mini Kit (Qiagen, #74804). Briefly, up to 100 mg of frozen tissue sections were homogenized in 1ml QIAzol Lysis reagent using the TissueLyzer II (Qiagen). The homogenate was placed on the benchtop at room temperature (15–25°C) for 5 min to allow nucleoprotein complexes dissociation. RNA was eluted with 40 µl of RNase-free water and quantified using a Qubit 4 Fluorometer (Invitrogen).
Total RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol.

treatment_protocol: 25mg/day oral dose of HT were given for 12 months in pre- and post-menopausal women at increased risk of breast cancer.

tag: tissue

value: breast

tag: treatment

value: 25mg/day oral dose of hydroxytyrosol (HT) for 12 months


title: Mouse liver tissue sEV-14 months-25

city: Beijing

first: XIAODONG

last: LUAN

address: DONGDAN SANTIAO 9, DONGCHENG District

department: Peking Union Medical College Hospital

country: China

institute: Peking Union Medical College & Chinese Academy of Medical Science

description:
Library name: sample25
E-micA182-25h

data_processing:
Raw reads were quality-checked using Agilent Bioanalyzer 2100 and qPCR.
Reads were aligned to the mouse genome using Bowtie tools.
Known miRNAs were identified by comparison with miRBase, and novel miRNAs were predicted.
Expression levels were quantified using UMI counts and normalized to CPM.
Differentially expressed miRNAs were identified using the EdgeR package in R.
Assembly: mm10
Supplementary files format and content: csv files include CPM values for each Sample

organism: Mus musculus

source_name: liver

growth_protocol: wild-type C57BL/6J, and allocated in the Central Laboratory Facility of GemPharmatech Co.,Ltd. All animal experiments were carried out in line with standard operating procedures (SOPs) of GemPharmatech Co., Ltd, and the experimental facilities of the center have been certified by the Association for Assessment and Accreditation of Laboratory Animal Care. All experimental procedures were approved by Institutional Animal Care and Use Committee (IACUC) (320727221100555368). Animal welfare and experimental operations comply with Association for Assessment and Accreditation of Laboratory Animal Care (AAALAC)'s requirements.Males and females are equally represented for mice that extracted liver tissue-derived EVs. The mice were kept in a specific environment free of pathogens with stable temperature, allowed access to food and water fed ad libitum, maintained in a 12 h dark/light cycle.

extract_protocol:
Tissues were collected under sterile conditions and stored at -80°C until processing. sEVs isolation was performed using a Miltenyi Human Tumor Dissociation Kit, followed by ultracentrifugation. Total RNA was extracted using the miRNeasy Serum/Plasma Advanced Kit (Qiagen).
The QIAseq miRNA Library Kit (Qiagen) was used to generate sequencing libraries. Libraries were sequenced on an Illumina Novaseq platform to generate paired-end reads.

value: liver

tag: cell type

value: small extracellular vesicles

tag: genotype

value: wild-type C57BL/6J

tag: batch

value: 14 months


title: Patient 16, end of treatment

description:
Library name: P16_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AB


title: Sample_4_plaque

city: New York

first: Michael

last: Gildea

state: New York

address: 550 1st avenue

institute: NYU Langone Health

description:
Library name: Sample_4_plaque
10x Genomics

library_source: transcriptomic single cell

data_processing:
Cell Ranger (10x Genomics, v7.1.0) was used to perform alignment (GRCh38, Ensembl 93), filtering, barcode counting and UMI counting of sequencing reads from fastq files.
Assembly: GRCh38
Supplementary files format and content: Tab -separated values files and matrix files

molecule: polyA RNA

source_name: coronary plaque

extract_protocol:
Left and right anterior descending arteries were washed, minced, and digested then filtered using cell strainers. Following a dead cell removal step, single-cell suspensions were counted and loaded onto a Chromium Controller (10x Genomics).
Libraries were prepared using the Chromium Single Cell 3’ Library v3 reagent, Gel Bead and Multiplex Kit and Chip Kit (10X Genomics; 1000268, 1000215 and 100127, respectively)

value: coronary plaque


title: Mouse liver tissue sEV-14 months-24

description:
Library name: sample24
E-micA182-24h


title: Patient 15, baseline

description:
Library name: P15_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column AA

value: baseline


title: Patient 13, baseline

description:
Library name: P13_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column Y


title: Patient 14, baseline

description:
Library name: P14_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column Z


title: Mouse liver tissue sEV-14 months-23

description:
Library name: sample23
E-micA182-23h


title: Mouse liver tissue sEV-14 months-21

description:
Library name: sample21
E-micA182-21h


title: Mouse liver tissue sEV-12 months-20

description:
Library name: sample20
E-micA182-20h

value: 12 months


title: Patient 10, baseline

description:
Library name: P10_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column V


title: Mouse liver tissue sEV-12 months-19

description:
Library name: sample19
E-micA182-19h


title: Patient 12, baseline

description:
Library name: P12_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column X


title: Patient 9, baseline

description:
Library name: P9_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column U


title: Mouse liver tissue sEV-12 months-18

description:
Library name: sample18
E-micA182-18h


title: Mouse liver tissue sEV-12 months-17

description:
Library name: sample17
E-micA182-17h


title: Patient 8, baseline

description:
Library name: P8_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column T


title: iMDF cells, Menuetto, T3, Rep3

city: Parkville

first: John

middle: E

last: La Marca

state: VIC

address: 1G Royal Parade

department: Blood Cells and Blood Cancer

country: Australia

institute: Walter and Eliza Hall Institute

description:
Library name: iMDF Menuetto Sample 12
T3-3

library_source: other

data_processing:
Reads were mapped to sgRNA library files using MAGeCK v0.5.9
Supplementary files format and content: Processed data files for each screen contain raw sgRNA counts for each sample
Library strategy: CRISPR Screen

molecule: other

source_name: Immortalised mouse dermal fibroblast

extract_protocol:
DNA was extracted using the DNeasy cell and tissue kit (QIAGEN) or Puregene kit (QIAGEN) according to the manufacturer's instructions.
Libraries were prepared and sequenced on the Illumina NextSeq 2000 using NextSeq 2000 P4 XLEAP-SBS Reagents, or on the Illumina MiSeq using a MiSeq Reagent Kit according to the manufacturer's instructions.

tag: cell line

value: Immortalised mouse dermal fibroblast

tag: crisprlibrary

value: Menuetto


title: iMDF cells, Menuetto, T2, Rep2

description:
Library name: iMDF Menuetto Sample 8
T2-2


title: Patient 7, baseline

description:
Library name: P7_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column S


title: iMDF cells, Menuetto, T2, Rep3

description:
Library name: iMDF Menuetto Sample 9
T2-3


title: Mouse liver tissue sEV-6 months-15

description:
Library name: sample15
E-micA182-15h

value: 6 months


title: iMDF cells, Menuetto, T3, Rep1

description:
Library name: iMDF Menuetto Sample 10
T3-1


title: Mouse liver tissue sEV-12 months-16

description:
Library name: sample16
E-micA182-16h


title: iMDF cells, Menuetto, T2, Rep1

description:
Library name: iMDF Menuetto Sample 7
T2-1


title: Patient 6, end of treatment

description:
Library name: P6_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column R


title: iMDF cells, Menuetto, T3, Rep2

description:
Library name: iMDF Menuetto Sample 11
T3-2


title: Patient 6, baseline

description:
Library name: P6_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column Q


title: iMDF cells, Menuetto, T1, Rep3

description:
Library name: iMDF Menuetto Sample 6
T1-3


title: Mouse liver tissue sEV-14 months-22

description:
Library name: sample22
E-micA182-22h


title: iMDF cells, Menuetto, T1, Rep2

description:
Library name: iMDF Menuetto Sample 5
T1-2


title: iMDF cells, Menuetto, T0, Rep1

description:
Library name: iMDF Menuetto Sample 1
T0-1


title: EuMyc cells, Scherzo, S63845, Rep6

description:
Library name: EuMyc Scherzo Sample 24
Q6s

source_name: Lymphoma cell line

value: Lymphoma cell line

value: Lymphoma

value: Scherzo


title: Patient 5, baseline

description:
Library name: P5_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column O


title: iMDF cells, Menuetto, T0, Rep2

description:
Library name: iMDF Menuetto Sample 2
T0-2


title: Patient 5, end of treatment

description:
Library name: P5_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column P


title: Mouse liver tissue sEV-6 months-13

description:
Library name: sample13
E-micA182-13h


title: Patient 11, baseline

description:
Library name: P11_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column W


title: iMDF cells, Menuetto, T1, Rep1

description:
Library name: iMDF Menuetto Sample 4
T1-1


title: iMDF cells, Menuetto, T0, Rep3

description:
Library name: iMDF Menuetto Sample 3
T0-3


title: Mouse liver tissue sEV-6 months-11

description:
Library name: sample11
E-micA182-11h


title: EuMyc cells, Scherzo, S63845, Rep5

description:
Library name: EuMyc Scherzo Sample 23
Q5s


title: EuMyc cells, Scherzo, S63845, Rep3

description:
Library name: EuMyc Scherzo Sample 21
Q3s


title: Mouse liver tissue sEV-6 weeks-10

description:
Library name: sample10
E-micA182-10h

value: 6 weeks


title: Patient 4, end of treatment

description:
Library name: P4_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column N


title: EuMyc cells, Scherzo, S63845, Rep4

description:
Library name: EuMyc Scherzo Sample 22
Q4s


title: Patient 4, baseline

description:
Library name: P4_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column M


title: EuMyc cells, Scherzo, S63845, Rep2

description:
Library name: EuMyc Scherzo Sample 20
Q2s


title: EuMyc cells, Scherzo, S63845, Rep1

description:
Library name: EuMyc Scherzo Sample 19
Q1s


title: EuMyc cells, Scherzo, Nutlin, Rep6

description:
Library name: EuMyc Scherzo Sample 18
Q6n

value: Nutlin


title: Mouse liver tissue sEV-6 weeks-9

description:
Library name: sample9
E-micA182-09h


title: Patient 3, end of treatment

description:
Library name: P3_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column L

value: breast


title: Mouse liver tissue sEV-6 weeks-8

description:
Library name: sample8
E-micA182-08h


title: EuMyc cells, Scherzo, Nutlin, Rep4

description:
Library name: EuMyc Scherzo Sample 16
Q4n


title: Mouse liver tissue sEV-6 months-14

description:
Library name: sample14
E-micA182-14h


title: EuMyc cells, Scherzo, Nutlin, Rep5

description:
Library name: EuMyc Scherzo Sample 17
Q5n


title: EuMyc cells, Scherzo, Nutlin, Rep3

description:
Library name: EuMyc Scherzo Sample 15
Q3n


title: Mouse liver tissue sEV-6 months-12

description:
Library name: sample12
E-micA182-12h


title: Mouse liver tissue sEV-6 weeks-7

description:
Library name: sample7
E-micA182-07h


title: Mouse liver tissue sEV-6 weeks-6

description:
Library name: sample6
E-micA182-06h


title: EuMyc cells, Scherzo, Nutlin, Rep1

description:
Library name: EuMyc Scherzo Sample 13
Q1n


title: Patient 2, baseline

description:
Library name: P2_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column I


title: EuMyc cells, Scherzo, Nutlin, Rep2

description:
Library name: EuMyc Scherzo Sample 14
Q2n


title: EuMyc cells, Scherzo, DMSO, Rep6

description:
Library name: EuMyc Scherzo Sample 12
Q6d

value: DMSO


title: EuMyc cells, Scherzo, DMSO, Rep5

description:
Library name: EuMyc Scherzo Sample 11
Q5d


title: Mouse liver tissue sEV-1 week-27

description:
Library name: sample5
E-micA182-27h

value: liver

value: 1 week


title: Patient 2, end of treatment

description:
Library name: P2_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column J

value: 25mg/day oral dose of hydroxytyrosol (HT) for 12 months


title: EuMyc cells, Scherzo, DMSO, Rep3

description:
Library name: EuMyc Scherzo Sample 9
Q3d


title: EuMyc cells, Scherzo, DMSO, Rep4

description:
Library name: EuMyc Scherzo Sample 10
Q4d


title: Patient 1, end of treatment

description:
Library name: P1_EOT
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column H


title: EuMyc cells, Scherzo, DMSO, Rep2

description:
Library name: EuMyc Scherzo Sample 8
Q2d


title: EuMyc cells, Scherzo, DMSO, Rep1

description:
Library name: EuMyc Scherzo Sample 7
Q1d


title: Patient 1, baseline

description:
Library name: P1_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column G


title: EuMyc cells, Scherzo, Input, Rep6

description:
Library name: EuMyc Scherzo Sample 6
Q6i

value: Input


title: Patient 3, baseline

description:
Library name: P3_BL
S1 flow cell
Puri_Yn_Chang_Counts_Jan02_2025.xlsx, Column K


title: EuMyc cells, Scherzo, Input, Rep5

description:
Library name: EuMyc Scherzo Sample 5
Q5i


title: 4C-seq, rs143558304 located CRE

city: Tianjin

first: Ke

last: Zhao

address: Qixiangtai Road, No.22

institute: Tianjin Medical University

description: Library name: 4C-seq_rs143558304

library_source: genomic

data_processing:
The processing and visualization of 4C-seq data was done using 4Cseqpipe(https://github.com/changegene/4Cseqpipe), pipe4C (https://github.com/deLaatLab/pipe4C) and peakC pipeline (https://github.com/deWitLab/peakC).
Assembly: hg19
Supplementary files format and content: wig.gz
Supplementary files format and content: nearcis.norm.txt.linear_mean.scales.txt-mean of normalized contact intensity in 1kb genomic bins.  Each row represents a genomic bin of size 1kb. Includes the following tab-delimited columns: column 1 – the starting coordinate of the 1kb bin column 2 – the median of values within a 2kb window, centered on the 1kb genomic bin column 3 – the 80th percentile of values in the window column 4 – the 20th percentile of values in the window column 5-148 – as columns 2-4, but with linearly increasing window size, going up to 50kb
Library strategy: 4C-Seq

molecule: genomic DNA

source_name: cell line

growth_protocol: HAP1 (Horizon Discovery) cells were cultured in IMDM (ThermoFisher) supplemented with 10% fetal bovine serum in 5% CO2 at 37°C.

