title: Head Kidney_MPLE.3

city: Santiago

first: Felipe

middle: E.

last: Reyes-López

state: Santiago

address: Av. Libertador Bernado O'Higgins 3363

country: Chile

institute: Universidad de Santiago de Chile

description:
Gene expression for head kidney of Atlantic salmon fed 0.1% MPLE diet pool 3
MPLE_head kidney_3

hyb_protocol: The hybridization protocol was carried out according to Agilent's instructions. Briefly, 1.65 μg of Cy3-labeled cRNA (specific activity >6.0 pmol Cy3/mg cRNA) was fragmented at 60°C for 30 min in a total reaction volume of 55 µl containing 25X Agilent fragmentation buffer and 10X Agilent blocking agent. On completion of the fragmentation reaction, 55 µl of 2X GEx hybridization buffer was added to the fragmentation mixture and hybridized to the custom-commercial Salmo salar oligonucleotide microarray platform (AMADID 084881; Agilent Technologies; USA) at 65°C and 10 rpm for 17 hours in a rotating hybridization oven.

scan_protocol: After hybridization, microarrays were washed 1 min at room temperature (RT) with GEWash Buffer 1 (Agilent), 1 min with GE Wash buffer 2 (Agilent) pre-incubated at 37°C, 45 s at RT with Acetonitrile (Sigma, St Louis, MO, USA), and 30 s at RT with stabilization and drying solution (Agilent). Slides were scanned immediately afterwashing on the Agilent DNA Microarray Scanner (G2505B) using one color scan setting for 4x44k array slides (Scan Area: 61 x21.6 mm; Scan resolution: 5 µm; Dye channel set to green; Green PMT: 100%). Spot intensities and other quality control features were extracted with Feature Extraction software version 10.4.0.0 (Agilent).

data_processing: Nofima's bioinformatic package STARS was used for data processing and mining. After filtration of low quality spots, Lowess normalization of log2-expression ratios (ER) was performed. The differentially expressed genes were selected by difference between the control and Aquolive-supplemented diet based on an unpaired t-test statistical analysis and following the criteria: p < 0.05 and log2-ER >|0.8|.

organism: Salmo salar

source_name: MPLE_head kidney

label_protocol: One-color microarray was carried out according to manufacturer’s protocols. Briefly, 200 ng of total RNA was reversed transcribed along with spike-in (Agilent One-Color RNA Spike-In kit, Agilent Technologies, USA). Then, the solution was used as template for Cyanine-3 (Cy3) labeled cRNA synthesis and amplification with the Low Input Quick Amp Labelling kit (Agilent).  Samples of cRNA were purified using the RNeasy micro kit (Qiagen). Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: At the end of the nutritional assay, total RNA from HK of individual fish (n = 18 fish per dietary treatment) was extracted using TRI reagent (Sigma-Aldrich, Sant Louis, MO, USA), according to manufacturer’s instructions. Total RNA concentration and purity were quantified using a Nanodrop-2000® spectrophotometer (Thermo Scientific, USA) and stored at -80 °C for further analysis. Samples were diluted to 133.33 ng/µL concentration and checked for integrity using an Agilent 2100 Bioanalyzer (Agilent Technologies, Spain). All the samples used in this study were selected by the criteria of a RNA Integrity Number (RIN) value > 8.5.

treatment_protocol:
[test animals]  A total of 1.500 unvaccinated Atlantic salmon parrs (body weight, BW = 55.0 ± 0.1 g; mean ± standard deviation) were obtained from a commercial fish farm (SARL SALMO, Gonneville-Le Thiel, France) and transported by road to IRTA-Sant Carles de la Ràpita research facilities (Sant Carles de la Ràpita, Spain).
All animal experimental procedures were complied with the Guiding Principles for Biomedical Research Involving Animals (EU2010/63), the guidelines of the Spanish laws (law 32/2007 and RD 1201/2015), and authorized by the Ethical Committee of the Institute for Research and Technology in Food and Agriculture (IRTA, Spain) for the use of laboratory animals (FUE-2020-01314717). After transport, fish received three treatments with hydrogen peroxide and two treatments with formaldehyde (150 ppm, during one hour each) to treat injuries and avoid the presence of any parasite. After the on-growing period of 133 days, 696 fish (BW = 55.0 ± 0.1 g) were randomly distributed in eight aerated 450 L square-shaped tanks with smoothed corners, using an IRTAmar® recirculation system (5-10 % water replacement per day) under natural photoperiod. Water temperature (12.2 ± 1.0 °C), oxygen (9.4 ± 0.8 mg/L) and pH (7.4 ± 0.3) were daily controlled, whereas salinity (35‰) as well as ammonia (0.13 ± 0.1 mg NH4+ L−1) and nitrite (0.18 ± 0.1 mg NO2- L−1) levels were weekly monitored. The nutritional assay was carried out in six replicate tanks with an initial density of 2 kg/m3 (58 fish per tank). Fish were fed both diets two times per day at the daily rate of 3.0% of the stocked biomass, which approached apparent satiation.  At day 133 of feeding, three fish were randomly selected from each tank (n total= 18 fish per dietary treatment), euthanized with anaesthetic (MS-222, Sigma-Aldrich) and a section from the head kidney was sampled and stored in RNAlater™, incubated overnight at 4 °C, and stored at -80 °C until analysed.

value: Head kidney

value: juveniles, 252 g

value: MPLE diet


title: Mel202_H3K4me3

status: Public on Sep 20 2024

type: SRA

city: Miami

first: Stefan

last: Kurtenbach

address: 1501 NW 10th Avenue

country: USA

institute: University of Miami

library_source: genomic

data_processing:
FASTQ files were trimmed with Trim Galore!
Reads were aligned with Bowtie2
Peak files and coverage tracks were computed by MACS2
Assembly: hg38
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

molecule: genomic DNA

organism: Homo sapiens

source_name: uveal melanoma

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin was sonicated using a E220 focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using the NEB Next Ultra 2 library prep kit according to the manufacturers reccomendations.

tag: tissue

value: uveal melanoma

tag: cell line

tag: cell type

value: cancer

tag: chip antibody


title: Head Kidney_MPLE.2

type: RNA

description:
Gene expression for head kidney of Atlantic salmon fed 0.1% MPLE diet pool 2
MPLE_head kidney_2

molecule: total RNA

tag: age

tag: treatment


title: Head Kidney_control.3

description:
Gene expression for control group pool 3
Control_head kidney_3

source_name: Control_head kidney

value: control


title: Daunorubicin.Brain.JS8

city: Kuopio

first: Merja

last: Heinäniemi

address: Yliopistonranta 1E

department: School of Medicine, Institute of Biomedicine

country: Finland

institute: University of Eastern Finland

description:
scRNAseq in daunorubicin, Chromium Single Cell 3ʹ Reagent Kits v3
10x Genomics

library_source: transcriptomic single cell

data_processing:
Data was aligned with Cell Ranger 3.1.0 version to human+mouse combined reference (hg19 & mm10) from 10x Genomics with default parameters.
Cells were filtered with Cell Ranger 3.1.0 following alignment.
The human cells were left out by filtering cells which cellranger characterized as human or doublet cells or had more than 500 counts assigned to human genes.
The human genes were filtered out from the count matrix.
Assembly: mm10
Supplementary files format and content: barcode annotation: filtered barcode annotation; feature annotation: filtered feature list; count matrix: filtered UMI count matrix

molecule: polyA RNA

organism: Mus musculus

source_name: Brain

extract_protocol:
Subsequently 10 million cells were methanol fixated according to 10X Genomics Methanol Fixation of Cells for Single Cell RNA Sequencing protocol User guide CG000136 Rev E, using a mix of two RNAse inhibitors (RNase Inhibitor, Thermo Fisher, Carlsbad, CA, USA and RNasin® Plus RNase Inhibitor, Promega, Madison, WI, USA). Samples were stored < 6 weeks before proceeding with Chromium run.
Cells were rehydrated following the MetOH fixation protocol and processed for loading following the Chromium Single Cell 3´Reagent Kits v3 User guide CG000183 Rev C. Mouse cells were prepared into pools together with human cells (not part of this study) and mouse cell singlets separated in data analysis step. Using 10X GemCode Technology, the poly-A transcripts are barcoded with an Illumina R1 sequence, a 16 bp 10X barcode and a 10 bp Unique Molecular Identifier (UMI). 13 cycles of PCR were used to amplify the cDNA. Sequencing was performed at Novogene UK sequencing core facility aiming at 50 000 reads per cell depth.

treatment_protocol: vehicle (DMSO), chemotherapy (prednisolone, daunorubicin)

tag: genotype

value: Brain

tag: time

value: leukemia development

tag: construct/treatment

value: daunorubicin


title: Head Kidney_control.2

description:
Gene expression for control group pool 2
Control_head kidney_2


title: MVIR1-HS236-D7ETA1-MNGS1

city: San Francisco

first: Charles

last: Langelier

state: CA

address: HSE 401, 513 Parnassus Ave

department: Medicine

institute: University of California San Francisco

library_source: transcriptomic

data_processing:
Alignment against human genome- kallisto
Differential expression with R package Limma
Assembly: HG-38, ENSEMBL v. 99
Supplementary files format and content: .csv file with genecounts

source_name: tracheal aspirate

growth_protocol: Clinical tracheal aspirate specimens

extract_protocol:
Zymo DNA/RNA magbead
NEBnext with Qiagen Fastselect rRNA depletion
Random hexamer RNAseq

treatment_protocol: DNAse

tag: gender

value: Male

tag: race

value: American Indian/Alaska Native

tag: ethnicity

value: Hispanic


title: Head Kidney_MPLE.1

description:
Gene expression for head kidney of Atlantic salmon fed 0.1% MPLE diet pool 1
MPLE_head kidney_1


title: MVIR1-HS238-DN1ETA1-MNGS1

value: Other/Multiple


title: MVIR1-HS231-D4ETA1-MNGS1


title: Daunorubicin.Lymphnode.JS6

source_name: Lymph node

value: Lymph node


title: Mel202_H3K27AC


title: 921_H3K4me3


title: Mel202_RNApol

value: RNApol


title: 921_RNApol


title: Mel202_Input


title: CN_CT rep8

city: yunnan

first: wang

middle: yi

last: chao

state: postgraduation

address: Jingming South Road, Chenggong District, Kunming City, Yunnan Province

country: China

institute: Kunming University of Science and Technology

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v7.0.1 (https://www.10xgenomics.com/cn/support/software/cell-ranger)
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

organism: Macaca fascicularis

source_name: Caudal nucleus

extract_protocol:
The Cell nucleus in the Macaca_mulatta brain tissues were isolated according to manufacturer’s protocol(Nuclei PURE Prep,Sigma-Aldrich ).
The Cell nucleus were loaded onto the 10X Chromium Single Cell Platform (10X Genomics) at a concentration of 1,000 cells per μl (Single Cell 3′ library and Gel Bead Kit v.3) as described in the manufacturer’s protocol. Generation of gel beads in emulsion (GEMs), barcoding, GEM-RT clean-up, complementary DNA amplification and library construction were all performed as per the manufacturer’s protocol.Qubit

value: Caudal nucleus

value: brain

value: CT


title: CN_CT rep5


title: MVIR1-HS223-D3ETA1-MNGS1

value: Not Hispanic

value: No-BP


title: Daunorubicin.Spinalcord.JS7

source_name: Spinal cord

value: Spinal cord


title: Daunorubicin.BM.JS9

source_name: Bone marrow

value: Bone marrow


title: CN_CT rep7


title: CN_CT rep6


title: MVIR1-HS233-D3ETA1-MNGS1

value: Caucasian


title: Head Kidney_control.1

description:
Gene expression for control group pool 1
Control_head kidney_1

value: Head kidney

value: juveniles, 252 g

value: control


title: CN_CT rep4


title: PP3_3D_3

city: Bethesda

first: Howard

last: Yang

state: MD

address: 37 CONVENT DR, Room 5120

department: CCR

institute: NCI

data_processing:
Illumina software RTA 3.4.4 was used for basecalling.
Reads of the samples were trimmed for adapters and low-quality bases using Cutadapt before alignment with the reference genome (hg38) and the annotated transcripts using STAR and RSEM.
Assembly: hg38
Supplementary files format and content: *.txt: Tab-delimited text files including raw counts and RPKM values for each Sample.

source_name: cell line

growth_protocol: SW620 WT (sgNT) and PPP6C KO (sgPPP6C#2, sgPPP6C#3) were cultured in normal petri dish (2D culture) or U-bottom plates (3D culture) for 3 days with three independent replicates for each cell sample.