extract_protocol:
The 4C assay was carried out in diploid HAP1 cells, using a published protocol.
Viewpoint-specific amplification was performed with 8 × 200 ng 4C template using 2 × Phanta Max Master Mix. The next-generation library was constructed using the VAHTS Universal DNA Library Prep Kit for Illumina V3 and purified by AMPure XP beads following the manufacturer's instructions. The 4C-seq library were sequenced on the Illumina NovaSeq 6000 platform, producing pair-end reads of 150 bp.

treatment_protocol: Diploid HAP1 cells were isolated from Hoechst (MCE)-stained HAP1 cells by flow sorting.

value: cell line

tag: enzyme

value: NlaIII, DpnII


title: EuMyc cells, Scherzo, Input, Rep4

description:
Library name: EuMyc Scherzo Sample 4
Q4i


title: 4C-seq, rs73156934 located CRE

description: Library name: 4C-seq_rs73156934

value: CviQI, DpnII


title: Mouse liver tissue sEV-1 week-3

description:
Library name: sample2
E-micA182-03h

value: small extracellular vesicles

value: wild-type C57BL/6J


title: Mouse liver tissue sEV-1 week-1

description:
Library name: sample1
E-micA182-01h


title: 4C-seq, rs79423520 located CRE

description: Library name: 4C-seq_rs79423519

value: CviQI, EcoRI


title: pituitary gland, anti-CD115 depletion, biol rep 4

city: Turku

first: Pia

last: Rantakari

address: Tykistökatu 6B

department: Turku Bioscience Centre

country: Finland

institute: University of Turku

description:
Library name: aCD115 biol rep 4
Column name in processed data files: CD115_4

data_processing:
The quality of the sequenced reads was investigated. The reads were aligned to the mouse reference genome (GRCm38 release 94) using HISAT2 v2.0.5.
The novel gene assembly was predicted using StringTie v1.3.3b using the mapping information from all the samples and the novel gene annotation was performed using Pfam, Swissprot, Go, and KEGG.
The number of uniquely mapped reads associated with each gene was counted using the featureCounts v1.5.0-p3 tool using Ensembl annotations.
Assembly: GRCm38 release 94
Supplementary files format and content: xlx files containing raw count data
Supplementary files format and content: xlx files containing FPKM normalized count data

source_name: pituitary gland

extract_protocol:
RNA was isolated with RNeasy Plus Micro Kit (Qiagen) according to the manufacturer's protocol and analyzed on Advanced Analytical Fragment Analyzer for quality assessment. A starting amount of 100 ng total RNA was used for libary construction.
Library preparation was performed using the llumina Stranded mRNA Library Preparation Kit (1000000124518) according to the manufacturer's protocol. The quality of the samples was ensured using Advanced Analytical Fragment Analyzer. Sample concentration was measured with Qubit Fluorometric Quantitation (Life Technologies).

treatment_protocol: To specifically target yolk sac-derived macrophages in the offspring, pregnant C57BL/6N females at embryonic day 6.5 (E6.5) were treated with a single intraperitoneal (i.p.) injection of a neutralizing antibody against CSF1R (AFS98; Bio X Cell) or received rat IgG2a control antibody (clone 2A3; Bio X Cell). Each injection consisted of 3 mg of the respective antibody dissolved in sterile PBS. Additionally 100, 150, and 200 µg of antibody were given on postnatal day (P) 2, P14, and 4 weeks of age.

value: pituitary gland

tag: strain

value: depletion with anti-CD115

tag: age

tag: Sex

value: male


title: EuMyc cells, Scherzo, Input, Rep1

description:
Library name: EuMyc Scherzo Sample 1
Q1i

value: Lymphoma cell line

value: Lymphoma

value: Scherzo


title: HAP1-KRAB, non-targeting control (NTC) sgRNA, H2AK119ub

description: Library name: H2AK119ub(sgNTC)

data_processing:
The CUT&Tag data was processed using CUT-RUNTools-2.0 0 (Yu et al., 2021). First, the input FASTQ files underwent read trimming, mapping, and filtering. Trimmed reads were aligned to the reference genome, and only those with high mapping quality, unique alignment, and proper mapping were retained for further analysis. Simultaneously, spike-in controls were aligned to the E. coli genome.  The aligned reads were then normalized based on spike-in sequence depth to account for differences in library size across samples. Peak identification was performed using MACS2 (Zhang et al., 2008), calling narrow peaks for histone modifications H3K27ac, H3K4me3, and H3K9me3, and broad peaks for H2AK119ub, H3K27me3, and H3K4me1.
Assembly: hg19
Supplementary files format and content: CUT&Tag output files: bigwig.
Library strategy: CUT&Tag

extract_protocol:
Adherent cells were digested with 0.25% trypsin and collected in a 15mL tube containing serum-containing medium, followed by centrifugation and washing of the cell pellet with serum-free basal medium to obtain a single-cell suspension.
CUT&Tag experiments were performed using the Hyperactive Universal CUT&Tag Assay Kit for Illumina (Vazyme, TD903). Briefly, 1 × 10⁵ freshly cultured cells were centrifuged (500 × g, 5 min) and resuspended in 500 μL Wash Buffer. After adding 10 μL ConA Beads and incubating at room temperature for 10 min, the beads were collected with a magnetic rack. The beads were incubated with 50 μL of primary antibody (H3K27ac antibody, Cell Signaling Technology, 8173S; H3K4me1 antibody, Cell Signaling Technology, 5326S; H3K4me3 antibody, Abcam, 8898; H2AK119ub antibody, Cell Signaling Technology, 8240T; H3K27me3 antibody, Cell Signaling Technology, 9733S; H3K9me3 antibody, Cell Signaling Technology, 13969) for 2 h, followed by incubation with 50 μL secondary antibody-dig-wash Buffer for 1 h. After washing with dig-wash Buffer, cells were treated with 100 μL Hyperactive pA-Tn5 Transposon (0.04 μM) for 1 h, washed, and resuspended in 300 μL Tagmentation Buffer. After 1 h of incubation at 37°C, the reaction was terminated with 10 μL EDTA, 3 μL SDS, and 2.5 μL Proteinase K, followed by incubation at 50°C for 1 h. DNA was extracted using phenol-chloroform-isoamyl alcohol (25:24:1) and dissolved in 25 μL TE buffer. The CUT&Tag library was amplified with 13 PCR cycles and sequenced on a Novogene HiSeq PE150 platform. Two biological replicates were performed for each condition.

treatment_protocol: HAP1-sgURE and HAP1-sgNTC cells were  generated by  transduced KRAB-blast stably expressed HAP1 cell with sgRNA targeted rs73156934-tagged CRE or non-targeting control(NTC) .

value: KRAB-blast stably expressed HAP1 cell

value: transduced with non-targeting control (NTC) sgRNA


title: EuMyc cells, Scherzo, Input, Rep3

description:
Library name: EuMyc Scherzo Sample 3
Q3i


title: EuMyc cells, Menuetto, S63845, Rep5

description:
Library name: EuMyc Menuetto Sample 23
D5s

value: Menuetto


title: pituitary gland, anti-CD115 depletion, biol rep 2

description:
Library name: aCD115 biol rep 2
Column name in processed data files: CD115_2


title: EuMyc cells, Menuetto, S63845, Rep4

description:
Library name: EuMyc Menuetto Sample 22
D4s


title: HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K4me3

description: Library name: H3K4me3(sgNTC)


title: EuMyc cells, Menuetto, S63845, Rep6

description:
Library name: EuMyc Menuetto Sample 24
D6s


title: HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K9me3

description: Library name: H3K9me3(sgNTC)


title: EuMyc cells, Scherzo, Input, Rep2

description:
Library name: EuMyc Scherzo Sample 2
Q2i


title: pituitary gland, anti-CD115 depletion, biol rep 3

description:
Library name: aCD115 biol rep 3
Column name in processed data files: CD115_3


title: Mouse liver tissue sEV-1 week-4

description:
Library name: sample3
E-micA182-04h

value: liver

value: 1 week


title: EuMyc cells, Menuetto, S63845, Rep2

description:
Library name: EuMyc Menuetto Sample 20
D2s


title: Mouse liver tissue sEV-1 week-5

description:
Library name: sample4
E-micA182-05h


title: pituitary gland, anti-CD115 depletion, biol rep 1

description:
Library name: aCD115 biol rep 1
Column name in processed data files: CD115_1

value: female


title: EuMyc cells, Menuetto, Nutlin, Rep6

description:
Library name: EuMyc Menuetto Sample 18
D6n

value: Nutlin


title: HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K4me1

description: Library name: H3K4me1(sgNTC)


title: EuMyc cells, Menuetto, S63845, Rep3

description:
Library name: EuMyc Menuetto Sample 21
D3s


title: HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K27me3

description: Library name: H3K27me3(sgNTC)


title: EuMyc cells, Menuetto, Nutlin, Rep4

description:
Library name: EuMyc Menuetto Sample 16
D4n


title: EuMyc cells, Menuetto, Nutlin, Rep3

description:
Library name: EuMyc Menuetto Sample 15
D3n


title: HAP1-KRAB, non-targeting control (NTC) sgRNA, H3K27ac

description: Library name: H3K27ac(sgNTC)


title: pituitary gland, isotype control, biol rep 3

description:
Library name: Control biol rep 3
Column name in processed data files: IgG2a_3

value: isotype control


title: EuMyc cells, Menuetto, Nutlin, Rep2

description:
Library name: EuMyc Menuetto Sample 14
D2n


title: pituitary gland, isotype control, biol rep 2

description:
Library name: Control biol rep 2
Column name in processed data files: IgG2a_2


title: EuMyc cells, Menuetto, Nutlin, Rep1

description:
Library name: EuMyc Menuetto Sample 13
D1n


title: EuMyc cells, Menuetto, DMSO, Rep6

description:
Library name: EuMyc Menuetto Sample 12
D6d

value: DMSO


title: HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H2AK119ub

description: Library name: H2AK119ub(sgURE)

value: transduced with sgRNA targeted rs73156934-tagged CRE


title: pituitary gland, isotype control, biol rep 1

description:
Library name: Control biol rep 1
Column name in processed data files: IgG2a_1


title: EuMyc cells, Menuetto, DMSO, Rep5

description:
Library name: EuMyc Menuetto Sample 11
D5d


title: HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K9me3

description: Library name: H3K9me3(sgURE)


title: EuMyc cells, Menuetto, DMSO, Rep4

description:
Library name: EuMyc Menuetto Sample 10
D4d


title: CD45+ pituitary cells, 8-weeks old

description:
Library name: 8-weeks old
10X Genomics

data_processing:
The Cell Ranger (ver. 7.1.0) "count" function was used to align samples to the mm10-2020-A reference genome, quantify reads, and filter reads and barcodes.
Assembly: gex-mm10-2020-A
Supplementary files format and content: Cell Ranger generated filtered Tab-seperated feature&barcode and matrix output files.