extract_protocol:
RNA was isolated from cultured 2D and 3D cells by RNeasy Plus Mini Kit (Qiagen).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: crispr guide

value: #3 sgRNA targeting PPP6C

tag: culture condition

value: U-bottom plates (3D culture)


title: Daunorubicin.Spleen.JS10

source_name: Spleen

value: Spleen

value: leukemia development

value: daunorubicin


title: MVIR1-HS204-D0ETA1-MNGS1

value: Female

value: Other/Multiple

value: Hispanic


title: CN_CT rep3

value: Caudal nucleus

value: brain

value: CT


title: MVIR1-HS196-D19ETA1-MNGS1


title: Prednisolone.Lymphnode.JS3

description:
scRNAseq in prednisolone, Chromium Single Cell 3ʹ Reagent Kits v3
10x Genomics

value: Lymph node

value: prednisolone


title: MVIR1-HS185-D1ETA1-MNGS1

value: No-BP


title: CN_CT rep2


title: PP3_3D_1


title: 921_H3K27AC

value: uveal melanoma

value: cancer


title: MVIR1-HS172-D8ETA1-MNGS1

value: Male


title: Prednisolone.Spinalcord.JS4

value: Spinal cord


title: PP2_3D_3

value: #2 sgRNA targeting PPP6C

value: U-bottom plates (3D culture)


title: Prednisolone.BM.JS1

value: Bone marrow

value: leukemia development


title: MVIR1-HS168-D0ETA1-MNGS1

value: Black

value: Not Hispanic


title: MVIR1-HS161-D10ETA1-MNGS1

value: Female

value: Other/Multiple

value: Hispanic


title: PP2_3D_1


title: Vehicle.Lymphnode.JS15

description:
scRNAseq in control, Chromium Single Cell 3ʹ Reagent Kits v3
10x Genomics

value: vehicle


title: CN_PD rep2

value: Caudal nucleus

value: brain

value: PD


title: PP2_3D_2


title: CN_PD rep4


title: Prednisolone.Brain.JS5

value: Brain

value: prednisolone


title: Prednisolone.Spleen.JS2

value: Spleen


title: CN_PD rep1


title: MVIR1-HS158-D6ETA1-MNGS1

value: Male

value: Caucasian

value: No-BP


title: NT_3D_3

value: non-targeting control sgRNA

value: U-bottom plates (3D culture)


title: CN_PD rep3


title: NT_3D_2


title: Vehicle.BM.JS14

value: Bone marrow

value: leukemia development


title: PP3_3D_2

value: #3 sgRNA targeting PPP6C


title: PUT_CT rep8

source_name: Putamen

value: Putamen

value: CT


title: NT_3D_1


title: Vehicle.Spinalcord.JS13

value: Spinal cord

value: vehicle


title: MVIR1-HS154-D15ETA1-MNGS1

value: Other/Multiple

value: Hispanic


title: CN_CT rep1

value: Caudal nucleus

value: brain


title: PUT_CT rep7


title: MVIR1-HS145-D1ETA1-MNGS1


title: PP3_2D_3

value: normal petri dish (2D culture)


title: PUT_CT rep6


title: MVIR1-HS115-D16ETA1-MNGS1

value: Male


title: PP3_2D_2


title: PUT_CT rep5


title: Vehicle.Spleen.JS12

value: Spleen


title: SPLN_CNT_3

description:
replicate 3
salmon.merged.gene_counts_scaled.tsv

data_processing:
Sequencing data was processed using nf-core/rna-seq pipeline (version 3.8) (45). Briefly, read quality was assessed by FastQC and MultiQC. Reads were first trimmed to remove adapter sequences and poor-quality reads were removed with TrimGalore.
Filtered reads were then aligned to the Mouse genome (mm10) using STAR and read counts per gene were quantified using Salmon and post-processed with SAMtools and picard MarkDuplicates.
The differential gene expression analysis was performed with the limma voom pipeline (v. 3.16). Genes were filtered by using edgeR package filterByExpr function removing low count genes across all the libraries and keeping as many genes as possible with significant counts. Filtered counts were transformed to log2-counts per million (log-CPM) with voom function in limma package. Differential gene expression analysis was performed by using limma package for linear model fitting (lmFit), making comparisons of interest (contrast.fit), and computing standard errors and t-statistics (eBayes) (46). The significance threshold was set to adjusted p-value < 0.05.
Assembly: mm10
Supplementary files format and content: bigWig RNA-seq signal files, separately for plus and minus strand
Supplementary files format and content: tab-delimited text file include scaled and bias corrected count matrix for each samples

extract_protocol:
RNeasy Plus Micro Kit (Qiagen) according to the manufacturer’s instructions
Truseq stranded mRNA kit (Illumina), Ligation with Ribo-Zero Plus kit.

treatment_protocol: vehicle (DMSO)

value: ALL leukemia cell


title: MVIR1-HS97-D8ETA1-MNGS1

value: No-BP


title: PP3_2D_1


title: MVIR1-HS156-D0ETA1-MNGS1


title: PUT_CT rep4


title: PUT_CT rep3


title: PUT_CT rep2


title: LN_CNT_3

source_name: Lymph nodes

value: Lymph nodes


title: MVIR1-HS94-D20ETA1-MNGS1

value: Female


title: SPLN_CNT_2

description:
replicate 2
salmon.merged.gene_counts_scaled.tsv


title: PP2_2D_1

value: #2 sgRNA targeting PPP6C


title: PUT_CT rep1


title: MVIR1-HS78-D4ETA1-MNGS1


title: MVIR1-HS72-D14ETA1-MNGS1

value: Not Hispanic


title: LN_CNT_1

description:
replicate 1
salmon.merged.gene_counts_scaled.tsv


title: LN_CNT_2


title: Vehicle.Brain.JS11

value: Brain

value: leukemia development


title: PUT_PD rep4

value: Putamen

value: PD


title: NT_2D_2

value: non-targeting control sgRNA


title: MVIR1-HS114-D3ETA1-MNGS1

value: Black


title: MVIR1-HS55-D9ETA1-MNGS1

value: Other/Multiple

value: Hispanic


title: PP2_2D_3

value: normal petri dish (2D culture)


title: SpinalCord_CNT_3

source_name: Spinal cord/brain

value: Spinal cord/brain

value: vehicle


title: PUT_PD rep3

value: brain


title: MVIR1-HS51-D1ETA1-MNGS1

value: Male


title: PUT_PD rep2


title: PP2_2D_2


title: SPLN_CNT_1

value: Spleen

value: ALL leukemia cell


title: SpinalCord_CNT_2


title: MVIR1-HS47-D19ETA1-MNGS1

value: Female

value: Caucasian


title: SpinalCord_CNT_1


title: MVIR1-HS2-D2ETA1-MNGS1

value: Not Hispanic

value: No-BP


title: PUT_PD rep1

value: Putamen


title: MVIR1-HS1-D3ETA1-MNGS1


title: SN_CT rep4

source_name: Substantia nigra

value: Substantia nigra

value: CT


title: NT_2D_3

value: non-targeting control sgRNA


title: BMC_CNT_3

source_name: Bone Marrow

value: Bone Marrow


title: SN_CT rep3


title: 3d_s1

city: guangzhou

first: ming

last: zhou

address: jinsui road 7

institute: Sun Yat-sen University,

data_processing:
Illumina library preparation was performed using the Chromium Single Cell 3′ Reagent Kits User Guide (V3 Chemistry). After the cDNA cleanup step (Step 2.1), half of the purified cDNA was used for PacBio library preparation, and the rest was used for downstream Illumina library preparation. Illumina libraries were sequenced on a NextSeq 550 system (SY-415-1002, Illumina) by using NextSeq High Output Kits (150 cycles; 20024907, Illumina) with the following read protocol: read 1, 118 cycles; i7 index read, 8 cycles; read 2, 40 cycles.
Assembly: Ensembl Macaca_fascicularis_5.0.99
Supplementary files format and content: Read count matrices for each sample were generated by CellRanger counting.

source_name: cornea

extract_protocol:
The cells were filtered through a 30-µm cell strainer and were re-suspended in 60 µL PBS containing 0.04% BSA to achieve 1,000 cells µl-1 for capture on the 10× Genomics Chromium controller.
The dissociated single cells were processed on the GemCode Single Cell Platform per the manufacturer’s recommendations using the Chromium Single Cell 3′ GEM, Library, and Gel Bead Kit v3 (10× Genomics; PN-1000075) with a recovered quantity of ~2000 cells.

value: cornea

value: WT

value: 3-day healing stage


title: 1d_s2

value: 1-day healing stage


title: 1d_s1


title: BMC_CNT_2

value: vehicle


title: NT_2D_1

value: normal petri dish (2D culture)


title: SN_CT rep2

value: brain


title: BMC_CNT_1

value: ALL leukemia cell


title: Trametes versicolor colonised wood block single species control replicate 3

city: SWANSEA

first: Daniel

last: Eastwood

state: West Glamorgan

address: Wallace Building Science, Swansea University, Singleton Park Campus

department: Biosciences

country: United Kingdom

institute: Swansea University

data_processing:
The raw fastq files were trimmed to remove Illumina adapter sequences using Cutadapt version 1.2.1 (Martin, 2011). The option “-O 3” was set, so the 3' end of any reads which matched the adapter sequence over at least 3 bp was trimmed off.  The reads were further trimmed to remove low quality bases, using Sickle version 1.200 with a minimum window quality score of 20
R1/R2 read pairs were mapped to the reference sequences (T. versicolorv1 and H. sublateritium reference genomes available through the JGI mycocosm portal) using HISAT2 version 2.0.3beta
Differential transcripts between samples were calculated from reads alignment files using HTSeq count. All the differential gene expression analyses were performed in R environment using edgeR
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample

organism: Trametes versicolor

source_name: Trametes versicolor TvFPH

extract_protocol:
RNA was extracted using MoBIO Laboratories Inc Powersoil Total RNA Isolation Kit. 0.1 ng mRNA per sample was purified polyA separation using Dynabead kit (Ambion)
RNA libraries for RNA-seq were prepared using the SMARTer mRNA-Seq library prep kit following manufacturer's instructions

value: Beechwood block

value: Control


title: 0d_s2

value: uninjured


title: SN_CT rep1


title: Trametes versicolor colonised wood block single species control replicate 1


title: 3d_s2


title: SN_PD rep4

value: PD


title: Trametes versicolor colonised wood block single species control replicate 2


title: 0d_s1


title: Hypholoma fasciculare-Trametes vesicolor interaction wood block replicate 1

organism:
Trametes versicolor
Hypholoma fasciculare

source_name: Hypholoma fasciculare GTWV2 and Trametes versicolor TvFPH

value: Interspecoific interaction


title: smart-Seq3 transcriptomic data

city: New York

first: Benjamin

last: Fait

state: NY

address: 1230 York Ave

institute: The Rockefeller University

data_processing:
We used bcl2fast2 (version 2.20; RRID:SCR_015058) with no lane splitting to convert binary base-call files to fastq. zUMIs150 (version 2.9.7; RRID:SCR_016139) was used to process the remainder of the data. We used a barcode “whitelist” given to zUMIs to align only known barcodes. Barcodes were filtered to 3 bases under a phred score of 20 and UMIs to a score of 2 under 20. The hamming distance for binning of barcodes was set to 1, and only barcodes with > 1000 reads were processed. For alignment of reads and processing into error-corrected UMI counts, we created a genome index with STAR151 (version 2.7.9a; RRID:SCR_004463) using GENCODE’s M27 mouse assembly (https://www.gencodegenes.org/mouse/release_M27.html). Because data was from nuclei, counts from both intronic and exonic reads were used for analysis.
Assembly: mm39
Supplementary files format and content: RDS file

molecule: nuclear RNA

source_name: cervical spinal cord

extract_protocol:
To purify nuclei, we used a modified density gradient centrifugation protocol similar to those previously published.142–144 “Buffer A” consisted of OptiPrep™ 60% iodixanol (Sigma-Aldrich, D1556). “Buffer B” consisted of 900 mM KCl (Invitrogen, AM9640G), 30 mM MgCl2 (Invitrogen, AM9530G), 120 mM Tricine-KOH (pH = 7.8) (Thermo Scientific, 15426389) in UltraPure™ water (Invitrogen, 10977015). “Buffer C” consisted of 5 volumes of Buffer A, 1 volume of Buffer B, 0.5 mM spermidine (Thermo Scientific, A19096.03), 0.15 mM spermine (Sigma-Aldrich, S3256), 1 mM DTT (Thermo Scientific, R0861), and 20 units/mL SUPERase•In™ RNase inhibitor (Invitrogen, AM2694), and 1 tablet per 10 mL of  cOmplete™ EDTA-free Protease Inhibitor Cocktail (Roche, 11836170001). “Buffer D” consisted of 0.25 M sucrose (Thermo Scientific, AC419762500), 150 mM KCl (Invitrogen, AM9640G), 5 mM MgCl2 (Invitrogen, AM9530G), 20 mM Tricine-KOH (pH 7.8) (Thermo Scientific, 15426389), 0.5 mM spermidine (Thermo Scientific, A19096.03), 0.15 mM spermine (Sigma-Aldrich, S3256), 1 mM DTT (Thermo Scientific, R0861), 20 units/mL  SUPERase•In™ RNase inhibitor (Invitrogen, AM2694), and 40 units/mL RNAsin Plus RNase inhibitor (Promega, N2611). “Buffer E” consisted of 1.17 parts Buffer C to 1 part Buffer D. In each buffer, DTT, spermine, and spermidine were added immediately before commencing purification. Buffer E was also mixed immediately before purification.
Tissue pieces for each replicate were added to 4.5 mL of Buffer D in a dounce homogenizer (DWK Life Sciences, 357542) at 4° C, dounced 40 times on ice with the loose (0.089 - 0.14 mm clearance range), and then 40 times with the tight (0.025 - 0.076 mm clearance range) pestles, taking care not to cause bubbles. The result was placed in a 15 mL protein LoBind® conical tube (Eppendorf, 0030122216). The total liquid was brought to 5 mL, and 4.6 mL Buffer C was added. The mixture was inverted ten times. 2 mL of Buffer E was added to a 13.2 mL thin-wall clear centrifuge tube (Beckman Coulter Life Sciences, 344059), and the 9.6 mL of solution was carefully layered on top 1 mL at a time. The solution was spun at 10,000 rpm (max acceleration, level 7 deceleration, max 17,136 g, average 12,320 g, K-factor 2,089) at 4°C in a swinging bucket rotor (SW41) for 30 minutes in a Beckman Coulter XL-70 ultracentrifuge. The supernatant was emptied from the tube by inverting it and “flicking” the liquid out. The nuclei were resuspended in 1 mL of Buffer D with 1:10,000 DAPI and passed through a cell strainer (Corning Life Sciences, 352235) into a 1.5 mL protein LoBind® tube (Eppendorf, 022431064) before being quantified on a Countess II FL Cell Counter (Thermo Fisher Scientific).