extract_protocol:
Whole pituitaries or separate posterior and anterior pituitaries were mechanically lysed by suspending and digested with 50 µg/ml DNase 1 (Roche) and 1 mg/ml Collagenase D (Roche) in Hank's Buffered Saline (HBSS; Sigma-Aldrich) at 37 °C for 30-45 minutes. The cell suspension was filtered through silk (pore size 77 µm), pelleted (1006G, 1.5 minutes), and washed with 500 µl of HBSS to remove enzymes. Finally, cells were eluted to Phosphate Buffered Saline (PBS; Sigma-Aldrich) and stained with Fixable Viability Dye eFluor 780 (eBioscience) to label the dead cells. Unspecific binding to low-affinity Fc-receptors was blocked by incubating the cells with unconjugated CD16/32 antibody (BioXCell, clone 2.4G2). Cells were subsequently stained for 30 min at 4 °C with antibodies diluted to the FACS buffer. The cells were sorted with Sony SH800 Cell Sorter (Sony Biotechnology Inc.). Single cells were gated with the FSC-H versus FCS-W plot and the SSC-H versus SSC-W plot to avoid doublets and dead cells were excluded. Live single CD45+ cells were sorted into the RPMI medium containing 2 % FCS.
Single cell RNA-sequencing libraries were prepared according to the manufacturer's instructions (CG00052 RevB) using Chromium Single Cell 3′ Library and Gel Bead Kit v2 (10X Genomics, 120237) and Chromium Single Cell A Chip Kit (10X Genomics). Prepared libraries were sequenced using the Illumina Novaseq6000 Sequencing System (RRID: SCR_016387). Library preparation was done in the Single Cell Omics core, and sequencing was done in the Finnish Functional Genomics Center at Turku Bioscience.

value: CD45+ cells

value: 8-weeks old


title: EuMyc cells, Menuetto, DMSO, Rep3

description:
Library name: EuMyc Menuetto Sample 9
D3d


title: EuMyc cells, Menuetto, DMSO, Rep2

description:
Library name: EuMyc Menuetto Sample 8
D2d


title: EuMyc cells, Menuetto, S63845, Rep1

description:
Library name: EuMyc Menuetto Sample 19
D1s


title: HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K4me3

description: Library name: H3K4me3(sgURE)


title: pituitary gland, isotype control, biol rep 4

description:
Library name: Control biol rep 4
Column name in processed data files: IgG2a_4

value: pituitary gland


title: CD45+ pituitary cells, 3-weeks old

description:
Library name: 3-weeks old
10X Genomics

value: 3-weeks old

value: male


title: EuMyc cells, Menuetto, Input, Rep6

description:
Library name: EuMyc Menuetto Sample 6
D6i

value: Lymphoma cell line

value: Lymphoma

value: Input


title: EuMyc cells, Menuetto, Nutlin, Rep5

description:
Library name: EuMyc Menuetto Sample 17
D5n


title: HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K4me1

description: Library name: H3K4me1(sgURE)

value: KRAB-blast stably expressed HAP1 cell


title: EuMyc cells, Menuetto, Input, Rep3

description:
Library name: EuMyc Menuetto Sample 3
D3i

value: Menuetto


title: CD45+ pituitary cells, newborn

description:
Library name: newborn
10X Genomics

value: newborn


title: CD45+ pituitary cells, 1-week old

description:
Library name: 1-week old
10X Genomics

value: 1-week old


title: HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K27ac

description: Library name: H3K27ac(sgURE)


title: EuMyc cells, Menuetto, Input, Rep4

description:
Library name: EuMyc Menuetto Sample 4
D4i


title: HAP1-KRAB, sgRNA targeted rs73156934-tagged CRE, H3K27me3

description: Library name: H3K27me3(sgURE)


title: EuMyc cells, Menuetto, Input, Rep2

description:
Library name: EuMyc Menuetto Sample 2
D2i


title: EuMyc cells, Menuetto, Input, Rep1

description:
Library name: EuMyc Menuetto Sample 1
D1i


title: Mouse_Cortex_bulk_nucleosome_depletion

first: Dongsheng

last: Bai

state: NY

address: 101 Avenue of the Americas

institute: New York Genome Center

description:
nucleosome_depletion_control
nucleosome_depletion_DNA_additional_bigwig.tar.gz

data_processing:
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Bigwig convert step: The sorted bam file are converted to bigiwg files with bamCoverage of deeptools software (--normalizeUsing RPKM --Offset 75 --smoothLength 500 --extendReads 200)
Assembly: hg38
Supplementary files format and content: bigwig file
Library strategy: CUT&Tag

source_name: Mus musculus

growth_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in DMEM (Gibco, 10569010) supplemented with 10% fetal bovine serum (Gibco, 16000044) and 1% penicillin-streptomycin (Gibco, 10378016) at 37 °C with 5% CO2. Cells were not authenticated or tested for mycoplasma. Cells were sown on plates 48 hours before treatment with H2O2 at the density of 3×105 cells per culture dish.

extract_protocol:
Damagenome libraries were diluted to 35 μl with 1× NIB-Tris buffer. Then, 5 μl of 4 M NaCl, 5 μl of 10% SDS (Invitrogen, 15553-035) and 5 μl of 10 mg ml−1 Protease K (NEB, P8107S) were added and nuclei were lysed at 850 r.p.m. at 55 °C for 2 hours in a ThermoMixer. The lysed solution was cooled to room temperature and then purified with 1× SPRI beads (Beckman Coulter, B23319) and eluted in 12.5 μl of H2O.
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome depletion; the DNA oxidative damage sites were treated with enzymatic labeling with biotin and tagmentated with identical barcoded assembled pA-Tn5, nuclei were lysed and gDNA and RNA were purified with 1X SPRI beads; next, DNA libraries were amplified by Kapa HiFi uracil plus DNA polymerase and used 0.8X Ampure XP beads to purify the product. The final libraries were sequenced using Nova-seq platform (illumina) with the following read lengths: PE 100 + 8 + 8 + 50 (Read 1 + Index 1 + Index 2 + Read 2).

treatment_protocol: Subconfluent cells were treated with H2O2, in a complete medium, at the final concentration of 200 µM (Thermo Scientific Chemicals, 202465000) for 2 hours at 37°C 5% CO2. After treatment, the medium was replaced with complete medium without H2O2 for additional incubation from 0 hour to 48 hours.

value: Mus musculus

value: Mouse cortex

value: WT

value: No


title: HAP1,wild-type, H2AK119ub

description: Library name: H2AK119ub(wild-type)

value: wild-type


title: DEK.CUT_DTA64_2

city: Chongqing

first: Zhe

last: Chen

address: 1 Yixueyuan Road, Yuzhong District

institute: Chongqing Medical University

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
Clean reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.2.9. MarkDuplicates was used to mark PCR duplicate and unmapped reads. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS2 and ChIPseeker package, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak
Library strategy: CUT&Tag

source_name: Bone marrow

extract_protocol:
The CUT&Tag assay was performed using NovoNGS CUT&Tag 3.0 High-Sensitivity Kit (Novoprotein) according to the manufacturer’s protocol. 2,000-5,000 HSCs were harvested and resuspended in 45 µL wash buffer. Then 6 µL ConA beads were added to the sample and incubated at 37°C for 10 min. Then the supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL antibody buffer (20 mM Hepes, pH 7.5, 150 mM Nacl, 0.5 mM Spermidine, 0.0125% Digitonin, 2 mM EDTA, 0.1% BSA, 1× PIC).
Then, 0.5 µL antibody was added to the sample and incubated at 4°C overnight. The supernatant was removed by magnet adsorption and the beads were resuspended in 50 µL secondary antibody buffer, containing 0.5 µL goat anti-rabbit IgG antibody. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL ChiTag Buffer, containing 0.5 µL ChiTag transposome. After incubation at 37°C for 60 min, the beads were resuspended in 50 µL tagmentation buffer. Then, 1 µL 10% SDS was added to the sample and incubated at 55°C for 10 min, and DNA was extracted using 2×DNA clean beads (Vazyme) and amplified with i5 and i7 primers (Vazyme) by 17-20 PCR cycles. The libraries were purified by 1.2×DNA clean beads (Vazyme).

treatment_protocol: HSCs (CD48-CD150+LSK) from Wild-type, DekTg, and Dek-cKO mice were sorted, followed by DEK CUT&Tag-seq. Besides, HSCs (CD48-CD150+LSK) from DekTg mice were sorted and treated control aptamer and DTA-64 (2 µM), followed by DEK CUT&Tag-seq

value: Bone marrow

value: Hematopoietic stem cell

value: DekTg

value: Aptamer (DTA-64)

tag: cut&tag antibody

value: DEK (16448–1-AP, Proteintech)


title: HAP1,wild-type, H3K9me3

description: Library name: H3K9me3(wild-type)


title: cerebellum, Thap1+/-, nerve-injured, RNA, biol rep6

city: Würzburg

first: Chi Wang

last: Ip

address: Josef-Schneider-Strasse 11

department: Neurology

country: Germany

institute: Neurologische Klinik und poliklinik

data_processing:
R version 4.1.0
Sequence reads were trimmed for adaptor sequence using Cutadapt version 4.6
Trimmed sequence reads were mapped to  the mouse genome GRCm39 using STAR version 2.7.2b
Read counts were summarized for each gene using featureCounts version 1.6.4
Count output was used to to calculate differentially expressed genes using DESeq2 package
Assembly: GRCm39
Supplementary files format and content: tab-delimited text files include raw count and r-log transformed count for each sample, as well as log2Foldchange, pvalue and p.adjust value

source_name: Right cerebellum

growth_protocol: Mice were housed in the animal facility of the University Hospital of Würzburg and kept in standard condition (21°C, 12-h light/dark cycle)

extract_protocol:
RNA was harvested using miRneasy mini kit(Qiagen) for the cerebellum and miRNeasy micro kit (Qiagen) for cortex and striatum . 500 ng of total RNA was used for the construction of sequencing libraries.
DNA libraries for RNA-seq were prepared using Illumina TruSeq Stranded mRNA Library Preparation Kit following manufacturer's protocols.
RNA-seq, Samples were sequenced twice to achieve a higher depth

treatment_protocol: A right sciatic nerve crush injury was performed for 1 minute on isoflurane- anesthetized 12 week-old wt and Thap1+/- mice

value: Right cerebellum

value: male

value: right sciatic nerve crush

tag: time

value: 12 weeks post injury


title: cerebellum, Thap1+/-, nerve-injured, RNA, biol rep5


title: cerebellum, Thap1+/-, nerve-injured, RNA, biol rep4


title: DEK.CUT_DTA64_1


title: cerebellum, Thap1+/-, nerve-injured, RNA, biol rep3


title: EuMyc cells, Menuetto, DMSO, Rep1

description:
Library name: EuMyc Menuetto Sample 7
D1d

value: Lymphoma cell line

value: Lymphoma

value: DMSO

value: Menuetto


title: HAP1,wild-type, H3K4me3

description: Library name: H3K4me3(wild-type)


title: cerebellum, Thap1+/-, nerve-injured, RNA, biol rep1


title: EuMyc cells, Menuetto, Input, Rep5

description:
Library name: EuMyc Menuetto Sample 5
D5i

value: Input


title: cerebelum, Thap1+/-,  naive, RNA, biol rep5

value: naive


title: HAP1,wild-type, H3K4me1

description: Library name: H3K4me1(wild-type)


title: DEK.CUT_Control_1

value: Control aptamer


title: cerebelum, Thap1+/-,  naive, RNA, biol rep6


title: DEK_CUT_Wt_2

value: Wild-type


title: HAP1,wild-type, H3K27me3

description: Library name: H3K27me3(wild-type)

value: wild-type


title: cerebelum, Thap1+/-,  naive, RNA, biol rep4


title: cerebelum, Thap1+/-,  naive, RNA, biol rep3


title: cerebelum, Thap1+/-,  naive, RNA, biol rep1


title: cerebelum, Thap1+/-,  naive, RNA, biol rep2


title: cerebellum, wt, nerve-injured, RNA, biol rep6

value: WT


title: ischemic 3, PBMCSs ADT

city: Hamburg

first: Berenike

last: Rutz

address: Martinistrasse 52

institute: University Medical Center Hamburg-Eppendorf

description:
Library name: Sample 6_ADT
ADT
Antibody-derived Oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads

data_processing:
The demultiplexing, barcoded processing, gene couting and aggregation were made using the Cell Ranger software v6.0.2 (https://www.10xgenomics.com/support/software/cell-ranger/latest/getting-started/cr-what-is-cell-ranger)
Assembly: GRCh38-2020-A
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: CITE-seq

molecule: protein

source_name: blood

extract_protocol:
Whole blood from ischemic stroke patients was acquired by  cathether intervention  from the ischemic hemisphere and from the carotid artery. Blood was immediately transfered to heparin tubes. Whole blood was  layered on Ficoll-Paque Plus  and centrifuged for 25 min at 1850 rpm with break off at RT. The mononuclear cell rich layer was then collected and stored  at -80° in liqud nitrogen. Prior to the library preperation cells were thawn and incubated with TotalSeq-C Human Universal Cocktail (Biolegend #399905) according to the manufacturers instructions. PBMCs were washed in Cell staining Buffer (Biolegend #420201).  After filtering through a 40µm cell strainer and resuspension in 0,04% w/v BSA cells were loaded on the chip.
Library was generated using the Chromium Single Cell 5' reagent kits v2 according to the manufactures protocol (10x Genomics).

value: blood

value: PBMCs


title: DEK_CUT_Wt_1

value: Bone marrow

value: Hematopoietic stem cell

value: DEK (16448–1-AP, Proteintech)


title: cerebellum, wt, nerve-injured, RNA, biol rep5

value: Right cerebellum

value: male

value: right sciatic nerve crush


title: HAP1,wild-type, H3K27ac

description: Library name: H3K27ac(wild-type)


title: cerebellum, wt, nerve-injured, RNA, biol rep3

value: 12 weeks post injury


title: DEK_CUT_Dek.Tg_1

value: DekTg


title: arterial, 3, PBMCSs ADT

description:
Library name: Sample 5_ADT
ADT
Antibody-derived Oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: cerebellum, Thap1+/-, nerve-injured, RNA, biol rep2


title: cerebellum, wt, nerve-injured, RNA, biol rep2


title: DEK_CUT_Dek.KO_2

value: Dek-cKO


title: cerebellum, wt, nerve-injured, RNA, biol rep4


title: DEK.CUT_Control_2


title: arterial, 3, PBMCSs GEX

description:
Library name: Sample 5_mRNA
mRNA
polyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 fle contains transcript


title: cerebellum, wt, nerve-injured, RNA, biol rep1


title: cerebelum, wt, naive, RNA, biol rep5


title: cerebelum, wt, naive, RNA, biol rep6


title: ischemic 2, PBMCSs ADT

description:
Library name: Sample 4_ADT
ADT
Antibody-derived Oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: cerebelum, wt, naive, RNA, biol rep4


title: HPCs_ATAC_DekTg_HU_2

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters “-q 10 -length 30 -stringency 5’.”
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 version 2.2.9. Reads that aligned to the mitochondrial genome were filtered, and PCR duplicates were removed with picard MarkDuplicates.
To identify peaks, the bam files containing unique, nonchrM reads were used to call peaks with MACS2 using parameters ‘‘-nomodel-keep-dup all -q 0.01-shift -100-extsize 200-call-summits -g mm’’.
For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATACseq reads were counted by featureCounts.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
About 1,000 HSCs was resuspended in 50 µL of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin) and incubated on ice for 5 min. After lysis, 950 µL wash buffer was added to the sample. The supernatant was removed by centrifugation (500 g, 10 min).
Then, 4 µLPBS, 0.4 µL 10% Tween 20, 0.4 µL 1% Digitonin, 13.6 µL ddH2O, 20 µl 2×TD buffer, and 1.6 µL Transposome Mix were added to the sample, which was mixed and incubated at 37°C for 30 min. The reaction was terminated by incubating with 10 µL stop buffer. Then the tagment DNA was extracted using 2×DNA Extract Beads (Novoprotein). Total 35 µL DNA was transferred to a 0.2 ml PCR tube, and 2.5 µL N5 primer, 2.5 µL N7 primer, and 10 µL 5×AmpliMix were added. PCR was performed to amplify the library for 13-16 cycles. After the PCR reaction, libraries were purified using the 1.2×DNA Clean Beads (Novoprotein).

treatment_protocol: HPCs (Lin-Sca-1-c-Kit+) from DekCon and DekTg mice were sorted and cultured with DMSO or Hydroxyurea (HU, 100 µM) for 48 h, followed by ATAC-seq

value: Hydroxyurea


title: cerebelum, wt, naive, RNA, biol rep3

value: naive


title: DEK_CUT_Dek.KO_1


title: cerebelum, wt, naive, RNA, biol rep1


title: HPCs_ATAC_DekTg_HU_1


title: ischemic, 3, PBMCSs GEX

description:
Library name: Sample 6_mRNA
mRNA
polyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 fle contains transcript


title: cerebelum, wt, naive, RNA, biol rep2


title: ischemic, 2, PBMCSs GEX

description:
Library name: Sample 4_mRNA
mRNA
polyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 fle contains transcript


title: DEK_CUT_Dek.Tg_2


title: arterial, 2, PBMCSs ADT

description:
Library name: Sample 3_ADT
ADT
Antibody-derived Oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: striatum, THap1+/-, nerve-injured, RNA, biol rep5

source_name: Left striatum

value: Left striatum


title: striatum, THap1+/-, nerve-injured, RNA, biol rep6


title: HPCs_ATAC_DekTg_2

value: DMSO


title: striatum, THap1+/-, nerve-injured, RNA, biol rep4


title: arterial, 2, PBMCSs GEX

description:
Library name: Sample 3_mRNA
mRNA
polyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 fle contains transcript


title: HPCs_ATAC_DekTg_1


title: striatum, THap1+/-, nerve-injured, RNA, biol rep3


title: ischemic 1, PBMCSs ADT

description:
Library name: Sample 2_ADT
ADT
Antibody-derived Oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: striatum, THap1+/-, nerve-injured, RNA, biol rep2


title: ischemic, 1, PBMCSs GEX

description:
Library name: Sample 2_mRNA
mRNA
polyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 fle contains transcript


title: striatum, Thap1+/-, naive, RNA, biol rep6


title: HPCs_ATAC_DekCon_HU_2

value: DekCon


title: HPCs_ATAC_DekCon_HU_1


title: striatum, THap1+/-, nerve-injured, RNA, biol rep1


title: striatum, Thap1+/-, naive, RNA, biol rep5


title: arterial, 1, PBMCSs ADT

description:
Library name: Sample 1_ADT
ADT
Antibody-derived Oligonucleotide (ADT)
ADT: read1 file contains cell barcode and UMI; read2 file contains Antibody Derived Tag reads


title: HPCs_ATAC_DekCon_2


title: striatum, Thap1+/-, naive, RNA, biol rep4


title: striatum, Thap1+/-, naive, RNA, biol rep2


title: arterial, 1, PBMCSs GEX

description:
Library name: Sample 1_mRNA
mRNA
polyA RNA
GEX (5' mRNA) library: read1 file contains cell barcode and UMI; read2 fle contains transcript


title: HPCs_ATAC_DekCon_1


title: striatum, wt, nerve-injured, RNA, biol rep6

value: WT


title: striatum, Thap1+/-, naive, RNA, biol rep1


title: NC_3

city: Wenzhou

first: Xinyu

last: Yang

state: Not applicable

address: Department of Medicinal Chemistry, School of Pharmaceutical Sciences, Wenzhou Medical University, Wenzhou, 325035, China.

department: School of Pharmaceutical Sciences

institute: Wenzhou Medical University

description:
Library name: sample6
FPKM.NC_3

data_processing:
Reads obtained from the sequencing machines includes raw reads containing adapters or low quality bases which will affect the following assembly and analysis. Thus, to get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9). We aligned reads of all samples to the research species reference genome using HISAT2 (https://daehwankimlab.github.io/hisat2/,version:hisat2-2.2.1) package, which initially remove a portion of the reads based on quality information accompanying each read and then maps the reads to the reference genome.
The mapped reads of each sample were assembled using StringTie (http://ccb.jhu.edu/software/stringtie/,version:stringtie-2.1.6) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare software(http://ccb.jhu.edu/software/stringtie/gffcompare.shtml,version:gffcompare-0.9.8). After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
Genes differential expression analysis was performed by DESeq2 software between two different groups (and by edgeR between two samples). The genes with the parameter of false discovery rate (FDR) below 0.05 and absolute fold change ≥ 2 were considered differentially expressed genes. Differentially expressed genes were then subjected to enrichment analysis of GO functions and KEGG pathways.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: synovium

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
mRNA was purified from total RNA (5ug) using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) with two rounds of purification. Following purification, the mRNA was fragmented into short fragments using divalent cations under elevated temperature (Magnesium RNA Fragmentation Module (NEB, cat.e6150, USA) under 94℃ 5-7min). Then the cleaved RNA fragments were reverse-transcribed to create the cDNA by SuperScript™ II Reverse Transcriptase (Invitrogen, cat. 1896649, USA), which were next used to synthesise U-labeled second-stranded DNAs with E. coli DNA polymerase I (NEB, cat.m0209, USA), RNase H (NEB, cat.m0297, USA) and dUTP Solution (Thermo Fisher, cat.R0133, USA). An A-base was then added to the blunt ends of each strand, preparing them for ligation to the indexed adapters. Each adapter contained a T-base overhang for ligating the adapter to the A-tailed fragmented DNA. Dual-index adapters were ligated to the fragments, and size selection was performed with AMPureXP beads. After the heat-labile UDG enzyme (NEB, cat.m0280, USA) treatment of the U-labeled second-stranded DNAs, the ligated products were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 8 cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA librarys were 300±50 bp. At last, we performed the 2×150bp paired-end sequencing (PE150) on an Illumina NovaseqTM 6000 following the vendor's recommended protocol.

value: synovium

value: fibroblast-like synoviocytes

value: IGF2BP1 wildtype


title: NC_2

description:
Library name: sample5
FPKM.NC_2


title: striatum, Thap1+/-, naive, RNA, biol rep3


title: striatum, wt, nerve-injured, RNA, biol rep4


title: LDR infection 1, 48hr

city: Kharagpur

first: Budhaditya

last: Mukherjee

state: West Bengal

address: Life Science Building

department: School of Medical Science and Technology

country: India

institute: Indian Institute of Technology Kharagpur

data_processing:
Raw sequence data were saved in FASTQ format. Each file was considered for various quality control, before process further downstream analysis.
Quality control and preprocessing of FASTQ files are essential to providing clean data for downstream analysis. Fastp (v0.20.0) was used for quality filtering and adapter trimming of the raw data. A cutoff of 30 was set for the quality phred score and only high quality reads were retained. Hisat2, a splice-aware aligner was used to align the reads against the Mus musculus (mm10) genome from the NCBI database. The transcriptome was assembled and quantified from the aligned reads for each sample using StringTie.
Assembly: mm10
Supplementary files format and content: Tab-delimited text file containing raw counts host(murine) genes of each sample

source_name: Peritonial Macrphages

growth_protocol: For in-vitro infection, peritoneal macrophages from BALB/c mice were collected from 48hrs starch-boosted mice after sacrifice. The cells were maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum and 100 U PenStrep. The cells were left to adhere for 48hrs in humidified atmosphere at 37ºC and 5% CO2 before infection.

extract_protocol:
Cells were treated with Trizol and kept at -80ºC until frozen. RNA isolation was done by using Thermo Fisher Invitrogen™ PureLink™ Plant RNA Reagent, as per manufacturer's protocols, followed by quantification was done by using Qubit BR Assay kit, and the Quality of RNA was checked by using Qubit Fluorometer 4 and Tapestatoin2200.
QC passed RNA samples were considered for library preparation by using NEBNext® Ultra™ II Directional RNA Library Prep Kit for Illumina using manufacturer's protocols. The quality of the prepared library was determined by using Qubit 1X dsDNA Assay Kit and Agilent D1000 Screen Tape on TapeStation. Qualified libraries were considered further for sequencing using paired-end(PE) reads of 151bp length format on the Illumina Novaseq 6000 platform.

treatment_protocol: Peritoneal macrophages were infected with LD strains at a ratio of 1:10 (macrophage: parasite) for 4 hours (considered as 0 hours), followed by washing and incubation for specific time points, i.e., 4 hours, 24 hours, and 48 hours post-infection.