value: cervical spinal cord


title: SN_PD rep3

value: Substantia nigra


title: Hypholoma fasciculare colonised wood block single species control replicate 3

organism: Hypholoma fasciculare

source_name: Hypholoma fasciculare GTWV2


title: Hypholoma fasciculare-Trametes vesicolor interaction wood block replicate 2


title: SN_PD rep2


title: Hypholoma fasciculare colonised wood block single species control replicate 2


title: S1pr2 f/f K14-Cre, skin, IMQ

city: La Jolla

first: Kana

last: Kuroki

address: 9500 Gilman Drive

department: Dermatology

institute: University of California San Diego

data_processing:
Raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were aligned to mm10 genome to gene expression count using Space Ranger's default settings.
Gene expression level of RefSeq coding genes were quantified using Space Ranger's default settings.
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scalefactors in jason format
Supplementary files format and content: tissue_hires_image.png.gz: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-res image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics

source_name: Skin

extract_protocol:
FFPE mouse skin samples were sectioned into 10 μm and deparaffinized.
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium CytAssist for FFPE Spatial Gene Expression 11mm Kit, Mouse, 2rxns.

value: Skin

value: S1pr2 f/f K14-Cre

value: IMQ


title: CS,root tip, replicate 1, scRNAseq

city: shanghai

first: yijing

last: zhang

address: 2005 Songhu Road

department: Biochemistry

institute: Fudan University

description: 10x Genomics

data_processing:
Firstly, we used cutadapt (v2.7) to remove 122bp and 59 bp from the R1 and R2 reads ends of raw scRNA-seq data according to the library structure of 10X Genomics. The TruSeq Read 1 was composed of 28bp Spatial Barcode and UMI, the TruSeq Read 2 was composed of 90 bp insert fragment. Secondly, the cleaned data were analyzed by Cell Ranger (v7.0.0) (https://support.10xgenomics.com/singlecell-gene-expression/software/pipelines/latest/what-is-cell-ranger). The reference genome (version 1.0) and GTF annotation files (version 1.1) of Triticum aestivum were downloaded from the International Wheat Genome Sequencing Consortium (IWGSC). Lastly, we performed downstream analysis with R package Seurat (v4.0), including quality control (filtering out low-quality cells and genes, evaluating reproducibility between replicates), data normalization (“Normalize” function with LogNormalize), scaling the data (“ScaleData”) and clustering cells (“FindClusters”).
Assembly: IWGSC RefSeq v1.0
Supplementary files format and content: Tab-separated values files and matrix files

organism: Triticum aestivum

source_name: 0.5cm root tip

extract_protocol:
The root tips (0.5 cm) of the seedlings were harvested for scRNA-seq experiment. The root tips were harvested and digested for 2 h at room temperature in digestion buffer (1.5% cellulase R10, 1.5% macerozyme R10, 0.3 M mannitol, 3 mM β-mercaptoethanol, 10 mM CaCl2, and 0.3% BSA).
Single-cell suspensions were loaded onto 10× GENOMICS Chromium to capture approximately 6000 single cells following the manufacturer’s instructions for the 10× Genomics Chromium Single-Cell 3′ kit (V3). cDNA amplification, library construction, and sequencing on the Illumina NovaSeq 6000 platform (paired-end multiplexing run, 150 bp) were performed by LC-Bio Technology (HangZhou, China)

value: root tip cells

value: 0.5cm root tip


title: SN_PD rep1


title: CS,root tip, replicate 2, scRNAseq

description: 10x Genomics


title: Patient 7, Non-FSGS

status: Public on Sep 19 2024

city: Chicago

first: Eunsil

last: Hahm

address: 735 W Harrison St. , 753

institute: Rush University Medical Center

data_processing:
Bioinformatics analysis was performed using Cytonaut™ cloud software v1.4 (www.cytonaut-scipio.bio, Scipio Bioscience) as follows: 1) pre-processing step applied to each pair of FASTQ files using the reference genome sequences and annotations based on Ensemble  and the knee point method for cell detection double-checked by manual inspection 2) post-processing step applied to the count matrixes, based on Scanpy with these main parameters: ≥ 10 cells per gene, ≥175 genes per cell, ≤20% mitochondrial transcripts per cell, top 2750 HVG, UMAP embedding, Louvain clustering with resolution 1.5, DGE with Wilcoxon rank-sum test.
A manual cluster annotation was performed with Cytonaut™ Rover based on the visual exploration of gene expression for the biomarkers as previously published (Baron et al., 2016). DEG between clusters were used with published canonical markers to manually identify clusters. Further DGE with Wilcoxon rank-sum test was performed on specific clusters (all monocytic cells for example) to identify DEGs for Patient vs Control.
Assembly: GRCh38
Supplementary files format and content: For each sample, output files (barcodes.tsv, features.tsv, matrix.mtx)

extract_protocol:
Single-cell suspensions, with 15,000 input cells per sample at the coupling step, were prepared using Scipio Bioscience’s reversible hydrogel technology RevGel-seq™ with the instrument-free 3’ scRNA-seq benchtop kit Asteria™, allowing for coupling of solid polymer-barcoded beads (NxSeq Single-cell RNA-seq Beads, LGC Biosearch Technologies) and cells in a homogenous phase (Komatsu et al., 2023). Cell capture was followed by cell lysis, mRNA capture on barcoded beads, reverse transcription, PCR amplification and cDNA sequencing.
Library was constructed by NEBNext Ultra II FS DNA Library Prep Kit for Illumina (New England Biolabs) with some adaptations according to the instruction of Asteria kit and were then sequenced on the Illumina NovaSeq x 25B sequencer with a medium of 60,000 reads per sample.

value: Bone marrow

value: Mononuclear cells


title: S1pr2 f/f, skin, IMQ

value: S1pr2 f/f


title: Patient 10, Non-FSGS


title: Hypholoma fasciculare-Trametes vesicolor interaction wood block replicate 3


title: Patient 8, 2° FSGS


title: Patient 5, 2° FSGS


title: Patient 4, 2° FSGS


title: Patient 6, 1° FSGS


title: Patient 3, 2° FSGS


title: Control 1, Healthy


title: Patient 2, 1° FSGS


title: H4K20me3.12h.rep3

city: Philadelphia

first: Gregory

last: Donahue

state: PA

address: 3400 Civic Center Blvd, Bldg 421

department: Cell & Developmental Biology

institute: The University of Pennsylvania

data_processing:
Index creation: mouse mm10 and drosophila dm6 assemblies were merged to create a hybrid genome, and a bowtie2 index for the hybrid genome was generated using bowtie2-build -f.
Alignment: FASTQs were aligned to the hybrid genome with bowtie2 v2.3.4.1 -p 16 --local -X 1000.
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3 -F 4 -F 8
Replicate merge: bam files of the three biological replicates of each sample were merged using samtools merge.
Scalar calculation: the percentage of drosophila reads in each ChIP sample was used to calculate the scalars for library size adjustment. RPM was used for input samples.
Track creation: bigWig files were created using deeptools bamCompare (log2(ChIP/Input) and scaled based on the ratio of the spike-in reads).
Domain calling: merged BAM files were converted into bed files using bedtools bamtoBed and then processed with RSEG v0.4.8 rseg-diff -i 20 -v -mode 2 -d deadzones-k36-mm10.bed with deadzones downloaded from the RSEG website and lifted from mm9 to mm10 over using UCSC Genome Browser's liftOver tool.
Assembly: GRCm38 / mm10
Supplementary files format and content: BigWig files reflect unpooled replicates with input subtraction and spike-in adjustment.
Supplementary files format and content: The BED file H4K20me3-RSEG.bed has RSEG domains called from the 0hr H4K20me3 chIP-seq data.

source_name: dTKO

growth_protocol: Mouse ESCs are maintained in LIF/FCS medium (DMEM-high glucose, 15% FBS, 2 mM GlutaMAX, 1 mM sodium pyruvate, 0.1 mM MEM NEAA, 0.1 mM 2-mercaptoethanol, 1,000 IU ESGRO) on 0.1% gelatin treated plates.

extract_protocol:
Briefly, cells were crosslinked with 1% formaldehyde at room temperature for 10 mins, and quenched with 0.125 mM Glycine at room temperature for 5 minutes. The cells were then washed 3 times with ice cold DPBS and incubated with seven ml swelling buffer (25mM HEPES-KCl, pH7.2, 1.5 mM MgCl2, 20mM KCl, 0.1% NP-40) per 15cm dish incubated for 10 minutes at 4 °C. The cells were scrapped off the plates, collected and pelleted in 15 ml falcon tubes and immediately snap frozen in the liquid nitrogen, and stored in -80 °C freezer. On the day of sonication, the crosslinked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM DTT, and 1x complete protease inhibitors cocktail) and lysis buffer 2 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1x complete protease inhibitors cocktail) for 5 minutes each at 4 °C. The nuclei were then resuspended in the lysis buffers 3 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x complete protease inhibitors cocktail) for 10 minutes on ice, followed by centrifugation at 1350g for 5 minutes. The nuclei pellets were then resuspended in lysis buffer 3 and sonicated with Covaris with (Incident peak power: 140; Duty Cycle: 5; Burst/Cycle: 200) for 15 minutes. The sonicated chromatin was centrifuging at 20,000g for 20 minutes and the soluble chromatin were collected, and 20 μl chromatin was de-crosslinked in 200 μl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65 °C over night and the rest of the chromatin was aliquoted, snap frozen in liquid nitrogen and stored in -80 °C freezer. The de-crosslinked chromatin was treated with proteinase K and RNase, followed by ethanol precipitation. For H4K20me3 ChIP-seq, 24 μg of chromatin was combined with 1.5 μg of Drosophila spike-in chromatin, and incubated with 20 μl of Protein A/G dynabeads, 3 μg of H4K20me3 (Millipore, 07-463) and 0.5 μg of drosophila spike-in antibody on a rotating wheel at 4 °C overnight.. The chromatin-antibody-dynabeads slurry was then washed 5 times with The RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x complete protease inhibitors cocktail) and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The chromatin was eluted with elution buffer by incubating at 65 C for 20 minutes and de-crosslinked at 65 °C over night, followed by proteinase and RNase treatment and ethanol precipitation. The DNA concentration was quantified with Qubit HS DNA kit and stored in -20 °C.
ChIP-seq DNA libraries was prepared with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645) following the manufacturer’s instructions. Briefly, 10 ng of ChIP DNA was used for each library and amplified with 11 PCR cycles and the library DNA was purified with Ampure XP beads and the distribution of the DNA fragments of the libraries was analyzed using High Sensitivity DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

treatment_protocol: For the degradation timecourse, the auxin and dTAG13 were added to the medium at the final concentration of 100 μg/ml and 0.5 μM, respectively.

value: dTKO

value: ES cells

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl

value: + auxin + dTAG13

tag: antibody

value: Millipore, 07-463

tag: time (hours_post_treatment)

tag: replicate


title: H4K20me3.48h.rep2


title: H4K20me3.0h.rep3


title: H4K20me3.24h.rep3


title: Control 2, Healthy

tag: tissue


title: H4K20me3.12h.rep1

tag: cell line


title: H4K20me3.0h.rep2

tag: cell type


title: Hypholoma fasciculare colonised wood block single species control replicate 1

value: Beechwood block

value: Control


title: H4K20me3.24h.rep2


title: H4K20me3.0h.rep1


title: H4K20me3.48h.rep1


title: H4K20me3.24h.rep1


title: 4OHT + siSMARCA4_4; 3V

city: London

first: LMS

last: Bioinformatics Core

address: Hammersmith Hospital Campus, Du Cane Road

department: Bioinformatics Core

institute: MRC London Institute of Medical Sciences

data_processing:
Illumina reads were adapter and quality trimmed with cutadapt v4.7 using the following settings: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT -m 31 --max-n 0 --nextseq-trim 20
Trimmed reads were aligned to the GRCh38 reference (Ensembl release 110) with HISAT2 v2.2.1 using the following settings: --score-min L,0,-0.66 --pen-noncansplice 20 --no-discordant --no-mixed --no-unal
Gene-leveland TE-level counts were calculated by expectation maximisation with TElocal v1.1.2 (https://github.com/mhammell-laboratory/TElocal) using Ensembl GRCh38 release 100 transcripts, a prepared TE index, and the following settings: --stranded reverse --mode multi --sortByPos
The TElocal index was prepared using the TElocal_Indexer program using TE annotations generated by RepeatMasker v4.15 (settings: -s -norna -spec Homo sapiens) configured with HMMER v3.3.2 against the Dfam 3.7 HMM database.
Assembly: GRCh38
Supplementary files format and content: comma-delimited text file include raw counts for each Sample.

source_name: Lung

growth_protocol: Inducible IMR90 RASG12V (IMR90 ER:RAS) cells were generated through the retroviral infection of the pLNC ER:RAS-neo retroviral vector. The construct comprises an ER:RAS fusion protein inducible with 4-hydroxytamoxifen (4OHT).

extract_protocol:
RNA was extracted following the Qiagen Rneasy Mini Kit
NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module

treatment_protocol: IMR90 ER:RAS cells were reverse transfected with siRNAs (non-targeting or targeting specific genes) to induce knockdown of target genes.

value: Lung

value: IMR90 ER:RAS

value: Fibroblast


title: H4K20me3.48h.rep3


title: 4OHT + siSMARCA4_4; 2VM


title: 4OHT + siSMARCA4_2; 3VM


title: 4OHT + siSMARCA4_4; 2V


title: 4OHT Control + siNT 4; 3VM


title: 4OHT + siSMARCA4_2; 1VM


title: Patient 1, 1° FSGS

source_name: Bone marrow


title: 4OHT Control + siNT 2; 3VM


title: 4OHT Control + siNT 2; 1VM


title: 4OHT Control + siNT 2; 2VM


title: 4OHT Control + siNT 4; 1VM


title: DMSO Control + siNT 4; 3VM


title: 4OHT Control + siNT 4; 2VM


title: H4K20me3.12h.rep2


title: DMSO Control + siNT 4; 2VM


title: DMSO Control + siNT 2; 2VM


title: DMSO Control + siNT 2; 1V


title: DMSO Control + siNT 2; 2V


title: BJ STING KO plus cGAMP 12 hours brep3

city: Pittsburgh

first: Jay Xiaojun

last: Tan

state: Pennsylvania

address: Bridgeside Point 1, 4th Floor, 100 Technology Drive

institute: Aging Institute, University of Pittsburgh

data_processing:
Trim Galore! done through "usegalaxy.org"
Salmon quant  done through "usegalaxy.org"
Reference transcriptome was "refMrna.fa.gz" from "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/"
Reference genome was "hg38.fa.gz" from "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/"
TPMs generated using the 3D RNA-seq online app "https://3drnaseq.hutton.ac.uk/app_direct/3DRNAseq/"
hg38.refGene.gtf.gz was the GTF file use for 3D RNA-seq from "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/genes/"
Assembly: hg38
Supplementary files format and content: .tabular files that can be used with the aforementioned 3D RNA-seq
Supplementary files format and content: .xlsx file with gene expression quantification for all samples

growth_protocol: BJ-5ta and U2OS cells were grown at 37°C in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 8% fetal bovine serum (Invitrogen), penicillin (100 U/mL), and streptomycin (100 mg/mL) (Gibco), InvivoGen plasmocin (2.5 μg/mL) in a humidified 5% CO2 atmosphere.

extract_protocol:
PureLink RNA Mini Kit (Thermo Fisher Scientific, ref 12183018A)
NextSeq 2000, P3 200 flow cell
Illumina Stranded mRNA Library Prep kit (Illumina: 20040534)

treatment_protocol: DMXAA dissolved in DMSO was directly added to cell cullture dishes and mixed well. For cGAMP treatment, a mild digitonin buffer was used for cGAMP delivery into the cells. Specifically, cells were cultured until 90% confluent. Then, the media were transferred to new plates or dishes. Cells were incubated with pre-warmed digitonin buffer (50 mM HEPES-KOH, pH 7.2, 100 mM KCl, 3 mM MgCl2, 0.1 mM DTT, 85 mM Sucrose, 0.2% BSA, 1 mM ATP, 10 μg/mL digitonin) containing 1 μM 2’3’-cGAMP or the buffer alone as negative control. After 10 min treatment, the digitonin buffer was aspirated, and the original media added back. Incubation was carried out for the specified duration in the incubator.

value: STING knockout

value: Digitonin buffer + 1 μM cGAMP 10 min, incubate for 12 h


title: BJ STING KO plus cGAMP 12 hours brep1


title: BJ STING KO minus cGAMP 12 hours brep1

value: Digitonin buffer 10 min, incubate for 12 h


title: BJ STING KO plus cGAMP 12 hours brep2


title: BJ STING KO minus cGAMP 12 hours brep3


title: BJ STING KO minus cGAMP 12 hours brep2


title: 4OHT + siSMARCA4_2; 3V


title: BJ plus cGAMP 12 hours brep1

value: wildtype


title: BJ minus cGAMP 12 hours brep3


title: BJ minus cGAMP 12 hours brep2


title: BJ STING KO plus cGAMP 6 hours brep2

value: Digitonin buffer + 1 μM cGAMP 10 min, incubate for 6 h


title: BJ minus cGAMP 12 hours brep1


title: BJ plus cGAMP 12 hours brep2


title: BJ STING KO plus cGAMP 6 hours brep1


title: BJ STING KO minus cGAMP 6 hours brep1

value: Digitonin buffer 10 min, incubate for 6 h


title: BJ STING KO plus cGAMP 6 hours brep3


title: BJ STING KO minus cGAMP 6 hours brep3


title: BJ STING KO minus cGAMP 6 hours brep2


title: BJ plus cGAMP 6 hours brep3


title: BJ plus cGAMP 6 hours brep2


title: BJ minus cGAMP 6 hours brep2


title: BJ plus cGAMP 6 hours brep1


title: BJ minus cGAMP 6 hours brep1


title: U2OS MmSting350 plus DMXAA 8 hours brep3

value: Stable overexpression of mouse STING 1-350

value: DMXAA 70 μM 8 h


title: BJ minus cGAMP 6 hours brep3


title: U2OS MmSting350 plus DMXAA 8 hours brep 2


title: BJ plus cGAMP 12 hours brep3


title: U2OS MmSting350 plus DMXAA 8 hours brep1


title: U2OS MmSting350 minus DMXAA 8 hours brep3

value: DMSO 8 h


title: U2OS MmSting350 minus DMXAA 8 hours brep 2


title: 4OHT + siSMARCA4_4, 3VM

data_processing:
Sequencing was conducted on an Illumina NextSeq 2000 system with 72 base pair single-end reads + dual 8bp indexing
Sequencing reads were mapped to hg38 genome using STAR aligner (version 2.7.8a)
Gene based counting was performed using the STAR aligner
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.36.0)
Assembly: hg38
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.


title: U2OS MmSting350 minus DMXAA 8 hours brep1


title: 4OHT Control + siNT 4, 3VM


title: 4OHT Control + siNT 2, 3VM


title: 4OHT + siSMARCA4_2, 2VM


title: 4OHT + siSMARCA4_4, 2VM


title: DMSO Control + siNT 2, 3VM


title: 4OHT + siSMARCA4_2, 3VM


title: DMSO Control + siNT 2, 2VM


title: 4OHT Control + siNT 2, 2VM


title: 4OHT Control + siNT 4, 1VM


title: 4OHT Control + siNT 4, 2VM


title: 4OHT + siSMARCA4_2, 1V


title: DMSO Control + siNT 4, 1V


title: 4OHT Control + siNT 2, 3V


title: 4OHT Control + siNT 4, 3V


title: 4OHT Control + siNT 2, 1VM


title: 4OHT + siSMARCA4_4, 3V


title: 4OHT + siSMARCA4_4, 1V


title: DMSO Control + siNT 2, 3V


title: DMSO Control + siNT 4, 3V


title: DMSO Control + siNT 2, 1V


title: DMSO Control + siNT 2, 2V


title: GNP_ZIC1NF_WT1_IP_2

city: Toronto

first: Michael

middle: D

last: Taylor

state: ON

address: 686 Bay St.

country: Canada

institute: Hospital for Sick Children

description: ChIP-Seq library

data_processing:
ChIP-Seq - alignment with bowtie2, peakcalling with MACS2. Differential peak analysis with DESeq2
counts were collected by bedtools multicov
Assembly: mm10
Supplementary files format and content: Raw counts for each sample for each gene or ChIP-Seq peak
Supplementary files format and content: narrowpeak outputs from MACS2 for GNP

extract_protocol:
ChIP-Seq libraries were generated with home made reagents
NEB Ultra DNA library prep kit was used for ChIP-Seq (NEB7645) library prep

value: Primary cell

value: Murine Granule Neuron Progenitor

value: WT

value: enrichment of gDNA for FLAG tagged ZIC1 (WT)


title: DMSO Control + siNT 4, 2V


title: DMSO Control + siNT 4, 2VM


title: GNP_ZIC1NF_WT1_IP_1

description: ChIP-Seq library


title: 4OHT + siSMARCA4_2, 3V


title: 4OHT + siSMARCA4_4, 2V


title: GNP_ZIC1NF_294_IP

description: ChIP-Seq library

value: G4 MB mutant

value: enrichment of gDNA for FLAG tagged ZIC1 (G4 mutant)


title: GNP_ZIC1NF_301_IP_2

description: ChIP-Seq library


title: 4OHT Control + siNT 4, 2V

value: Lung

value: IMR90 ER:RAS


title: TUMOR IN THE OMENTUM, CISPLATIN(2X), MOUSE 6

data_processing:
Sequencing was conducted on an Illumina NextSeq 2000 system with 72 base pair single-end reads + dual 8bp indexing
Sequencing reads were mapped to mm10 genome using STAR aligner (version 2.7.1a)
Gene based counting was performed using the STAR aligner
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.36.0)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

source_name: OMENTUM

growth_protocol: 5*10^6 ID8 cells were injected IP in 24 mice.

extract_protocol:
RNA was extracted performing the lysis of the tissue with the use of Trizol and Chloroform. Then we extracted the RNA using the Qiagen Rneasy Mini Kit
NEBNext Ultra II Directional RNA library prep kit with the NEBNext PolyA Enrichment module

treatment_protocol: After 1 month, 6 mice receive vehicle (PBS), 6 mice receive cisplatin (4mg/kg) for one week, 4 mice receive vehicle (PBS), 6 mice receive cisplatin (4mg/kg) for two weeks.

value: OMENTUM

value: ID8 P53 KO

value: OVARIAN CANCER

value: P53 KO


title: TUMOR IN THE OMENTUM, CISPLATIN(2X), MOUSE 5


title: DMSO Control + siNT 4, 3VM

value: Fibroblast


title: GNP_ZIC1NF_no_virus_IP

description: ChIP-Seq library

value: no virus

value: enrichment of gDNA for FLAG tagged ZIC1 (no virus)


title: TUMOR IN THE OMENTUM, CISPLATIN(2X), MOUSE 4


title: 4OHT + siSMARCA4_2, 2V


title: GNP_ZIC1NF_301_IP_1

description: ChIP-Seq library


title: TUMOR IN THE OMENTUM, CISPLATIN(2X), MOUSE 3


title: TUMOR IN THE OMENTUM, CISPLATIN(2X), MOUSE 2


title: TUMOR IN THE OMENTUM, VEHICLE(2X), MOUSE 3


title: TUMOR IN THE OMENTUM, CISPLATIN(2X), MOUSE 1


title: TUMOR IN THE OMENTUM, CISPLATIN(1X), MOUSE 6


title: TUMOR IN THE OMENTUM, VEHICLE(2X), MOUSE 4


title: TUMOR IN THE OMENTUM, VEHICLE(2X), MOUSE 1


title: TUMOR IN THE OMENTUM, CISPLATIN(1X), MOUSE 4


title: TUMOR IN THE OMENTUM, CISPLATIN(1X), MOUSE 3


title: TUMOR IN THE OMENTUM, CISPLATIN(1X), MOUSE 2


title: TUMOR IN THE OMENTUM, CISPLATIN(1X), MOUSE 1


title: TUMOR IN THE OMENTUM, VEHICLE(1X), MOUSE 6


title: TUMOR IN THE OMENTUM, VEHICLE(1X), MOUSE 3


title: TUMOR IN THE OMENTUM, VEHICLE(1X), MOUSE 2


title: TUMOR IN THE OMENTUM, VEHICLE(1X), MOUSE 4


title: DMSO, replicate 6

data_processing:
Sequencing was conducted on an Illumina NextSeq 2000 system with 70 base pair single-end reads + dual 8bp indexing
Sequencing reads were mapped to mm10 genome using STAR aligner (version 2.7.1a)
Gene based counting was performed using the STAR aligner
Gene expression analysis was performed using the DESeq2 Bioconductor package (DESeq2_1.36.0)
Assembly: mm10
Supplementary files format and content: comma-delimited text file include raw counts for each Sample generated by STAR aligner.

source_name: ID8 P53 KO

growth_protocol: ID8 P53 KO cells are mouse ovarian cancer cells. They grow in DMEM with high glucose and pyruvate with 4% FBS, 1% insulin-transferrin-selenium and 1% Anti-Anti.

treatment_protocol: ID8 P53 KO are treated with DMSO, or AU15330 (Smarca4 protac) 2.5 uM, Cisplatin 750 nM or a combination of both for 6 days, before to be used for RNA extraction.