value: Peritonial Macrphages

value: LDR-infected


title: striatum, wt, nerve-injured, RNA, biol rep1


title: NC_1

description:
Library name: sample4
FPKM.NC_1


title: striatum, wt, nerve-injured, RNA, biol rep3


title: MUT_3

description:
Library name: sample3
FPKM.MUT_3

value: IGF2BP1 R167K point mutation


title: striatum, wt, nerve-injured, RNA, biol rep2

value: male


title: striatum, wt, naive, RNA, biol rep5


title: LDS infection 2, 48hr

value: LDS-infected


title: LDR infection 2, 24hr


title: MUT_2

description:
Library name: sample2
FPKM.MUT_2


title: striatum, wt, naive, RNA, biol rep2

value: 12 weeks post injury


title: striatum, wt, naive, RNA, biol rep3


title: striatum, wt, naive, RNA, biol rep4


title: LDS infection 1, 48hr


title: LDR infection 1, 24hr


title: cortex, Thap1+/-, nerve-injured, RNA, biol rep6

source_name: Left cortex

value: Left cortex

value: right sciatic nerve crush


title: LDS infection 2, 24hr


title: striatum, wt, naive, RNA, biol rep1


title: striatum, wt, nerve-injured, RNA, biol rep5


title: GES-1,Ulcer-healing Decoction

city: Hangzhou

first: Xiaohong

last: Shi

address: No.280 Xiangshan Road, Xihu District

department: Department of Traditional Chinese Medicine

description:
Library name: Sample 2
Column name in gene_counts.txt:sample2

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts..In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: GRCh38/hg38
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

extract_protocol:
Total RNA was isolated using TRIzol  according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

value: gastric epithelial cells

value: wt

value: Ulcer-healing Decoction


title: GES-1, Placebo

description:
Library name: Sample 1
Column name in gene_counts.txt:sample1

value: Placebo


title: cortex, Thap1+/-, nerve-injured, RNA, biol rep4


title: Hela_Paired_Damage_RNA_batch2

description: Paired-Damage

data_processing:
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Bigwig convert step: The sorted bam file are converted to bigiwg files with bamCoverage of deeptools software (--normalizeUsing RPKM --Offset 75 --smoothLength 500 --extendReads 200)
Assembly: hg38,mm10
Supplementary files format and content: bigwig file
Library strategy: CUT&Tag

molecule: nuclear RNA

source_name: Hela cell

extract_protocol:
Sub-libraries were diluted to 35 μl with 1× NIB-Tris buffer. Then, 5 μl of 4 M NaCl, 5 μl of 10% SDS (Invitrogen, 15553-035) and 5 μl of 10 mg ml−1 Protease K (NEB, P8107S) were added and nuclei were lysed at 850 r.p.m. at 55 °C for 2 hours in a ThermoMixer. The lysed solution was cooled to room temperature and then purified with 1× SPRI beads (Beckman Coulter, B23319) and eluted in 12.5 μl of H2O.
The formaldehyde fixed cells are collected and re-suspended in ice cold NIB buffer for nucleosome depletion; the DNA oxidative damage sites were treated with enzymatic labeling with biotin and tagmentated with identical barcoded assembled pA-Tn5, followed by reverse transcription with paired barcoded RT primers. After 2 rounds of Ligation-based combinatorial barcoding, nuclei were lysed and gDNA and RNA were purified with 1X SPRI beads; next, DNA and RNA libraries were amplified by Kapa HiFi uracil plus DNA polymerase and used 0.8X Ampure XP beads to purify the product. The final libraries were sequenced using Nova-seq platform (illumina) with the following read lengths: PE 100 + 8 + 8 + 50 (Read 1 + Index 1 + Index 2 + Read 2).

treatment_protocol: HeLa S3 (human, ATCC CCL-2.2) cells were cultured according to standard procedures in DMEM (Gibco, 10569010) supplemented with 10% fetal bovine serum (Gibco, 16000044) and 1% penicillin-streptomycin (Gibco, 10378016) at 37 °C with 5% CO2. Cells were not authenticated or tested for mycoplasma. Cells were sown on plates 48 hours before treatment with H2O2 at the density of 3×105 cells per culture dish. Subconfluent cells were treated with H2O2, in a complete medium, at the final concentration of 200 µM (Thermo Scientific Chemicals, 202465000) for 2 hours at 37°C 5% CO2. After treatment, the medium was replaced with complete medium without H2O2 for additional incubation. The frontal cortex of male C57BL/6J mice at 8 weeks and 11 months was purchased from Jackson Laboratories and maintained in dry ice. Single-cell suspensions were prepared from douncing of the frozen tissues, in Douncing Buffer with protease/RNase inhibitor cocktail (DBI: 0.25 M sucrose (Sigma, S7903), 25 mM KCl (Sigma, P9333), 5 mM MgCl2, 10 mM Tris-HCl pH 7.5 (Invitrogen, 15567027), 1 mM DTT (Sigma, D9779), 1× Protease Inhibitor, 0.5 U μL−1 RNase OUT and 0.5 U μL−1 SUPERase Inhibitor) supplemented with 0.1% Triton-X100 (Sigma T9284). The cell suspension was then filtered by 30-μm Cell-Tric (Sysmex) and spun down for 10 min, at 1,000 g and 4 °C. After the cell pellets were washed with DBI and spun down again, cold NIB-HEPES buffer was added to resuspend the nuclei pellets, incubated on ice for 10 min and centrifuged for 10 min at 600 g, 4 °C. Cells were washed with 1 mL cold NIB-HEPES buffer and centrifuged for 10 min at 600 g, 4 °C before proceeding to Paired-Damage experiments. The nuclei were counted by a cell counter before proceeding to Paired-Damage experiments immediately.

value: Hela cell

value: Cancer cell

value: No


title: LDR infection 2, 48hr


title: cortex, Thap1+/-, nerve-injured, RNA, biol rep3


title: cortex, Thap1+/-, nerve-injured, RNA, biol rep2


title: striatum, wt, naive, RNA, biol rep6

value: Left striatum

value: WT

value: naive


title: LDR infection 2, 4hr

value: Peritonial Macrphages

value: LDR-infected


title: LDS infection 1, 24hr


title: cortex, Thap1+/-, nerve-injured, RNA, biol rep1

value: male


title: LDR infection 1, 4hr


title: cortex, Thap1+/-, naive, RNA, biol rep6


title: MUT_1

description:
Library name: sample1
FPKM.MUT_1

value: synovium

value: fibroblast-like synoviocytes

value: IGF2BP1 R167K point mutation


title: LDS infection 2, 4hr

value: LDS-infected


title: Hela_Paired_Damage_DNA_batch2

description: Paired-Damage


title: cortex, Thap1+/-, naive, RNA, biol rep4

value: Left cortex

value: 12 weeks post injury


title: cortex, Thap1+/-, naive, RNA, biol rep5


title: Hela_nickase_bulk_damage

description:
bulk damagenome
Damage_HeLa_DNA_additional_bigwig.tar.gz


title: Hela_10mM_bulk_damage

value: hydrogen peroxide treatment


title: cortex, Thap1+/-, naive, RNA, biol rep1


title: cortex, Thap1+/-, naive, RNA, biol rep3


title: cortex, Thap1+/-, naive, RNA, biol rep2


title: LDS infection 1, 4hr


title: Hela_5mM_bulk_damage


title: cortex, Thap1+/-, nerve-injured, RNA, biol rep5

value: right sciatic nerve crush


title: cortex, wt, nerve-injured, RNA, biol rep6


title: cortex, wt, nerve-injured, RNA, biol rep5


title: Unifected Control 2

value: UI


title: Hela_prerepair_bulk_damage

value: Hela cell

value: Cancer cell


title: cortex, wt, nerve-injured, RNA, biol rep4


title: Hela_bulk_nucleosome_depletion

description:
nucleosome_depletion_control
nucleosome_depletion_DNA_additional_bigwig.tar.gz

value: No


title: cortex, wt, nerve-injured, RNA, biol rep1

value: WT


title: cortex, wt, nerve-injured, RNA, biol rep3


title: Unifected Control 1

value: Ui


title: PVA_HSC_Aged_Control_3

first: David

last: Redmond

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Reads were checked for quality (FastQC v0.11.5) and processed using the Digital Expression Explorer 2 (DEE2) workflow
Adapter trimming was performed with Skewer (v0.2.2)
Further quality control was performed with Minion, part of the Kraken package
Filtered reads were mapped to the mouse reference genome GRCm38 using STAR aligner and gene-wise expression counts were generated using the “-quantMode GeneCounts” parameter.
The R package edgeR was used to calculate FPKM
Assembly: mm10
Supplementary files format and content: tab-delimited text file include FPKM values for all samples in this subseries

source_name: Bone Marrow

growth_protocol: FACS purified HSCs were cultured ex vivo for 11 days in a polyvinyl alcohol based expansion medium containing 10 ng/mL murine SCF and 100 ng/mL murine TPO.

extract_protocol:
Cells were FACS sorted into TRIzol-LS and total RNA was purified as per manufacturer’s protocol. 2 ng total RNA was utilized as input for library preparation.
Libraries for RNA-seq were prepared using SMART-Seq v4 Ultra Low Input RNA Kit following manufacturer's protocols.

treatment_protocol: To analyze transcriptional alterations within HSCs cultured in the presence of recombinant Thbs1 and its neutralizing antibody, RNA Seq analysis was performed on FACS purified HSPCs.

value: Bone Marrow

value: Primary cells

value: Hematopoietic stem cell

value: Control

value: 18 month old

value: Vehicle (PBS)


title: ATAC_Healthy_5

data_processing:
Low-quality reads and adaptor sequences were removed by Trim Galore v0.4.4 with parameters “-q 10 -length 30 -stringency 5’.”
Paired-end reads were mapped to the mm10 reference genome using Bowtie2 version 2.2.9. Reads that aligned to the mitochondrial genome were filtered, and PCR duplicates were removed with picard MarkDuplicates.
To identify peaks, the bam files containing unique, nonchrM reads were used to call peaks with MACS2 using parameters ‘‘-nomodel-keep-dup all -q 0.01-shift -100-extsize 200-call-summits -g mm’’.
For differential coverage, corresponding bam files were merged to call peaks to get a union peak set. For each peak in the peak set, raw ATACseq reads were counted by featureCounts.
Assembly: hg38
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

extract_protocol:
About 1,000 cells was resuspended in 50 µL of lysis buffer (10 mM Tris-HCl pH7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% NP40, 0.1% Tween 20, 0.01% Digitonin) and incubated on ice for 5 min. After lysis, 950 µL wash buffer was added to the sample. The supernatant was removed by centrifugation (500 g, 10 min).
Then, 4 µLPBS, 0.4 µL 10% Tween 20, 0.4 µL 1% Digitonin, 13.6 µL ddH2O, 20 µl 2×TD buffer, and 1.6 µL Transposome Mix were added to the sample, which was mixed and incubated at 37°C for 30 min. The reaction was terminated by incubating with 10 µL stop buffer. Then the tagment DNA was extracted using 2×DNA Extract Beads (Novoprotein). Total 35 µL DNA was transferred to a 0.2 ml PCR tube, and 2.5 µL N5 primer, 2.5 µL N7 primer, and 10 µL 5×AmpliMix were added. PCR was performed to amplify the library for 13-16 cycles. After the PCR reaction, libraries were purified using the 1.2×DNA Clean Beads (Novoprotein).

treatment_protocol: Bone marrow CD34+ cells from five healthy donors and five patients with FA were isolated, followed by ATAC-seq

value: Bone marrow

value: CD34+ cells

tag: disease state

value: Healthy


title: cortex, wt, nerve-injured, RNA, biol rep2

value: Left cortex

value: male

value: 12 weeks post injury


title: PVA_HSC_Aged_Control_2


title: cortex,wt, naive, RNA, biol rep5

value: naive


title: cortex,wt, naive, RNA, biol rep4


title: ATAC_Healthy_4


title: PVA_HSC_Aged_Control_1


title: cortex,wt, naive, RNA, biol rep3


title: cortex,wt, naive, RNA, biol rep1


title: ATAC_Healthy_3


title: ATAC_Healthy_2


title: cerebellum, Thap1+/-, nerve-injured, miRNA, biol rep6

data_processing:
R version 4.1.0
Sequence reads were annoted, adapter-trimmed and mapped using miRge3.0
Read counts were summarized for each gene using featureCounts version 1.6.4
Assembly: Mouse
Supplementary files format and content: tab-delimited text files include raw count and r-log transformed count for each sample, as well as log2Foldchange, pvalue and p.adjust value

extract_protocol:
miRNA was harvested using miRneasy mini kit(Qiagen) for the cerebellum and miRNeasy micro kit (Qiagen) for cortex and striatum . 10 ng of enriched miRNA samples were used for the construction of sequencing libraries.
DNA libraries for miRNA-seq were prepared using QIASeq miRNA UDI Library Kit following manufacturer's protocols.