value: DMSO


title: AU15330 2.5uM, replicate 6


title: CISPLATIN 750nM+AU15330 2.5uM, replicate 6


title: TUMOR IN THE OMENTUM, VEHICLE(1X), MOUSE 5


title: AU15330 2.5uM, replicate 5


title: CISPLATIN 750nM, replicate 6

value: CISPLATIN


title: CISPLATIN 750nM+AU15330 2.5uM, replicate 5


title: DMSO, replicate 5


title: CISPLATIN 750nM, replicate 5


title: DMSO, replicate 4


title: AU15330 2.5uM, replicate 4


title: CISPLATIN 750nM, replicate 4


title: TUMOR IN THE OMENTUM, CISPLATIN(1X), MOUSE 5


title: CISPLATIN 750nM, replicate 3


title: AU15330 2.5uM, replicate 3


title: CISPLATIN 750nM+AU15330 2.5uM, replicate 2


title: DMSO, replicate 2


title: CISPLATIN 750nM+AU15330 2.5uM, replicate 1


title: CISPLATIN 750nM, replicate 2


title: AU15330 2.5uM, replicate 2


title: TUMOR IN THE OMENTUM, VEHICLE(1X), MOUSE 1


title: CISPLATIN 750nM, replicate 1


title: Breast fibroblast, scRNA-seq [TNBC-P021]

city: Shenzhen

first: Yang

last: Gao

address: Guangqiao Road, Guangming District

institute: Shenzhen Bay Laboratory

data_processing:
The scRNA-seq data we generated were aligned and quantified using the Cell Ranger Single-Cell toolkit (v.3.1.0) against the GRCh38 human reference genome.
Assembly: GRCh38
Supplementary files format and content: Fibroblast_counts.csv.gz: gene expression count data in csv format
Supplementary files format and content: Fibroblast_metadata.csv.gz: metadata in csv format

source_name: Breast

extract_protocol:
Tumors and adjacent non-cancer tissues were cut into approximately 1-2-mm3 pieces in RPMI-1640 medium (Gibco) with 10% fetal bovine serum (FBS, Gibco) and enzymatically digested with gentle MACS (Miltenyi) for 60min on a rotor at 37°C, according to the manufacturer's instructions. Dissociated cells were subsequently passed through a 100-um Smart Strainer and centrifuged at 400g for 5min. After the removal of supernatant the pelleted cells were suspended in red blood cell lysis buffer (TIANDZ) and incubated on ice for 1-2 min to lyse red blood cells. After washing twice with 1×PBS (Gibco), cell pellets were resuspended in sorting buffer (PBS supplemented with 1% FBS). The concentration of single-cell suspensions was adjusted to ~500-1,200 cells ul-1. All subsequent steps were performed following the standard manufacturer's instructions. Purified libraries were analyzed using an Illumina Hiseq X Ten sequencer with 150-base pair (bp) paired-end reads.
Cells were loaded for library construction using the 10x Chromium Single cell 5' Library (10x Genomics), according to the manufacturer's instructions

value: Breast

value: Fibroblast cells

tag: cancer type

value: Triple-negative breast cancer (TNBC)


title: DMSO, replicate 1


title: Breast fibroblast, scRNA-seq [TNBC-P024]


title: CISPLATIN 750nM+AU15330 2.5uM, replicate 4


title: Breast fibroblast, scRNA-seq [TNBC-P020]


title: Breast fibroblast, scRNA-seq [TNBC-P023]


title: Breast fibroblast, scRNA-seq [TNBC-P001]


title: CISPLATIN 750nM+AU15330 2.5uM, replicate 3


title: Breast fibroblast, scRNA-seq [TNBC-P016]


title: Breast fibroblast, scRNA-seq [TNBC-P004]


title: Breast fibroblast, scRNA-seq [TNBC-P017]


title: Breast fibroblast, scRNA-seq [TNBC-P007]


title: Lung fibroblast, scRNA-seq [NSCLC-P25]

value: Non-small-cell lung cancer (NSCLC)


title: Breast fibroblast, scRNA-seq [TNBC-P002]


title: Lung fibroblast, scRNA-seq [NSCLC-P22]


title: Breast fibroblast, scRNA-seq [TNBC-P018]


title: DMSO, replicate 3


title: Lung fibroblast, scRNA-seq [NSCLC-P6]


title: Lung fibroblast, scRNA-seq [NSCLC-P28]


title: Lung fibroblast, scRNA-seq [NSCLC-P18]


title: Lung fibroblast, scRNA-seq [NSCLC-P16]


title: Lung fibroblast, scRNA-seq [NSCLC-P23]


title: Lung fibroblast, scRNA-seq [NSCLC-P15]


title: AU15330 2.5uM, replicate 1


title: Lung fibroblast, scRNA-seq [NSCLC-P14]


title: Lung fibroblast, scRNA-seq [NSCLC-P24]


title: Lung fibroblast, scRNA-seq [NSCLC-P10]


title: Breast fibroblast, scRNA-seq [TNBC-P022]


title: Liver fibroblast, scRNA-seq [HCC-P20180108]

source_name: Liver

value: Liver

value: Hepatocellular carcinoma (HCC)


title: Lung fibroblast, scRNA-seq [NSCLC-P1]

value: Lung


title: Stomach fibroblast, scRNA-seq [GC-P190124]

source_name: Stomach

value: Stomach

value: Gastric cancer (GC)


title: Liver fibroblast, scRNA-seq [HCC-P20171220]


title: Stomach fibroblast, scRNA-seq [GC-P190103]


title: Stomach fibroblast, scRNA-seq [GC-P190118]


title: Stomach fibroblast, scRNA-seq [GC-P190123]


title: Stomach fibroblast, scRNA-seq [GC-P181227]


title: Breast fibroblast, scRNA-seq [TNBC-P013]


title: Stomach fibroblast, scRNA-seq [GC-P181019]


title: Lung fibroblast, scRNA-seq [NSCLC-P12]


title: Stomach fibroblast, scRNA-seq [GC-P181025]


title: Stomach fibroblast, scRNA-seq [GC-P180308]


title: Stomach fibroblast, scRNA-seq [GC-P180118]


title: Mutant_JA-untreatment, replicate 3

city: Bei Jing

first: Wang

last: Qun

address: West Campus, China Agricultural University, 2 Yuanmingyuan West Road, Haidian District, Beijing

institute: China Agricultural University

data_processing:
The MP3RNA-seq method generated the sequencing data, comprising both R1 and R2 fastq files. However, during data analysis, the processed data files were generated solely from the R1 files.
Trimmomatic  (version 0.39) was used to trim the sequence reads and Hisat2 (version 2.2.1) was used to align them to the B73 v4 reference genome.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: Matrix table with raw counts for every sample (column) and gene (rows)

organism: Zea mays

source_name: Endosperm

extract_protocol:
5-10 of 15 DAP endosperms of wild type and mutant were pooled for extracting total RNA with an RNAprep Pure Plant Kit (cat. no. DP441, TIANGEN)
MP3RNA-seq

value: Endosperm

tag: Stage

value: wild type

value: JA-untreatment


title: Mutant_JA-treatment, replicate 2

value: mutant

tag: treatment

value: JA-treatment


title: Mutant_JA-treatment, replicate 3

tag: genotype


title: Mutant_JA-untreatment, replicate 2


title: Wild type_JA-treatment, replicate 2


title: Mutant_JA-untreatment, replicate 1


title: Mutant_JA-treatment, replicate 1


title: Wild type_JA-treatment, replicate 3


title: Wild type_JA-treatment, replicate 1


title: Wild type_JA-untreatment, replicate 1


title: Stomach fibroblast, scRNA-seq [GC-P180611]


title: Wild type_IAA-untreatment, replicate 2

value: IAA-untreatment


title: Wild type_IAA-untreatment, replicate 1


title: Mutant ZmICE1a, replicate 2

value: control


title: Mutant ZmICE1a, replicate 1


title: Wild type_JA-untreatment, replicate 3


title: Wild type ZmICE1a, replicate 1


title: Wild type ZmICE1a, replicate 2


title: Wild type_JA-untreatment, replicate 2


title: ZmICE1a-wildtype-biorep1

data_processing:
Illumina software used for base calling
The raw reads obtained were processed using the fastp program (version 0.23.1) with default settings to remove any low-quality reads.
The resulting high-quality reads were then aligned to the maize B73 RefGen_version 4.47 using Bowtie2 (version 2.4.1) with default parameters
The unique aligned reads were extracted using samtools (version 1.12).
Peak calling was performed separately for each biological replicate using MACS2 (version 2.1.0) with specific parameters (bandwidth = 300; model fold = [5, 50]; Q-value cutoff = 0.01) to identify binding regions of ZmICE1a.
Assembly: Zea mays ssp mays B73 v4
Supplementary files format and content: bigWig, narrowPeak
Library strategy: CUT&Tag-seq

source_name: maize endosperm

extract_protocol:
About 100 mg of endosperm powder was resuspended in pre-cold nuclear isolation buffer A (10 mM Tris-HCl (pH 8.0), 10 mM KCl, and 0.5 mM spermidine) and filtered through Miracloth (Millipore, Burlington, MA, USA; cat. no. 475855-1R). Cell nuclei were extracted using pre-cold nuclear isolation buffer B (10 mM Tris-HCl (pH 8.0), 10 mM KCl, 0.5 mM spermidine, 0.5 % Triton X-100, and 1X cocktail) and then washed three times.
Cell nuclei were incubated with ZmICE1a antibody (final concentration, 20 μg/mL) for 2 h at room temperature. Goat anti-rabbit IgG (secondary antibody) was added to each sample (final concentration, 10 μg/mL). After washing the samples three times, they were incubated with pA-Tn5 transposome at room temperature for 1 h. The samples were washed three times to remove unbound pA-Tn5 transposome and then incubated in tagmentation buffer (10 mM TAPS-NaOH (pH 8.5), 10 mM MgCl2, 10% (v/v) DMF, 0.5 mM spermidine, 0.05% (v/v) digitonin, and 1% (v/v) plant cocktail) at 37°C for 1 h. The reactions were stopped, and then the DNA was extracted from the samples. Finally, CUT&Tag-DNA libraries were constructed and sequenced using an Illumina NovaSeq 6000 platform (Illumina, San Diego, CA, USA) by BerryGenomics (China).

value: maize endosperm

value: wildtype


title: Wild type_IAA-treatment, replicate 2

value: IAA-treatment


title: Wild type_IAA-treatment, replicate 1


title: Wild type_IAA-untreatment, replicate 3


title: Mutant ZmICE1a, replicate 3


title: 4-OI, replicate 1, RNAseq

city: Ann Arbor

first: Weiping

last: Zou

state: MI

address: 109 Zina Pitcher Pl

department: Surgery

institute: University of Michigan

data_processing:
BCL Convert Conversion Software v4.0 (Illumina) was used to generate de-multiplexed Fastq files. The reads were trimmed using Cutadapt v2.3. The reads were evaluated with FastQC (v0.11.8) to determine quality of the data. Reads were mapped to the reference genome GRCm38 (ENSEMBL 102), using STAR v2.7.8a and assigned count estimates to genes with RSEM v1.3.3. Alignment options followed ENCODE standards for RNA-seq. QC metrics from several different steps in the pipeline were aggregated by multiQC v1.7.
Assembly: GRCm38
Supplementary files format and content: Tab-delimited text file contains raw counts for each sample
Supplementary files format and content: Tab-delimited text file contains TPM for each sample
Supplementary files format and content: Tab-delimited text file contains FPKM for each sample

extract_protocol:
Total RNA extraction utilized the Direct-zol RNA Miniprep Plus kit (Zymo Research)
mRNA libraries were prepared using Illumina TruSeq technology.  Sequencing was performed on an Illumina NextSeq sequencer at 150 bp, paired-end reads with an approximate yield of 30 million reads per sample. Each condition was independently sequenced in four experiments.

tag: strain

value: Itaconate-treated


title: Wild type ZmICE1a, replicate 3


title: ZmICE1a-mutant-biorep1


title: ZmICE1a-mutant-biorep2


title: ZmICE1a-wildtype-biorep2


title: PF_WT_rep2

city: Memphis

first: Paul

middle: A.

last: Northcott

address: 262 Danny Thomas Place

department: Developmental Neurobiology

institute: St. Jude Children's Research Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the CellRanger (v7.0.0)
Assembly: mm10
Supplementary files format and content: Tab-separated files

source_name: paraflocculus/flocculus

extract_protocol:
The petrous bone and paraflocculus/flocculus (PF/F) were dissected from P5.5 Tbx1+/- mice and their matched littermates. Each sample was flash frozen and stored at -80°C until used. The frozen bones (5 mice per group) were placed into the prechilled tissue tubes (Covaris, cat. no. 520001) on dry ice and pulverized using a prechilled CP01 cryoPREP manual dry pulverizer (Covaris, cat. no. 500230). The coarsely powdered bone was placed into a well of 6 well plate with 1ml of CHAPS/salt-Tris solution (ST buffer) containing 980 µl of 1 % CHAPS (Millipore, cat. no. 220201) mixed with 1 ml of 2xST buffer (292 mM NaCl, 20 mM Tris-HCl pH 7.5, 2 mM CaCl2 and 42 mM MgCl2), 10 µl of 2 % BSA (New England Biolabs, cat. no. B9000S) and 10 µl of nuclease-free water, and gently chopped using Noyes spring scissors (Fine Science Tools, cat. no. 15514-12) for 2 minutes on ice. The nuclei suspension was filtered through a 40 µm strainer into a 15 ml tube (pre-blocked with 2.5% BSA). The filter was washed with 1ml of 1x ST buffer and the filtered volume was brought up to 5 ml by addition of 1x ST buffer. Following additional filtration through a 30 µm strainer, the solution was centrifuged at 300xg for 5 minutes. The pellet was resuspended in 1% BSA in PBS (250-500 µl based on pellet size) and filtered through a strainer cap FACS tube (Corning, cat. no. 352235). Nuclei were counted and checked for integrity under a microscope and the volume was adjusted to a concentration of 1x106 nuclei/ml. The frozen PF/F (5 mice/group) was placed directly into 1 ml of CHAPS/ST buffer (without pulverization) and chopped for 3 minutes on ice and processed further as described above. All solutions used for nuclei isolation were amended with 0.2U/µl of RNase Inhibitor (Roche, cat. no. 3335399001).
Nuclei from developing mouse cerebellar tissue or petrous bone were isolated and processed using the 10x Chromium technology, specifically optimized for single nuclei RNA sequencing. The nuclei were processed using the Chromium Single Cell 3′ v3 or v3.1 Library & Gel Bead Kit, which is designed for nuclei and includes adjustments to the standard single-cell protocol to accommodate the unique characteristics of nuclei. All procedures were carried out in accordance with the manufacturer's recommendations for single nuclei RNA-seq
snRNA-seq

value: paraflocculus/flocculus

value: WT


title: Bone_MUT_rep1

description: 10x Genomics

source_name: petrous bone

value: petrous bone


title: Bone_WT_rep1

description: 10x Genomics


title: DMSO, replicate 3, RNAseq

value: Control


title: PF_MUT_rep2

description: 10x Genomics


title: 4-OI, replicate 4, RNAseq


title: 4-OI, replicate 2, RNAseq


title: DMSO, replicate 4, RNAseq


title: Muscle_4

city: Leiden

first: Clara

last: Martinez Mir

address: Einthovenweg 20

department: Anatomy and Embryology

country: Netherlands

institute: Leiden University Medical Center

description:
mRNA
section_barcodes.txt

data_processing:
Sequencing libraries were mapped using STAR (v.2.7.7a) with default parameters to the mouse GRCm38 genome (Ensembl 102). Only reads mapping to gene bodies (exons or introns) were used for downstream analysis. Reads mapping simultaneously to an exon and to an intron were assigned to the exon. Sections were filtered based on their total transcript counts. Genes linked to mapping errors (Kcnq1ot1, Mir5109, Lars2 and Malat1)44,46, spike-ins, ribosomal genes, low detected genes and genes with saturated UMI counts were excluded from downstream analysis. For each muscle, data was normalized to the median number of unique transcripts counts per section.
Assembly: Ensemble version 102 of the mouse genome (GRCm38)
Supplementary files format and content: Tabular-separated file indicating number of transcripts per section obtained as previously described (Grün, Dominic, Lennart Kester, and Alexander Van Oudenaarden. "Validation of noise models for single-cell transcriptomics." Nature methods 11.6 (2014): 637). We refer to transcripts as unique molecules based on UMI correction.

source_name: tibialis anterior muscle

extract_protocol:
After cryosectioning, total RNA is extracted from individual sections using TRIZOL.
Total RNA from individual sections is sorted into 96-well plates containing mineral oil, and uniquely barcoded section specific primers (read 1 contain the unique molecular identifier in the first 6 bases, followed by the 8-nucleotide long section barcode) for mRNA dection.
TOMO-seq-CELseq2

value: tibialis anterior muscle


title: DMSO, replicate 2, RNAseq


title: Muscle_1

description:
mRNA
section_barcodes.txt


title: PF_WT_rep1

description: 10x Genomics


title: Wild type_IAA-treatment, replicate 3


title: IMH-IIICD45, replicate 1, scRNAseq

city: Wuhan

first: Jiahong

last: Xia

state: Hubei

address: JieFang Road 1277

department: Department of Cardiovascular Surgery

institute: Union Hospital, Tongji Medical College,  Huazhong University of Science and Technology

description: FACS sorted nucleated living cells from multiple distinct aortic aneurysms with dissection/intramural hematoma

data_processing:
The Cell Ranger Single Cell Software Suite, version 3.1.0 (https://www.10xgenomics.com/) was used to perform sample de-multiplexing, barcode ad UMI processing, and single-cell 3′ gene counting. A detailed description of the pipeline and specific instructions to run it can be found at: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger.
Cloupe files were generated using the Cell Ranger 3.1.0 version. A description of the pipeline and instructions can be found at: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/latest/what-is-cell-ranger#header.
The CellRanger count command was run on the individual Fastq datasets to produce expression data.
R package Seurat v3.6.3 was used for cell filtration, normalization, principal component analysis, variable genes finding, clustering analysis, and Uniform Manifold Approximation and Projection (UMAP) dimensional reduction. Data were then log-normalized for the subsequent analyses. Principal component analysis (PCA) was used for dimension reduction, followed by clustering analysis in principal component analysis space using a graph-based clustering approach. UMAP was then used for the two-dimensional visualization of the identified clusters.
The Seurat functions Vlnplot, FeaturePlot, DotPlot and DoHeatmap were used to visualize the gene expression with violin plot, feature plot, dot plot and heatmap, respectively. Markers for a specific cluster against all remaining cells were found by using the Seurat function FindAllMarkers.
Assembly: Data were mapped to the pre-build mouse reference genome (mm10, version 3.0.0).
Supplementary files format and content: barcodes.tsv, features.tsv, matrix.mtx

source_name: abdominal aorta

extract_protocol:
The abdominal aortas pooled from mice in each group were digested with an enzymatic solution containing 2U/mL LiberaseTM (Cat# 05401127001, Switzerland, Roche) and 2U/mL elastase (Cat# LS002279, America, Worthington) in Hanks’ buffered saline solution (HBSS) for 1 hour at 37℃. The cell suspension was strained through a 40 μm filter and washed thrice with PBS. The single cells were resuspended in opti-MEM with 10% FBS. The cell suspensions were loaded on a 10x Genomics Chromium instrument to generate single-cell gel beads in emulsion (GEMs).
Library was performed according to the manufacturer’s instruction (single cell 3’ v2 protocol, 10x Genomics). Briefly, living cells in the abdominal aorta were resuspended in the master mix and loaded together with partitioning oil and gel beads into the 10x Genomics microfluidics chip to generate the gel bead-in-emulsion (GEM) in the GemCode instrument according to the manufacturer’s protocols, in which cell lysis and barcoded reversed transcription of RNA, then amplification, shearing, and 5′ adaptor and sample index attachment were performed.

value: abdominal aorta

value: nucleated immune living cells

value: ApoE-deficient

value: 4 weeks Angiotensin II-induction


title: shPde10a#1, snRNAseq

city: Bethesda

first: Nicholas

middle: Klose

last: Nuechterlein

address: 9000 Rockville Pike

institute: NIH

description: 10x Genomics

data_processing:
Sequenced reads from tumor samples were demultiplexed and aligned to the mm10 reference genome using CellRanger (v6.1; 10X Genomics) mkfastq function with default settings and subsequent counts were generated using the CellRanger count function.
To calculate RCAS expression, CellRanger version 7.1.0 was used to recover unmapped reads by converting BAM files processed by CellRanger back to fastq files. The RCAS virus sequence was then added to the genome reference file and CellRanger was used to realign the fastq files.
Expression of hPDGFA was computed in a similar manner
Assembly: mm10
Supplementary files format and content: matrix.h5 files

source_name: Brain

growth_protocol: Neural stem cells were isolated from P0 neonatal mouse brain tissue. Fresh media was prepared for each passage, containing 45 mL of NeuroCult Mouse Basal Medium (STEMCELL Technologies, 5700), 5mL NeuroCult Proliferation Supplement (STEMCELL Technologies, 5701), 125µL Heparin Solution (STEMCELL Technologies, 7980), 20ng/mL EGF, 10ng/mL bFGF, and 5,000U Penicillin-Streptomycin. Cells were maintained at 1x105 cells/mL in low-attachment flasks and stored at 37C in 5% CO2 humidified incubators. TrypLE Express (Invitrogen, 12604013) was applied to pelleted cells every 2-4 days to split into single-cell suspension. For retroviral transduction of murine neurospheres with RCAS-RFP-shPde10a#1,  RCAS-RFP-shPde10a#4, or RCAS-RFP-shScrambled, RCAS virus was produced in DF-1 packaging cells maintained with serum-free neurosphere medium and was then diluted 1:1 with collection media (fresh murine neurosphere media). RCAS transduced cells were passaged twice, and retroviral incorporation was enriched for by gating RFP-positive cells using a MoFlo Astrios Cell Sorter (Beckman Coulter Life Sciences) at the National Institute of Neurological Disorders and Stroke Flow & Imaging Cytometry Core Facility. Flow sorted RFP-positive cells were then grown again as neurospheres and were passaged twice prior to each of the subsequent assays.

extract_protocol:
Mouse tumors were macro-dissected from normal appearing brain and flash-frozen in liquid nitrogen. Tumor samples were removed from liquid nitrogen storage and nuclei were isolated from the frozen tissues using an adaptation of a previously established protocol. Briefly, each sample (two mice per condition were pooled for each sample) was placed on a clean petri dish and washed with 800 mL of Detergent-Lysis Buffer (0.1% Triton-X). A number 22 blade was used to dissociate tissue, which was then transferred into a 7 mL Dounce Homogenizer. Tissue was first homogenized with eight strokes of the loose Pestle, and then 12 strokes of the tight Pestle. The crude nuclei homogenate was then passed through a 40-micrometer strainer and spun down at 3,200 𝗑 g for 5 minutes at 4°C in a swing-bucket centrifuge. The pellet was resuspended in 1 mL of low-sucrose buffer and then gently layered above 4 mL of high sucrose buffer without disrupting the density gradient. The gradient was then spun down at 3,200 𝗑 g for 20 minutes at 4°C, and the ensuing pellet was resuspended in 25–150 mL of 0.04% BSA and 1 U/µL Sigma Protector RNase Inhibitor (3335399001) in 1X PBS. An aliquot was taken to be stained with Acridine Orange dye (1:10 dilution) and counted/imaged using a Luna-FL Dual-Fluorescence Cell Counter (Logos Biosystems). Following manufacturer’s recommendations, the nuclei suspensions were next processed via the Single Cell Gene Expression Assay (10X Genomics). Nuclei were loaded onto a Next GEM Chip G (10X Genomics) targeting a yield of 5,000 nuclei.
For all single-nuclei experiments, the Single Cell Gene Expression Kit (10X Genomics) was used according to the manufacturer’s protocol recommendations. Library preparation was performed according to the manufacturer’s instructions. Libraries were pooled and sequenced on the NextSeq 500 System (Illumina) using High-Output Reagent Kit v2.5 (150 cycles; Illumina).
single nucleus RNA-sequencing

treatment_protocol: Cells were not treated

value: Brain

value: Neural stem cell

value: Ink4a/Arf -/-; Pten fl/fl


title: Scrambled control, snRNAseq

description: 10x Genomics

value: Scrambled control


title: IMH-III, replicate 1, scRNAseq

description: nucleated living cells from multiple distinct aortic aneurysms with dissection/intramural hematoma

value: nucleated living cells


title: shPde10a#4, snRNAseq

description: 10x Genomics


title: Bone_MUT_rep2

description: 10x Genomics


title: Bone_WT_rep2

description: 10x Genomics


title: Muscle_3

description:
mRNA
section_barcodes.txt


title: Muscle_2

description:
mRNA
section_barcodes.txt


title: 4-OI, replicate 3, RNAseq


title: TTseq.48h.rep3-1

data_processing:
Index creation: to calculate spike-in scalar coefficients, a mouse and yeast hybrid genome was generated by merging the mouse mm10 and sarCer3 fasta files and applying STAR v2.5.2a with parameters --runMode genomeGenerate --sjdbOverhang 41.
Alignment: FASTQ files were aligned to the hybrid genome using STAR with parameters recommended by the TEtranscripts analysis pipeline (Jin et al. Bioinformatics 2015. 31, 3593-3599, https://github.com/mhammell-laboratory/TEtranscripts): --winAnchorMultimapNmax 100 --outFilterMultimapNmax 100. Data from runs was pooled to increase coverage.
Spike-in adjustment: the fraction of the reads aligned to the yeast genome in each sample was used to calculate a scalar for bigwig and DEseq2 normalization between different samples.
Transcription unit identification: transcription units were called using TU_filter (https://github.com/shaorray/TU_filter).
Quantitation: expression levels of genes, non-coding RNAs and transposable elements were quantified with TElocal (https://github.com/mhammell-laboratory/TElocal) with parameters --TE mm10_rmsk_TE.gtf.locInd --stranded reverse.
Differential analysis: transcription units were assessed for statistically significant differential expression with DEseq2 using spike-in scalars calculated above as size factors.
Track creation: bigwig files were generated with deeptools bamCoverage using RPKM normalization, with forward and reverse strands separated, after pooling all replicates.
Assembly: GRCm38/mm10
Supplementary files format and content: BigWig files reflect transcription data adjusted using RPKM adjustment for library size, with reference genome + (*.fw.bw) and - (*.rv.bw) separated
Supplementary files format and content: Tables reflect spike-in adjusted TU counts (TTseq_replicates_adjusted.txt) or the same, adjusted for the length of the nascent transcription unit (TTseq_replicates_Average_lengthNormalised.txt). For analysis purposes, it is better to use the length normalized counts as nascent RNA-seq covers entire gene models and not only the exons.