value: Right cerebellum

value: right sciatic nerve crush


title: cerebellum, Thap1+/-, nerve-injured, miRNA, biol rep5


title: Coretx_Paired_Damage_DNA

description: Paired-Damage

data_processing:
Cut adapter step: The raw FASTQ files are firstly but the sequencing adapters with cutadapt software
Alignment step: After the cut adapter step, all the FASTQ files are mapped to the reference genome
BAM convert step:The alignment SAM results are converted to sorted BAM files with samtools software
Assembly: hg38,mm10
Supplementary files format and content: bigwig file
Library strategy: paired-damage

source_name: Mouse cortex

value: Mouse cortex

value: Neuron and nonneuron cells

value: WT


title: ATAC_Healthy_1


title: pATF2(S490/498)-HSC-2

data_processing:
The quality control of each sample was accomplished using FASTQC V0.11.5.
Clean reads were aligned to mouse reference genome (mm10) using Bowtie 2 version 2.2.9. MarkDuplicates was used to mark PCR duplicate and unmapped reads. Only unique mapped reads were used in further analysis.
Peak calling and annotation were performed using MACS2 and ChIPseeker package, respectively.
Assembly: mm10
Supplementary files format and content: bigWig
Supplementary files format and content: narrowPeak

treatment_protocol: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted , followed by p-ATF2 CUT&Tag-seq

value: Wild-type


title: cerebellum, Thap1+/-, nerve-injured, miRNA, biol rep3


title: cerebellum, Thap1+/-, nerve-injured, miRNA, biol rep2


title: cerebellum, Thap1+/-, nerve-injured, miRNA, biol rep1


title: pATF2(S490/498)-HSC-1

value: Hematopoietic stem cell


title: ATAC_FA_5

value: Fanconi anemia (FA)


title: cortex,wt, naive, RNA, biol rep6


title: cerebelum, Thap1+/-,  naive, miRNA, biol rep6


title: ATAC_FA_3


title: cerebelum, Thap1+/-,  naive, miRNA, biol rep5


title: cerebelum, Thap1+/-,  naive, miRNA, biol rep4


title: pATF2(T69/71)-HSC-1


title: cerebelum, Thap1+/-,  naive, miRNA, biol rep3


title: cortex,wt, naive, RNA, biol rep2


title: Cortex_Paired_Damage_RNA

description: Paired-Damage


title: cerebelum, Thap1+/-,  naive, miRNA, biol rep1


title: ATAC_FA_1


title: cerebellum, wt, nerve-injured, miRNA, biol rep6


title: cerebellum, wt, nerve-injured, miRNA, biol rep5


title: Fancd2-/-Dek-HET HSC-1

treatment_protocol: HSCs (CD48-CD150+LSK) from Fancd2+/+Dekfl/+, Fancd2-/-Dekfl/+, Fancd2+/+Dek-HET, and Fancd2-/-Dek-HET mice were sorted, followed by ATAC-seq


title: cerebellum, Thap1+/-, nerve-injured, miRNA, biol rep4


title: cerebellum, wt, nerve-injured, miRNA, biol rep4


title: cerebellum, wt, nerve-injured, miRNA, biol rep3


title: cerebellum, wt, nerve-injured, miRNA, biol rep2


title: cerebelum, wt, naive, miRNA, biol rep6


title: P65_pDBF_rep3

city: Aurora

first: Matthew

last: Taliaferro

state: CO

department: Biochemistry and Molecular Genetics

institute: University of Colorado Anschutz Medical Campus

data_processing:
OINC-seq (Oxidation-Induced Nucleotide Conversion sequencing)
Adapters were trimmed from reads using Cutadapt.
RNA oxidation events (as seen as mutations) were quantified using PIGPEN (https://github.com/TaliaferroLab/OINC-seq)
Assembly: hg38 and GRCz11
Supplementary files format and content: Quantification of mutations in RNAseq data produced by PIGPEN.

source_name: HeLa

growth_protocol: HeLa cells were cultured in DMEM + pen/strep + 10% FBS. Zebrafish embryos were incubated at 28.5C in E3 medium.

extract_protocol:
RNA was extracted using Trizol and DNase treated for 30 min at 37C.
Single amplicon libraries were constructed using gene-specific RT-PCR. Whole transcriptome libraries were created using Lexogen Quantseq library kits.

value: HeLa

value: plus DBF


title: cerebellum, wt, nerve-injured, miRNA, biol rep1


title: Fancd2+/+Dek-HET HSC-1

value: Bone marrow


title: P65_pDBF_rep1


title: ATAC_FA_4

value: CD34+ cells


title: P65_pDBF_rep2


title: Fancd2-/-Dekfl/+ HSC-2


title: pATF2(T69/71)-HSC-2


title: cerebelum, wt, naive, miRNA, biol rep5


title: Fancd2-/-Dekfl/+ HSC-1


title: cerebelum, Thap1+/-,  naive, miRNA, biol rep2


title: Fancd2-/-Dek-HET HSC-2


title: ATAC_FA_2


title: Fancd2+/+Dekfl/+ HSC-2


title: P65_mDBF_rep3

value: minus DBF


title: cerebelum, wt, naive, miRNA, biol rep4


title: cerebelum, wt, naive, miRNA, biol rep2


title: cerebelum, wt, naive, miRNA, biol rep1


title: cerebelum, wt, naive, miRNA, biol rep3


title: P65_mDBF_rep2


title: striatum, THap1+/-, nerve-injured, miRNA, biol rep6

value: Left striatum


title: Fancd2+/+Dekfl/+ HSC-1


title: Fancd2+/+Dek-HET HSC-2


title: P65_mDBF_rep1


title: P65_GAPDH_intspan_Rep3_pDBF


title: striatum, THap1+/-, nerve-injured, miRNA, biol rep4

value: male


title: MSCV-H1C-HSC

treatment_protocol: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were transduced by pMSCV or MSCV-H1C retrovirus, followed by ATAC-seq

value: H1C overexpression


title: striatum, THap1+/-, nerve-injured, miRNA, biol rep5

value: 12 weeks post injury


title: striatum, THap1+/-, nerve-injured, miRNA, biol rep3


title: striatum, THap1+/-, nerve-injured, miRNA, biol rep1


title: MSCV-HSC

value: Control


title: DekTg-HSC-4

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome using bowtie v0.12.9.
Fragments per kilobase per million (FPKM) estimation was performed with Cufflinks v2.1.1, aligned reads were counted with HTSeq (a Python framework to work with high-throughput sequencing data), and differential expression analysis was performed with DESeq2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

extract_protocol:
Total RNA was extracted with miRNeasy Kit (QIAGEN).
The mRNA was reverse-transcribed and amplified according to the method Geo-seq, then the library was constructed using the TruePrep DNA Library Prep Kit V2 for Illumina (Vazyme) according to the manufacturer’s instruction.

treatment_protocol: Total RNA of HSCs (CD48-CD150+LSK) from DekCon and DekTg mice were extracted, followed by RNA-seq.

value: DekTg


title: P65_GAPDH_intspan_Rep2_pDBF


title: striatum, Thap1+/-, naive, miRNA, biol rep6

value: naive


title: striatum, Thap1+/-, naive, miRNA, biol rep4


title: striatum, Thap1+/-, naive, miRNA, biol rep3


title: striatum, Thap1+/-, naive, miRNA, biol rep5


title: DekTg-HSC-3


title: P65_GAPDH_intspan_Rep2_mDBF


title: striatum, Thap1+/-, naive, miRNA, biol rep2


title: striatum, Thap1+/-, naive, miRNA, biol rep1


title: striatum, wt, nerve-injured, miRNA, biol rep6

value: right sciatic nerve crush


title: DekTg-HSC-1


title: DekTg-HSC-2


title: P65_GAPDH_intspan_Rep1_pDBF


title: striatum, wt, nerve-injured, miRNA, biol rep5

value: WT


title: P65_GAPDH_intspan_Rep1_mDBF


title: P65_GAPDH_exon_Rep3_pDBF


title: striatum, wt, nerve-injured, miRNA, biol rep3


title: striatum, wt, nerve-injured, miRNA, biol rep2


title: P65_GAPDH_exon_Rep3_mDBF


title: DekCon-HSC-3

value: DekCon


title: P65_GAPDH_exon_Rep2_pDBF


title: DekCon-HSC-4

value: Hematopoietic stem cell


title: striatum, THap1+/-, nerve-injured, miRNA, biol rep2


title: P65_GAPDH_intspan_Rep3_mDBF


title: striatum, wt, naive, miRNA, biol rep6


title: DekCon-HSC-2


title: striatum, wt, naive, miRNA, biol rep5


title: striatum, wt, naive, miRNA, biol rep4


title: DekCon-HSC-1


title: P65_GAPDH_exon_Rep2_mDBF


title: striatum, wt, naive, miRNA, biol rep3


title: striatum, wt, naive, miRNA, biol rep2


title: striatum, wt, naive, miRNA, biol rep1


title: ATAC DekTg-HSC-HU-2

treatment_protocol: HSCs (CD48-CD150+LSK) from DekCon and DekTg mice were sorted and cultured with DMSO or Hydroxyurea (HU, 100 µM) for 48 h, followed by ATAC-seq

value: Hydroxyurea


title: P65_GAPDH_exon_Rep1_pDBF

value: HeLa


title: cortex, Thap1+/-, nerve-injured, miRNA, biol rep6

value: Left cortex


title: P65_GAPDH_exon_Rep1_mDBF


title: P65_CD9_rep3_pDBF

value: plus DBF


title: cortex, Thap1+/-, nerve-injured, miRNA, biol rep4


title: ATAC DekTg-HSC-HU-1

value: Bone marrow


title: ATAC DekTg-HSC-DMSO-2

value: DMSO


title: striatum, wt, nerve-injured, miRNA, biol rep4

value: Left striatum


title: cortex, Thap1+/-, nerve-injured, miRNA, biol rep3

value: male


title: ATAC DekTg-HSC-DMSO-1


title: P65_CD9_rep2_pDBF


title: cortex, Thap1+/-, nerve-injured, miRNA, biol rep1


title: cortex, Thap1+/-, naive, miRNA, biol rep6


title: cortex, Thap1+/-, nerve-injured, miRNA, biol rep5


title: P65_CD9_rep2_mDBF

value: minus DBF


title: cortex, Thap1+/-, nerve-injured, miRNA, biol rep2

value: 12 weeks post injury


title: cortex, Thap1+/-, naive, miRNA, biol rep4


title: ATAC DekCon-HSC-HU-2


title: cortex, Thap1+/-, naive, miRNA, biol rep3


title: P65_CD9_rep1_pDBF


title: ATAC DekCon-HSC-HU-1


title: cortex, Thap1+/-, naive, miRNA, biol rep2


title: striatum, wt, nerve-injured, miRNA, biol rep1


title: cortex, Thap1+/-, naive, miRNA, biol rep5


title: ATAC DekCon-HSC-DMSO-2


title: P65_CD9_rep1_mDBF


title: cortex, wt, nerve-injured, miRNA, biol rep6


title: cortex, wt, nerve-injured, miRNA, biol rep5


title: P65_CD9_rep3_mDBF


title: cortex, Thap1+/-, naive, miRNA, biol rep1


title: ATAC DekCon-HSC-DMSO-1


title: cortex, wt, nerve-injured, miRNA, biol rep4


title: cortex, wt, nerve-injured, miRNA, biol rep2


title: P450_pDBF_rep2


title: cortex, wt, nerve-injured, miRNA, biol rep1


title: DekTg-HSC-HU-1

treatment_protocol: HSCs (CD48-CD150+LSK) from DekCon and DekTg mice were sorted and cultured with DMSO or Hydroxyurea (HU, 100 µM) for 48 h, followed by H3K27ac CUT&Tag-seq


title: cortex,wt, naive, miRNA, biol rep6


title: cortex, wt, nerve-injured, miRNA, biol rep3


title: cortex,wt, naive, miRNA, biol rep4


title: DekTg-HSC-HU-2


title: P450_pDBF_rep1


title: DekTg-HSC-DMSO-2


title: DekTg-HSC-DMSO-1


title: P450_mDBF_rep3


title: P450_mDBF_rep2


title: cortex,wt, naive, miRNA, biol rep2


title: DekCon-HSC-HU-2


title: P450_mDBF_rep1


title: primary astrocytes, Prdm16os KD 6

city: Gottingen

first: Andre

last: Fischer

state: NS

address: Von Sieboldstr 3a

department: Epigenetic Mechanisms in Dementia

institute: German Center for Neurodegenerative Diseases (DZNE)

data_processing:
llumina’s conversion software bcl2fastq (v2.20.2) was used for adapter trimming and converting the base calls in the per-cycle BCL files to the per-read FASTQ format from raw images
FASTQ reads were aligned to mouse genome (mm10) using parameters --outFilterMismatchNmax 2   --sjdbOverhang 100
Read counts were generated with the featureCounts (v2.0.0) script from the R package subread with parameters "-t" "exon" "-g" "gene_id"
Assembly: mm10
Supplementary files format and content: Tab-delimited files include raw counts for each sample

source_name: Primary mouse astrocytes

growth_protocol: Primary mouse astrocytes were isolated from p1 mice and cultured in Neurobasal+ medium containing B27+ supplement and antibiotics in humified atmosphere with 5% CO2 at 37°C

extract_protocol:
RNA was isolated using Tri reagent (Sigma), followed by purification with the RNA Clean & Concentrator-5 kit (Zymo)
Libraries were generated from 300 ng RNA with the SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara)

treatment_protocol: Cells were treated on DIV12 with 50 nM control or Prdm16os KD Gapmers using Lipofectamine RNAiMAX in medium without antibiotics for 48 hours.