extract_protocol:
TT-seq was performed as previously described (Schwalb et al. Science 2016. 352, 1225-1228) with slight modifications. Cells were labeled with 4SU (Glentham Life Sciences, GN6085) at 1mM final concentration for 10 minutes in 37 °C incubator. The medium was then immediately decanted, and cells were lysed by directly adding 5 ml Trizol reagent onto the plates. Cells were scraped from the plates and collected in 15 mL falcon tubes and frozen in -80 °C. Total RNA were extracted using Trizol RNA extraction protocol following the manufacturer’s instructions and stored in -80 °C. S. cerevisiae 4-thiouracil (4TU, Sigma, 440736) labelled RNAs were prepared following the protocol described previously (Gregersen et al. Nature Protocols 2020. 15, 604-627).
110 μg total RNA, combined with 1 μg of spike-in S. cerevisiae 4TU-labeled RNA were fragmented with 166 mM NaOH for 30 minutes on ice, and stopped by adding 400 mM Tris-HCl, pH 6.8 and passed through Micro Bio-Spin P-30 gel columns twice. The total RNAs were then denatured at 65°C for 10min, followed by 5mins of incubation on ice, and mixed with 50 μL of 0.1 mg/ml MTSEA biotin-XX linker (Biotium, BT90066) on rotator at room temperature for 30 minutes in the dark. The RNA was then purified with phenol/chloroform/isoamyl alcohol (25:24:1 (vol/vol/vol)), followed by isopropanol precipitation. The RNA was then resuspended in nuclease-free H2O and denatured at 65°C for 10min, followed by 5 minutes of incubation on ice and mixed with 150 μL of μMACS streptavidin MicroBeads (Miltenyi, 130-074-101) for 15 minutes in cold room on a rotating wheel. The biotinylated RNA was retained on μMACS magnetic separator (Miltenyi, 130-042-602) placed on a MACS multistand (Miltenyi, 130-042-303) and washed three times with 900 μL of pre-warmed (65 °C) pull-down wash buffer (100 mM Tris-HCl, pH 7.4, 10 mM EDTA, 1 M NaCl and 0.1% Tween 20) and three more times with 900 μL of room temperature pull-down wash buffer. The biotinylated RNA was eluted twice from the column with 100 μl of 100 mM DTT and purified with RNeasy MinElute Cleanup Kit (Qiagen, 74204).

value: dTKO

value: ES cells

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl

value: + auxin + dTAG13


title: AAA, replicate 1, scRNAseq

description: nucleated living cells from single aortic aneurysm without dissection


title: TTseq.3h.rep2-2


title: DMSO, replicate 1, RNAseq


title: IMH-I, replicate 1, scRNAseq

description: nucleated living cells from aortic dissection/intramural hematoma without aneurysm


title: AAACD45, replicate 1, scRNAseq

description: FACS sorted nucleated living cells from single aortic aneurysm without dissection


title: IMH-IICD45, replicate 1, scRNAseq

description: FACS sorted nucleated living cells from single aortic aneurysm with dissection/intramural hematoma


title: TTseq.24h.rep3-2


title: TTseq.24h.rep2-2


title: IMH-II, replicate 1, scRNAseq

description: nucleated living cells from single aortic aneurysm with dissection/intramural hematoma


title: PF_MUT_rep1

description: 10x Genomics

value: paraflocculus/flocculus


title: TTseq.24h.rep2-1


title: TTseq.48h.rep2-2


title: TTseq.48h.rep3-2


title: TTseq.3h.rep3-2


title: TTseq.48h.rep1-2


title: TTseq.48h.rep2-1


title: TTseq.12h.rep2-1


title: TTseq.12h.rep1-2


title: TTseq.3h.rep2-1


title: AAD, replicate 1, scRNAseq

description: nucleated living cells from abdominal dilated aorta without dissection


title: TTseq.24h.rep3-1


title: TTseq.0h.rep3-1


title: TTseq.0h.rep3-2


title: TTseq.24h.rep1-2


title: TTseq.3h.rep1-2


title: TTseq.0h.rep1-1


title: NA, replicate 1, scRNAseq

description: nucleated living cells from normal aorta


title: TTseq.24h.rep1-1


title: TTseq.12h.rep2-2


title: TTseq.12h.rep3-1


title: TTseq.3h.rep3-1


title: ATAC.6h.rep1

data_processing:
Pipeline overview: data were aligned to mouse genome assembly mm10 and subsequent analysis was performed with CUT&RUNTools v2.0 (https://github.com/fl-yu/CUT-RUNTools-2.0) using the standard CUT&Tag pipeline.
Read trimming and alignment: reads were trimmed with trimmomatic v0.36 and aligned with bowtie2 v2.4.2.
Read shift: aligned reads were shifted +4bp and -5bp for positive and negative strand reference genome alignments, respectively, to account for the 9-bp duplication created by DNA repair of the nick by Tn5 transposase.
Filtering and peak calling: aligned reads were filtered by size and duplicates were marked; peaks were called using MACS2 v2.2.7.1.
Peak merge: peaks from individual replicates were merged where overlapping.
Track creation: nucleosome positioning analysis was performed using NucleoATAC with default settings. Bedgraphs from the smoothed NucleoATAC signals were converted into bigWig format using UCSC Genome Browser's bedGraphToBigWig utility.
Assembly: GRCm38/mm10
Supplementary files format and content: The BED file ATAC.all.narrowpeaks.merged.Named.bed contains all ATAC-seq peaks identified through the CUT&RUN Tools pipeline (MACS2 narrow peak calls) which were then merged if overlapping.
Supplementary files format and content: BigWig files are produced from NucleoATAC signals.

extract_protocol:
The ATAC-seq was performed following the protocol described previously (Grandi et al. Nature Protocols 2022. 17, 1518-1552) with slight modification. Briefly, 100,000 cells were collected and washed once with DPBS, and nuclei were isolated by incubating the cells with 50 μl ice-cold ATAC-RSB buffer (10 mM Tris-HCl pH 7.6, 10mM NaCl, 3mM MgCl2) with 0.1% NP40, 0.1% Tween 20, and 0.01% Digitonin for 3 minutes on ice. The nuclei were then washed once with ATAC-RSB buffer with 0.1% Tween 20 and incubated with 50 μl transposition mix (25 μl 2x TD buffer, 2.5 μl transposase (120 nM final), 16.5 μl PBS, 0.5 μl 1% digitonin, 0.5 μl 10% Tween-20, 5 μl H2O) at 37°C for 30 minutes and mixed in thermomixer at 1000 RPM. The transposition was stopped by adding 250 μl (five volumes) DNA binding buffer to the transposition mix and DNA was purified with Zymo DNA Clean and Concentrator-5 Kit (D4014) and eluted in 21 μl elution buffer.
For library preparation, 5 cycle of pre-amplification was performed, and the DNA concentration was then quantified, followed by an additional 5 cycles of amplifications. The library DNA was purified with Zymo DNA Clean and Concentrator-5 Kit and eluted in 20 μl of H2O.


title: TTseq.3h.rep1-1


title: TTseq.12h.rep1-1


title: TUMOR IN THE OMENTUM, VEHICLE(2X), MOUSE 2

value: OMENTUM

value: ID8 P53 KO

value: OVARIAN CANCER

value: P53 KO


title: ATAC.6h.rep3


title: TTseq.0h.rep2-1


title: TTseq.48h.rep1-1


title: TTseq.0h.rep2-2


title: TTseq.0h.rep1-2


title: ATAC.48h.rep1


title: ATAC.48h.rep2


title: ATAC.3h.rep2


title: ATAC.3h.rep3


title: ATAC.24h.rep2


title: ATAC.3h.rep1


title: ATAC.0h.rep3


title: ATAC.0h.rep2


title: ATAC.48h.rep3


title: ATAC.6h.rep2


title: ATAC.0h.rep1


title: ATAC.12h.rep1


title: ATAC.24h.rep1


title: Input_for_HP1b.48h.rep2-3

data_processing:
Index creation: mouse mm10 and drosophila dm6 assemblies were merged to create a hybrid genome, and a bowtie2 index for the hybrid genome was generated using bowtie2-build -f.
Alignment: FASTQs were aligned to the hybrid genome with bowtie2 v2.3.4.1 -p 16 --local -X 1000.
Filtering: unmapped/unpaired reads were filtered out using samtools v1.1 view -bS -h -f 3 -F 4 -F 8
Library repeat merge: reads from three sequencing runs of the same sample (technical repeats) were merged using samtools merge.
Replicate merge: bam files of the three biological replicates of each sample were merged using samtools merge.
Scalar calculation: the percentage of drosophila reads in each ChIP sample was used to calculate the scalars for library size adjustment. RPM was used for input samples.
Track creation: bigWig files were created using deeptools bamCompare (log2(ChIP/Input) and scaled based on the ratio of the spike-in reads).
Domain calling: merged BAM files were converted into bed files using bedtools bamtoBed and then processed with RSEG v0.4.8 rseg-diff -i 20 -v -mode 2 -d deadzones-k36-mm10.bed with deadzones downloaded from the RSEG website and lifted from mm9 to mm10 over using UCSC Genome Browser's liftOver tool.
Assembly: GRCm38 / mm10
Supplementary files format and content: BigWig files ending in *.merged.multimap.bw reflect the pool of three biological replicates with input subtraction and spike-in adjustment.
Supplementary files format and content: The table H3K9me3.DomainsByDecayRate.mm10.txt has a list of ~43k H3K9me3 domains identified at t=0hrs, with column 4 describing the decay kinetics (fast, intermediate, slow, residual).

extract_protocol:
Briefly, cells were crosslinked with 1% formaldehyde at room temperature for 10 mins, and quenched with 0.125 mM Glycine at room temperature for 5 minutes. The cells were then washed 3 times with ice cold DPBS and incubated with seven ml swelling buffer (25mM HEPES-KCl, pH7.2, 1.5 mM MgCl2, 20mM KCl, 0.1% NP-40) per 15cm dish incubated for 10 minutes at 4 °C. The cells were scrapped off the plates, collected and pelleted in 15 ml falcon tubes and immediately snap frozen in the liquid nitrogen, and stored in -80 °C freezer. On the day of sonication, the crosslinked cells were incubated with lysis buffer 1 (50 mM HEPES-KOH, pH7.5, 140 mM NaCl, 1mM EDTA, 10% glycerol, 0.5% NP-40, 0.25% Triton X-100, 1 mM DTT, and 1x complete protease inhibitors cocktail) and lysis buffer 2 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1x complete protease inhibitors cocktail) for 5 minutes each at 4 °C. The nuclei were then resuspended in the lysis buffers 3 (10 mM Tis-HCl, pH8, 200 mM NaCl, 1mM EDTA, 0.5 mM EGTA, 1 mM DTT, 0.1% Na-Deoxycholate, 0.5% N-lauroylsarcosine, 1x complete protease inhibitors cocktail) for 10 minutes on ice, followed by centrifugation at 1350g for 5 minutes. The nuclei pellets were then resuspended in lysis buffer 3 and sonicated with Covaris with (Incident peak power: 140; Duty Cycle: 5; Burst/Cycle: 200) for 15 minutes. The sonicated chromatin was centrifuging at 20,000g for 20 minutes and the soluble chromatin were collected, and 20 μl chromatin was de-crosslinked in 200 μl elution buffer (50 mM Tris-HCl, pH 8.0, 10 mM EDTA, 1% SDS) at 65 °C over night and the rest of the chromatin was aliquoted, snap frozen in liquid nitrogen and stored in -80 °C freezer. The de-crosslinked chromatin was treated with proteinase K and RNase, followed by ethanol precipitation. For H3K9me3 and HP1β ChIP-seq, 20 μg of chromatin was combined with 1.5 μg of Drosophila spike-in chromatin and incubated with 10 μl of Protein A/G dynabeads pre-coated with 0.5 μg of H3K9me3 (abcam, ab8898) or 1ug of HP1β antibody (Cell Signaling Technology, 8676) and 0.5 μg of drosophila spike-in antibody on a rotating wheel at 4 °C overnight. The chromatin-antibody-dynabeads slurry was then washed 5 times with The RIPA buffer (50 mM Hepes-KOH, pH 7.6, 500 mM LiCl, 1mM EDTA, 1% NP40, 0.7% Na-Deoxycholate, 1x complete protease inhibitors cocktail) and once with TE (10 mM Tris-HCl, pH 8.0, 1mM EDTA). The chromatin was eluted with elution buffer by incubating at 65 C for 20 minutes and de-crosslinked at 65 °C over night, followed by proteinase and RNase treatment and ethanol precipitation. The DNA concentration was quantified with Qubit HS DNA kit and stored in -20 °C.
ChIP-seq DNA libraries was prepared with NEBNext® Ultra™ II DNA Library Prep Kit (NEB, E7645) following the manufacturer’s instructions. Briefly, 10 ng of ChIP DNA was used for each library and amplified with 11 PCR cycles and the library DNA was purified with Ampure XP beads and the distribution of the DNA fragments of the libraries was analyzed using High Sensitivity DNA ScreenTape (Agilent, 5067-5584) on Agilent Tapestation 4150.

tag: chip antibody

tag: time (hours post treatment)


title: Input_for_HP1b.48h.rep2-2


title: TTseq.12h.rep3-2


title: Input_for_HP1b.48h.rep1-3


title: Input_for_HP1b.48h.rep3-3


title: Input_for_HP1b.48h.rep3-2


title: Input_for_HP1b.48h.rep2-1


title: Input_for_HP1b.48h.rep3-1


title: Input_for_HP1b.48h.rep1-2


title: Input_for_HP1b.48h.rep1-1


title: Input_for_HP1b.24h.rep3-2


title: ATAC.24h.rep3


title: Input_for_HP1b.24h.rep3-3


title: Input_for_HP1b.3h.rep1-3


title: Input_for_HP1b.3h.rep3-3


title: ATAC.12h.rep2


title: Input_for_HP1b.3h.rep3-1


title: Input_for_HP1b.3h.rep2-2


title: Input_for_HP1b.24h.rep1-2


title: Input_for_HP1b.3h.rep1-2


title: Input_for_HP1b.3h.rep1-1


title: Input_for_HP1b.24h.rep2-1


title: ATAC.12h.rep3


title: Input_for_HP1b.3h.rep2-1


title: Input_for_HP1b.24h.rep3-1


title: Input_for_HP1b.1h.rep3-2


title: Input_for_HP1b.24h.rep2-2


title: Input_for_HP1b.3h.rep3-2


title: Input_for_HP1b.24h.rep2-3


title: Input_for_HP1b.24h.rep1-3


title: Input_for_HP1b.12h.rep3-2


title: Input_for_HP1b.1h.rep2-2


title: Input_for_HP1b.1h.rep1-3


title: Input_for_HP1b.1h.rep2-1


title: Input_for_HP1b.1h.rep1-2


title: Input_for_HP1b.1h.rep1-1


title: Input_for_HP1b.12h.rep1-3


title: Input_for_HP1b.1h.rep2-3


title: Input_for_HP1b.1h.rep3-1


title: Input_for_HP1b.12h.rep2-3


title: Input_for_HP1b.12h.rep3-3


title: Input_for_HP1b.1h.rep3-3


title: Input_for_HP1b.24h.rep1-1


title: Input_for_HP1b.12h.rep2-2


title: Input_for_HP1b.0h.rep3-1


title: Input_for_HP1b.12h.rep2-1


title: Input_for_HP1b.12h.rep1-1


title: Input_for_HP1b.0h.rep3-2


title: Input_for_HP1b.0h.rep2-1


title: Input_for_HP1b.0h.rep2-3


title: Input_for_HP1b.0h.rep1-2


title: Input_for_HP1b.0h.rep1-1


title: Input_for_H3K9me3.48h.rep3-3


title: Input_for_HP1b.12h.rep3-1


title: Input_for_HP1b.12h.rep1-2


title: Input_for_H3K9me3.48h.rep3-1


title: Input_for_H3K9me3.48h.rep1-1


title: Input_for_H3K9me3.48h.rep2-3


title: Input_for_H3K9me3.48h.rep3-2


title: Input_for_H3K9me3.48h.rep1-2


title: Whole Lung, MCT-Fer-1 4

city: Minneapolis

first: Kurt

last: Prins

state: MN

address: 2231 6th St Se

institute: University of Minnesota

data_processing:
CLC Genomics Workbench
Assembly: Sequence reads were trimmed for quality and mapped to rat genome. Read count extraction and normalization were performed
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Rattus norvegicus

source_name: Whole Lung

extract_protocol:
RNA was harvested from whole lung extracts
RNA libraries from RNA-seq were prepared by the University of Minnesota Genomics center.

treatment_protocol: control, monocrotaline-vehicle, and monocrotalin-ferrostatin-1

value: Whole Lung

value: WT

tag: time

value: 25 days


title: Input_for_H3K9me3.3h.rep3-2


title: Input_for_H3K9me3.48h.rep1-3


title: Input_for_H3K9me3.48h.rep2-1


title: Input_for_HP1b.0h.rep3-3


title: Whole Lung, MCT-Fer-1 3


title: Input_for_H3K9me3.3h.rep3-1


title: Input_for_H3K9me3.3h.rep2-3


title: Whole Lung, MCT-Fer-1 1


title: Input_for_H3K9me3.3h.rep2-1


title: Whole Lung, MCT-Fer-1 2


title: Input_for_H3K9me3.3h.rep3-3


title: Whole Lung, MCT-Vehicle 4

value: Ferrostatin-1 Vehicle


title: Whole Lung, MCT-Vehicle 3


title: Input_for_HP1b.0h.rep1-3


title: Input_for_H3K9me3.3h.rep2-2


title: Input_for_H3K9me3.3h.rep1-1


title: Whole Lung, MCT-Vehicle 2


title: Input_for_H3K9me3.48h.rep2-2


title: Input_for_H3K9me3.24h.rep3-3


title: Whole Lung, MCT-Vehicle 1


title: Input_for_H3K9me3.3h.rep1-2


title: Whole Lung, Control 3

value: Control


title: Input_for_H3K9me3.24h.rep2-3


title: Whole Lung, Control 1


title: Whole Lung, Control 4


title: placenta_perfluorocarbon [62-F2]

type: genomic

city: Washington

first: Kristen

last: Kocher

state: DC

address: 111 Michigan Ave NW

institute: Children's National Hospital

hyb_protocol: Illumina Methylation EPIC array (v1) kit

scan_protocol: NextSeq 550 with beadchip adapter

data_processing:
R/Rstudio (ChAMP, minfi, limma)
processed value definition: functional normalization of beta values extracted from raw idat files (XY, SNPs, cross-reactive probes filtered out)

label: Qiagen Gentra Puregene Tissue Kit

label_protocol: cohort name - patient ID - sample processing type

extract_protocol: fresh placentas were couriered from local delivery hospitals- flash frozen tissue DNA was extracted using the Qiagen Gentra Puregene Tissue Kit, FFPE processed tissue was extracted using Zymo Quick-DNA FFPE

tag: processing type

value: female

tag: ga at birth

value: Fibroid uterus, Group B streptococcal infection


title: Input_for_H3K9me3.24h.rep1-2


title: Input_for_H3K9me3.24h.rep1-3


title: placenta_FFPE [62-F3]

label: Zymo Quick-DNA FFPE

value: FFPE


title: Input_for_H3K9me3.24h.rep3-2

value: dTKO


title: Input_for_H3K9me3.3h.rep1-3

value: ES cells


title: Whole Lung, Control 2


title: Input_for_H3K9me3.24h.rep3-1

value: Suv39h1fl/fl ; Suv39h2-/- ; Setdb1fl/fl


title: Input_for_H3K9me3.24h.rep2-1

value: + auxin + dTAG13


title: Input_for_H3K9me3.24h.rep1-1


title: placenta_FFPErestore [62-F4]

description: Infinium HD FFPE Restore protocol used


title: Input_for_H3K9me3.24h.rep2-2


title: placenta_perfluorocarbon [60-F2]

value: Intrauterine growth restriction; early term pregnancy


title: placenta_FFPErestore [60-F4]

description: Infinium HD FFPE Restore protocol used


title: placenta_flashfrozen [62-F1]


title: Input_for_H3K9me3.1h.rep3-2


title: placenta_FFPE [60-F3]


title: Input_for_H3K9me3.1h.rep3-3


title: Input_for_H3K9me3.1h.rep2-3


title: Input_for_H3K9me3.1h.rep2-2


title: Input_for_H3K9me3.1h.rep2-1


title: placenta_flashfrozen [60-F1]


title: placenta_FFPE [59-F3]

value: male

value: unremarkable


title: placenta_FFPErestore [59-F4]

description: Infinium HD FFPE Restore protocol used


title: Input_for_H3K9me3.1h.rep1-3


title: placenta_perfluorocarbon [59-F2]


title: placenta_FFPErestore [50-F4]

description: Infinium HD FFPE Restore protocol used


title: Input_for_H3K9me3.1h.rep1-2


title: Input_for_H3K9me3.1h.rep1-1


title: placenta_perfluorocarbon [50-F2]


title: placenta_flashfrozen [59-F1]


title: Input_for_H3K9me3.12h.rep3-3


title: Input_for_H3K9me3.12h.rep3-2


title: placenta_FFPE [50-F3]


title: Input_for_H3K9me3.12h.rep3-1


title: placenta_flashfrozen [50-F1]


title: Input_for_H3K9me3.12h.rep2-3


title: Input_for_H3K9me3.12h.rep2-2


title: Input_for_H3K9me3.1h.rep3-1


title: placenta_FFPErestore [48-F4]

description: Infinium HD FFPE Restore protocol used


title: placenta_FFPE [48-F3]


title: placenta_perfluorocarbon [48-F2]


title: placenta_flashfrozen [48-F1]


title: Input_for_H3K9me3.12h.rep1-1


title: Input_for_H3K9me3.12h.rep1-3


title: placenta_FFPE [40-F3]

value: Subchorionic bleed during delivery


title: Input_for_H3K9me3.0h.rep3-3


title: placenta_perfluorocarbon [40-F2]


title: placenta_flashfrozen [40-F1]


title: placenta_FFPErestore [40-F4]

description: Infinium HD FFPE Restore protocol used


title: Input_for_H3K9me3.0h.rep3-2


title: Input_for_H3K9me3.0h.rep2-3


title: Input_for_H3K9me3.0h.rep3-1


title: HK_20180813_Leaf_tree565

city: Fukuoka

first: Atsuko

last: Miyawaki-Kuwakado

address: 744 Motooka, Nishi-ku

department: Department of Biology, Faculty of Science

country: Japan

institute: Kyushu University

data_processing:
The quantification of expression was conducted as follows.
First, quality filtering was performed using the fastp v0.20.0 with default options (Chen et al., 2018).
Second, RNA-seq reads were mapped to the reference genome (Shirasawa et al., 2019) using STAR v1.5.2 (Dobin et al., 2013).
Third, RNA-seq reads were quantified using StringTie v1.3.5 (Pertea et al., 2015).
Assembly: Cerasus x yedoensis Somei-Yoshino Genome v1.0  (Shirasawa et al., 2019, https://www.rosaceae.org/species/cerasus_x_yedoensis/genome_v1.0)
Supplementary files format and content: tab-limited text files includes TPM values of all genes for each sample
Supplementary files format and content: tab-limited text files includes TPM values of the extracted genes whose expression levels across samples satisfy sum of TPM > 1.

organism: Prunus yedoensis

source_name: Leaf

growth_protocol: Samples were taken from the sun-exposed crown (approximately 2–3 m from the ground) using long pruning shears from 11:30 to 12:30 h.

extract_protocol:
Total RNA of leaf sample was extracted in accordance with the method described in a previous study. Total RNA of bud sample was extracted using the PureLink™ Plant RNA Reagent (Thermo Fisher Scientific, Waltham, MA, USA, DNase-processed using the TURBO DNA-free kit™ (Thermo Fisher Scientific, Waltham, MA, USA) according to their protocols, and purified using the RNeasy Plant Mini Kit (Qiagen, Hilden, Germany) according to its RNA cleanup protocol.
Five to six micrograms of RNA extracted from the leaves of each sample were sent to Hokkaido System Science Co., Ltd., where a cDNA library was prepared with a NovaSeq 6000 S4 Reagent Kit, and 151 base paired-end transcriptome sequencing of each sample was conducted using an Illumina NovaSeq6000 sequencer (Illumina, San Diego, CA, USA).

treatment_protocol: For each sample, 0.2–0.4 g of tissue was preserved in a 2 ml microtube containing 1.5 ml of RNA-stabilizing reagent (RNAlater; Thermo Fisher Scientific, Waltham, MA, USA) immediately after harvesting. The samples were transferred to the laboratory within 3 hr after sampling, stored at 4 Celsius overnight and then stored at -80 Celsius until RNA extraction. During transport to the laboratory, the samples were kept in a cooler box with ice to maintain a low temperature.

value: Leaf

tag: variety

value: Somei-yoshino

tag: year of_sampling

tag: day of_sampling

tag: site of_sampling

value: Hokkaido

tag: tree id

value: Hokkaido Tree565


title: Input_for_H3K9me3.12h.rep2-1

source_name: dTKO

tag: cell line

tag: replicate


title: Input_for_H3K9me3.12h.rep1-2

tag: cell type


title: HK_20180604_Leaf_tree565

tag: tissue


title: HK_20180709_Leaf_tree565


title: HK_20180907_Leaf_tree565


title: Input_for_HP1b.0h.rep2-2

tag: treatment


title: HK_20190207_Bud_tree565

source_name: Bud

value: Bud


title: Input_for_H3K9me3.0h.rep1-1

tag: genotype


title: Input_for_H3K9me3.0h.rep1-3


title: HK_20190408_Bud_tree565


title: HK_20181203_Bud_tree565


title: HP1b.48h.rep3-3

value: Cell Signaling Technology 8676


title: Input_for_H3K9me3.0h.rep1-2


title: HK_20190307_Bud_tree565