value: Primary mouse astrocytes

value: Prdm16os KD Gapmers


title: DekCon-HSC-HU-1


title: MAVS_pDBF_rep3

value: Halo-MAVS


title: P450_pDBF_rep3


title: DekCon-HSC-DMSO-2


title: primary astrocytes, Prdm16os KD 3


title: primary astrocytes, Prdm16os KD 4


title: MAVS_pDBF_rep2


title: DekCon-HSC-DMSO-1


title: primary astrocytes, Prdm16os KD 2


title: cortex,wt, naive, miRNA, biol rep5

value: naive


title: primary astrocytes, Prdm16os KD 5


title: MAVS_pDBF_rep1


title: primary astrocytes, Prdm16os KD 1


title: CUT-Tag-4 HSC-CUT-Tag-4 HU-2

treatment_protocol: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted and cultured with DMSO, Gemcitabine (Gem, 0.5 µM), or Hydroxyurea (HU, 100 µM) for 48 h, followed by H3K27ac CUT&Tag-seq

value: Wild-type


title: cortex,wt, naive, miRNA, biol rep3

value: WT


title: primary astrocytes, control 4

value: Control Gapmers


title: primary astrocytes, control 5


title: cortex,wt, naive, miRNA, biol rep1


title: MAVS_mDBF_rep2


title: MAVS_mDBF_rep3


title: CUT-Tag-4 HSC-CUT-Tag-4 HU-1

value: Hematopoietic stem cell

value: Hydroxyurea


title: primary astrocytes, control 3


title: CUT-Tag-4 HSC-Gem-2

value: Gemcitabine


title: primary astrocytes, control 2


title: CUT-Tag-4 HSC-Gem-1


title: cckAts-ntrC(A446P) replicate 3

city: East Lansing

first: Sean

last: Crosson

state: Michigan

address: 567 Wilson Rd

department: Dept. Microbiology and Molecular Genetics

institute: Michigan State University

description:
Library name: SCR_378
SCR_378

data_processing:
RNA-seq reads were aligned to the Caulobacter crescentus genome (accession CP001340) using CLC Genomics Workbench version 22.0.
Assembly: Caulobacter crescentus NA1000 (genbank accession CP001340)
Supplementary files format and content: processed data files contain total counts, RPKM, TPM, and CPM for each replicate sample.

organism: Caulobacter vibrioides

growth_protocol: Caulobacter strains were grown in peptone-yeast extract medium to mid-log phase (~0.3 OD 660 nm) at 37 C.

extract_protocol:
Pellets were immediately resuspended in 1ml TRIzol and stored at -80˚C until RNA extraction. To extract RNA, thawed samples were incubated at 65˚C for 10 min. After addition of 200 µl of chloroform, samples were vortexed for 20 s and incubated at room temperature (RT) for 5 min. Phases were separated by centrifugation (10 min at 17,000 x g). The aqueous phase was transferred to a fresh tube and an equal volume of isopropanol was added to precipitate the nucleic acid. Samples were stored at 80˚C (1 h to overnight), then thawed and centrifuged at 17,000 x g for 30 min at 4˚C to pellet the nucleic acid.  Pellets were washed with ice-cold 70% ethanol then centrifuged for at 17,000 x g for 5 min at 4˚C.  After discarding the supernatant, pellets were air-dried at RT, resuspended in 100 µl RNAse-free water, and incubated at 60˚C for 10 min. Samples were treated with TURBO DNAse (Invitrogen) following manufactures protocol for 30 min at RT and then column purified using RNeasy Mini Kit (Qiagen).  RNA samples were sequenced at SeqCenter (Pittsburgh, PA). Briefly, sequencing libraries were prepared using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and custom rRNA depletion probes.
RNA samples were sequenced at SeqCenter (Pittsburgh, PA). Briefly, sequencing libraries were prepared using Illumina’s Stranded Total RNA Prep Ligation with Ribo-Zero Plus kit and custom rRNA depletion probes.


title: cckAts-ntrC(A446P) replicate 2

description:
Library name: SCR_377
SCR_377


title: ntrC(A446P) replicate 3

description:
Library name: SCR_375
SCR_375


title: ntrC(A446P) replicate 1

description:
Library name: SCR_373
SCR_373


title: cckAts-ntrC(A446P) replicate 1

description:
Library name: SCR_376
SCR_376


title: cckAts-ntrC(L424P) replicate 3

description:
Library name: SCR_372
SCR_372


title: ntrC(A446P) replicate 2

description:
Library name: SCR_374
SCR_374


title: cckAts-ntrC(L424P) replicate 1

description:
Library name: SCR_370
SCR_370


title: CUT-Tag HSC-CUT-Tag HU-1

treatment_protocol: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted and cultured with DMSO, Gemcitabine (Gem, 0.5 µM), or Hydroxyurea (HU, 100 µM) for 48 h, followed by H3K4me3 CUT&Tag-seq


title: CUT-Tag-4 HSC-DMSO-2


title: cckAts-ntrC(L424P) replicate 2

description:
Library name: SCR_371
SCR_371


title: MAVS_ND3_Rep2_mDBF

value: HeLa


title: MAVS_ND3_Rep2_pDBF

value: plus DBF


title: MAVS_ND3_Rep1_mDBF


title: cckAts-delntrC replicate 3

description:
Library name: SCR_366
SCR_366

value: cckAts-delntrC


title: cckAts-delntrC replicate 2

description:
Library name: SCR_365
SCR_365


title: MAVS_ND3_Rep3_pDBF


title: MAVS_ND3_Rep3_mDBF


title: ntrC(L424P) replicate 1

description:
Library name: SCR_367
SCR_367


title: CUT-Tag HSC-CUT-Tag HU-2

value: Bone marrow


title: primary astrocytes, control 6


title: CUT-Tag-4 HSC-DMSO-1

value: DMSO


title: primary astrocytes, control 1


title: CUT-Tag HSC-Gem-1


title: cckAts-delntrC replicate 1

description:
Library name: SCR_364
SCR_364


title: CUT-Tag HSC-DMSO-2


title: ntrC(L424P) replicate 2

description:
Library name: SCR_368
SCR_368


title: ntrC(L424P) replicate 3

description:
Library name: SCR_369
SCR_369


title: MAVS_CO1_Rep3_pDBF


title: MAVS_mDBF_rep1

value: minus DBF


title: MAVS_ND3_Rep1_pDBF


title: CUT-Tag HSC-Gem-2


title: cckAts replicate 2

description:
Library name: SCR_359
SCR_359

value: cckAts


title: MAVS_CO1_Rep2_pDBF


title: cckAts replicate 1

description:
Library name: SCR_358
SCR_358


title: ATAC HSC-ATAC HU-2

treatment_protocol: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted and cultured with DMSO, Gemcitabine (Gem, 0.5 µM), or Hydroxyurea (HU, 100 µM) for 48 h, followed by ATAC-seq


title: ITAM-SK96-2

city: Madison

first: Igor

last: Slukvin

state: Wisconsin

address: 1220 Capital Ct

department: Wisconsin National Primate Research Center

institute: University of Wisconsin-Madison

description: Library name: ITAM-SK96-2

data_processing:
Illumina bcl2fastq v2.20.0.422
Read trimming with Skewer v0.2.2b -m pe -q 20 -k 15 -l 25
Read alignment with STAR v2.5.3a --runThreadN 10 --twopassMode Basic --quantMode TranscriptomeSAM GeneCounts --outSAMtype BAM SortedByCoordinate --outSAMstrandField intronMotif --outSAMattributes NH HI AS NM MD XS --outSAMunmapped Within --outFilterMultimapNmax 50
Expression estimation with RSEM rsem-calculate-expression v1.2.31 --alignments --no-bam-output --paired-end
Differential expression estimation with edgeR v3.28.0
Assembly: GRCh38.p10
Supplementary files format and content: Text file contains RSEM expected counts for each sample

source_name: SIRPA-ITAM BM9 hiPSC

growth_protocol: In vitro hematopoiesis of BM9 iPSCs to generate hematopoietic progenitors, then differentiation into iPSC-derived macrophages

extract_protocol:
Total RNA isolatioon according to Qiagen Rneasy mini kit
The RNA samples were rRNA depleted using QIAGEN FastSelect rRNA HMR Kit (Qiagen, Germantown, MD, USA). The kit NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (New England Biolabs, Ipswich, MA, USA) was used for library preparation following manufacture instructions.

treatment_protocol: Cultured in IF9S media

value: SIRPA-ITAM BM9 hiPSC

value: CD45+ iPSC-derived macrophage

value: SIRPA-ITAM

value: Cultured with SKOV-3 and anti-HER2 for 96 hours


title: CUT-Tag HSC-DMSO-1

value: Wild-type


title: MAVS_CO1_Rep3_mDBF

value: Halo-MAVS


title: ITAM-SK96-3

description: Library name: ITAM-SK96-3


title: ITAM-SK96-1

description: Library name: ITAM-SK96-1


title: ITAM-SK24-2

description: Library name: ITAM-SK24-2

value: Cultured with SKOV-3 and anti-HER2 for 24 hours


title: cckAts replicate 3

description:
Library name: SCR_360
SCR_360


title: ATAC HSC-ATAC HU-1

value: Hematopoietic stem cell


title: MAVS_CO1_Rep1_pDBF


title: ATAC HSC-Gem-2


title: ITAM-SK24-3

description: Library name: ITAM-SK24-3


title: ITAM-3

description: Library name: ITAM-3

value: Cultured alone in media


title: ITAM-2

description: Library name: ITAM-2


title: KO-SK96-3

description: Library name: KO-SK96-3

source_name: SIRPA-KO BM9 hiPSC

value: SIRPA-KO BM9 hiPSC

value: SIRPA-KO


title: HeLa_P65_MALAT1_Rep4_mDBF

value: HeLa


title: MAVS_CO1_Rep2_mDBF


title: MAVS_CO1_Rep1_mDBF


title: ATAC HSC-DMSO-2


title: KO-SK96-2

description: Library name: KO-SK96-2


title: ITAM-1

description: Library name: ITAM-1


title: HeLa_P65_MALAT1_Rep4_pDBF

value: plus DBF


title: ITAM-SK24-1

description: Library name: ITAM-SK24-1


title: ATAC HSC-DMSO-1

value: Bone marrow


title: KO-SK96-1

description: Library name: KO-SK96-1


title: HeLa_P65_MALAT1_Rep3_pDBF


title: KO-SK24-3

description: Library name: KO-SK24-3


title: KO-SK24-2

description: Library name: KO-SK24-2


title: HSC-HU-2

treatment_protocol: HSCs (CD48-CD150+LSK) from wild-type C57BL/6J mice were sorted and cultured with DMSO, Gemcitabine (Gem, 0.5 µM), or Hydroxyurea (HU, 100 µM) for 48 h, followed by RNA-seq

value: Hydroxyurea


title: ATAC HSC-Gem-1

value: Gemcitabine


title: HSC-HU-1


title: HeLa_P65_MALAT1_Rep3_mDBF

value: minus DBF


title: KO-SK24-1

description: Library name: KO-SK24-1


title: HeLa_P65_MALAT1_Rep2_pDBF


title: KO-3

description: Library name: KO-3


title: KO-1

description: Library name: KO-1


title: HSC-Gem-1


title: WT-SK96-3

description: Library name: WT-SK96-3

source_name: BM9 hiPSC

value: BM9 hiPSC

value: WT


title: HeLa_P65_MALAT1_Rep1_pDBF


title: HSC-Gem-2


title: KO-2

description: Library name: KO-2

value: CD45+ iPSC-derived macrophage


title: WT-SK96-2

description: Library name: WT-SK96-2

value: Cultured with SKOV-3 and anti-HER2 for 96 hours


title: WT-SK96-1

description: Library name: WT-SK96-1


title: HSC-DMSO-3

value: Wild-type

value: DMSO


title: WT-SK24-3

description: Library name: WT-SK24-3

value: Cultured with SKOV-3 and anti-HER2 for 24 hours


title: WT-SK24-2

description: Library name: WT-SK24-2


title: HeLa_P65_MALAT1_Rep2_mDBF


title: WT-SK24-1

description: Library name: WT-SK24-1


title: HSC-DMSO-2

value: Hematopoietic stem cell


title: WT-3

description: Library name: WT-3

value: Cultured alone in media


title: HSC-DMSO-1


title: WT-2

description: Library name: WT-2


title: HeLa_P65_GAPDH_Rep4_mDBF


title: WT-1

description: Library name: WT-1


title: HeLa_P65_GAPDH_Rep3_pDBF


title: INPUT for HA ChIP-seq at 28h

city: Thuwal

first: Valerio

last: Orlando

country: Saudi Arabia

institute: KAUST

data_processing:
Raw data was quality-checked and trimmed with BBDuk (version December 10, 2015) (https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/). Since the datasets contained a spike-in from Drosophila melanogaster, the high-quality reads were mapped against the mouse genome (version mm10) and against the D. melanogaster genome (version BDGP6) with the software BWA (version 0.7.17). Afterwards, from the mouse-derived mapping reads, PCR duplicates were removed with Picard MarkDuplicates (version 2.8.1) (http://broadinstitute.github.io/picard/) and only reads being properly paired with a mapping quality equal or higher than 30 were kept with SAMtools (version 1.7). Peak calling was performed using MACS2 (version 2.2.4) using a q-value cutoff of 0.05.
Assembly: mm10
Supplementary files format and content: ChIP-seq peaks (depending on the mark, narrowPeak or broadPeak format). BigWig files.

source_name: skeletal muscle

extract_protocol: TruSeq ChIP Library Preparation Kit followed by sequencing with NovaSeq6000

value: skeletal muscle


title: Tollip knockdown + IL-13 treatment sample

city: Bronx

first: Grace

middle: Yihua

last: Lee

address: 1300 Morris Park Ave, Forchheimer Bldg, Room 726

institute: Singulomics Corporation

data_processing:
The sequencing reads were processed using the 10x Genomics Cell Ranger analytical pipeline (v8.0.0) with the human GRCh38-2024-A reference (10X Genomics, Pleasanton, CA). Additional filtering steps were applied to the barcodes identified as cells by the Cell Ranger program.
Assembly: GRCh38-2024-A
Supplementary files format and content: RDS files with filtered cell-gene matrices

source_name: Tracheobronchial epithelium

extract_protocol:
Tollip knockdown primary healthy human tracheobronchial epithelial cells were generated using the CRISPR/Cas9 method. The cells were seeded into collagen-coated Transwell inserts in PneumaCult-ALI Medium (STEMCELL Technologies, Vancouver, BC, Canada) and grown at the air-liquid interface for 21 days to induce mucociliary function.
Viable single-cell suspensions were loaded into the Chromium Controller (10x Genomics, Pleasanton, CA) to generate gel beads-in-emulsion (GEMs), each containing a single cell and barcoded oligonucleotides. The GEMs were then subjected to reverse transcription (GEM-RT) in the SimpliAmp 96-well Thermal Cycler (Thermo Fisher Scientific, Wilmington, DE). After reverse transcription, the complementary cDNA was amplified and cleaned using Silane DynaBeads (10x Genomics, Pleasanton, CA) and the SPRIselect Reagent kit (Beckman Coulter, Indianapolis, IN). The amplified full-length cDNAs from polyadenylated mRNA were then used to generate 3ʹ Gene Expression libraries using the Chromium Next GEM 3’ Single Cell Reagent kits v3.1, following the manufacturer’s instructions (10x Genomics, Pleasanton, CA).

value: Tracheobronchial epithelium

value: Tollip knockdown + IL-13 treatment


title: HeLa_P65_GAPDH_Rep3_mDBF

value: HeLa


title: INPUT for HA ChIP-seq at 32h


title: Cell line, Menuetto, Mouse 1147

first: John

last: La Marca

description:
Library name: InVivo Menuetto Sample 26
mouse1147_cell

data_processing:
Reads were mapped to sgRNA library files using MAGeCK v0.5.9
Supplementary files format and content: Processed data files for each screen contain raw sgRNA counts for each sample
Library strategy: CRISPR Screen

source_name: Lymphoma cell line

extract_protocol:
DNA was extracted using the DNeasy cell and tissue kit (QIAGEN) or Puregene kit (QIAGEN) according to the manufacturer's instructions.
Libraries were prepared and sequenced on the Illumina NextSeq 2000 using NextSeq 2000 P4 XLEAP-SBS Reagents, or on the Illumina MiSeq using a MiSeq Reagent Kit according to the manufacturer's instructions.

value: Lymphoma cell line

value: Lymphoma

value: In vivo

value: Menuetto


title: Tollip knockdown sample

value: Tollip knockdown


title: IL-13 treatment sample

value: IL-13 treatment


title: INPUT for HA ChIP-seq at 20h


title: Cell line, Menuetto, Mouse 1146

description:
Library name: InVivo Menuetto Sample 25
mouse1146_cell


title: Cell line, Menuetto, Mouse 1141

description:
Library name: InVivo Menuetto Sample 22
mouse1141_cell


title: INPUT for HA ChIP-seq at 12h


title: Cell line, Menuetto, Mouse 1142

description:
Library name: InVivo Menuetto Sample 23
mouse1142_cell


title: INPUT for HA ChIP-seq at 24h


title: Cell line, Menuetto, Mouse 1130

description:
Library name: InVivo Menuetto Sample 20
mouse1130_cell


title: HeLa_P65_GAPDH_Rep4_pDBF

value: plus DBF


title: HA-EZH1 ChIP-seq at 32h, biological replicate 3


title: HeLa_P65_MALAT1_Rep1_mDBF

value: minus DBF


title: HeLa_P65_GAPDH_Rep1_pDBF


title: HeLa_P65_GAPDH_Rep1_mDBF


title: HeLa_P65_15min_Rep3_pDBF


title: Cell line, Menuetto, Mouse 1131

description:
Library name: InVivo Menuetto Sample 21
mouse1131_cell


title: Control sample

value: Control


title: HeLa_P65_GAPDH_Rep2_pDBF


title: INPUT for HA ChIP-seq at 16h


title: Tumour, Menuetto, Mouse1151

description:
Library name: InVivo Menuetto Sample 17
mouse1151_tumour

source_name: spleen

value: spleen


title: Cell line, Menuetto, Mouse 1145

description:
Library name: InVivo Menuetto Sample 24
mouse1145_cell


title: HA-EZH1 ChIP-seq at 32h, biological replicate 2


title: HeLa_P65_GAPDH_Rep2_mDBF


title: Tumour, Menuetto, Mouse1150

description:
Library name: InVivo Menuetto Sample 16
mouse1150_tumour


title: HeLa_P65_15min_Rep3_mDBF


title: Tumour, Menuetto, Mouse1147

description:
Library name: InVivo Menuetto Sample 14
mouse1147_tumour


title: HeLa_P65_15min_Rep2_pDBF


title: Cell line, Menuetto, Mouse 1128

description:
Library name: InVivo Menuetto Sample 19
mouse1128_cell


title: HA-EZH1 ChIP-seq at 32h, biological replicate 1


title: Tumour, Menuetto, Mouse1146

description:
Library name: InVivo Menuetto Sample 13
mouse1146_tumour


title: HA-EZH1 ChIP-seq at 28h, biological replicate 3


title: Tumour, Menuetto, Mouse1144

description:
Library name: InVivo Menuetto Sample 11
mouse1144_tumour


title: Tumour, Menuetto, Mouse1148

description:
Library name: InVivo Menuetto Sample 15
mouse1148_tumour


title: HA-EZH1 ChIP-seq at 28h, biological replicate 2


title: HeLa_P65_15min_Rep1_pDBF


title: HeLa_P65_15min_Rep2_mDBF


title: Tumour, Menuetto, Mouse1141

description:
Library name: InVivo Menuetto Sample 8
mouse1141_tumour


title: HA-EZH1 ChIP-seq at 28h, biological replicate 1


title: Tumour, Menuetto, Mouse1142

description:
Library name: InVivo Menuetto Sample 9
mouse1142_tumour


title: Tumour, Menuetto, Mouse1145

description:
Library name: InVivo Menuetto Sample 12
mouse1145_tumour


title: HA-EZH1 ChIP-seq at 24h, biological replicate 3


title: Tumour, Menuetto, Mouse1131

description:
Library name: InVivo Menuetto Sample 7
mouse1131_tumour


title: Cell line, Menuetto, Mouse 1126

description:
Library name: InVivo Menuetto Sample 18
mouse1126_cell


title: Tumour, Menuetto, Mouse1143

description:
Library name: InVivo Menuetto Sample 10
mouse1143_tumour


title: Tumour, Menuetto, Mouse1128

description:
Library name: InVivo Menuetto Sample 5
mouse1128_tumour


title: HeLa_P65_10uM_Rep3

value: 10uM DBF


title: HeLa_P65_15min_Rep1_mDBF


title: HeLa_P65_10uM_Rep2


title: HA-EZH1 ChIP-seq at 24h, biological replicate 2


title: Tumour, Menuetto, Mouse1127

description:
Library name: InVivo Menuetto Sample 4
mouse1127_tumour


title: Tumour, Menuetto, Mouse1126

description:
Library name: InVivo Menuetto Sample 3
mouse1126_tumour


title: HA-EZH1 ChIP-seq at 24h, biological replicate 1


title: HeLa_P65_10uM_Rep1


title: Tumour, Menuetto, Mouse1125

description:
Library name: InVivo Menuetto Sample 2
mouse1125_tumour


title: Tumour, Menuetto, Mouse1124

description:
Library name: InVivo Menuetto Sample 1
mouse1124_tumour


title: HA-EZH1 ChIP-seq at 20h, biological replicate 3


title: A549,sgUHRF1-2,WGBS,rep2

city: Beijing

first: Zhou

last: Xindi

state: Beijing

address: 30 Shuangqing Road

department: School of Medicine

institute: Tsinghua University

description: UHRF1-2 KO

data_processing:
Illumina HiSeq 2000 reads were trimmed and clipped for quality control.
Reads were mapped with Homo_sapiens.GRCh38 to the nuclear genome, allowing for 1 mismatch and retaining only uniquely mapping reads.
Identical reads (potential PCR or optical duplicates) were flattened to 1 read.
Assembly: Homo_sapiens.GRCh38
Supplementary files format and content: bedGraph

growth_protocol: A549 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
genomic DNA isolated  and bisulfite treated
The genomic DNAs of A549 control and UHRF1 KO tumor cells were isolated using the NucleoSpin Blood Mini kit for DNA from cells and tissue. The EZ DNA Methylation-GoldTM Kit  were used for DNA bisulfite conversion of genomic DNA (400ng) according to the manufacturers’ instructions. The DNA bisulfite converted DNA were then used for WGBS and focused bisulfite sequencing.

treatment_protocol: UHRF1 sgRNA was cloned in to lentiCRISPRv2-hygro and transfection with lentivirus then selected with hygromycin.

value: tumor cell

value: UHRF1 KO


title: A549,sgUHRF1-1,WGBS,rep1

description: UHRF1-1 KO


title: HA-EZH1 ChIP-seq at 20h, biological replicate 2

value: skeletal muscle