title: Excell_DMSO_rep2_amp4

city: Durham

first: Amanda

last: Hargrove

state: NC

address: 124 Science Dr

department: Chemistry

institute: Duke University

library_source: other

data_processing:
ShapeMapper (version 2.1.5)  for SHAPE-MaP libraries, using default parameters. For DMS probing, the DMS-MaPseq program (version 1.0) was used.
Assembly: reference_sequences_for_alignment.txt
Supplementary files format and content: Text files containing the raw output of SHAPEMapper for each amplicon from each experiment (SHAPE and DMSO for a given amplicon/experiment combined into one text file)
Supplementary files format and content: For DMS-MaPseq data, text files containing the mutation rate for each amplicon (DMS and EtOH separated into two separate files).

molecule: other

source_name: LNCaP

growth_protocol: For in cellulo and ex cellulo probing, LNCaP cells were grown in RPMI 1640 media with 10% FBS. For in vitro experiments, SChLAP1 was in vitro transcribed and isolated following a native purification workflow (10.1016/bs.mie.2019.04.002)

extract_protocol:
For in cellulo probing, LNCaP cells were treated with 25 mM 5-nitroisatoic anhydride (5NIA) in 6-well plates. RNA was isolated by TRIzol followed by treatment with DNAse I. For ex cellulo probing, RNA was isolated following previous protocols (10.1021/acs.biochem.5b00977) before 5NIA treatment. For in vitro probing, 5NIA treatment occured after isolation of RNA. For in vitro and ex cellulo probing, RNA was incubated in 50 mM K-HEPES pH 7.5, 150 mM KCl, 5 mM MgCl2, and 0.1 mM EDTA final.
RNA was reverse transcribed and amplified using targeted amplicons tiling the SChLAP1 transcript. Library prep was performed using a 2-step PCR approach (10.1038/nprot.2015.103)
DNA-seq of RT-PCR-derived targeted sequencing libraries for SChLAP1. For in cellulo and ex cellulo SChLAP1, amplicons were independently barcoded. For in vitro SChLAP1, amplicons from a given condition (e.g. DMSO or SHAPE) were barcoded identically and pooled together for sequencing.

tag: cell line

value: LNCaP


title: Invitro_DMSO_rep1

status: Public on Jan 12 2024

type: SRA

country: USA

organism: Homo sapiens

tag: treatment


title: Excell_SHAPE_rep2_amp4


title: Invitro_EtOH_rep1


title: Invitro_SHAPE_rep1


title: Excell_SHAPE_rep2_amp3


title: KO1CpG2h

city: Duesseldorf

first: Stefanie

last: Scheu

state: Nordrhein-Westfalen

address: Universitaetsstr. 1

department: Institute of Medical Microbiology and Hospital Hygiene

country: Germany

institute: University of Duesseldorf

library_source: transcriptomic

data_processing:
Illumina bcl2fastq v2.17.1.4 software was used for basecalling.
Sequenced reads were trimmed for adaptor sequence (Illumina TrueSeq) and quality trimmed (using the default parameters: bases below Q13 were trimmed from the end of the reads, ambiguous nucleotides maximal 2), then mapped to mm10 whole genome using CLC Genomics Workbench v11.0.1 with standard parameters.
Counts per million (cpm) were calculated using EdgeR on usegalaxy.org with standard parameters. Multi-group comparisons were calculated using edgeR after grouping of samples (three biological replicates each) according to their respective experimental condition and filtering of low expressing genes based on a formula from Chen, Y., Lun, A.T., and Smyth, G.K. (2016). From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline. F1000Res 5, 1438. . The resulting p values were corrected for multiple testing by FDR. A p value of ≤ 0.05 was considered significant. Cut-off for differential gene expression was set to 2 fold.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include cpm values for each sample.

molecule: total RNA

organism: Mus musculus

source_name: bone marrow

growth_protocol: BM-derived Flt3-L cultured pDCs were generated as previously described (Scheu et al, PNAS 2008).

extract_protocol:
purification protocol: For RNA-Seq, BM-derived pDCs (CD3-CD19-CD11c+CD11blowB220+SiglecH+mPDCA1+) from wild-type and Batf-deficient mice were FACS purified using FACS Aria III (BD).
Libraries were prepared according to Illumina® ‘TruSeq Stranded mRNA Library Prep Kit’. Briefly, 200 ng total RNA were used for mRNA capturing, fragmentation, the synthesis of cDNA, adapter ligation and library amplification. Bead purified libraries were normalized and finally sequenced on the HiSeq 3000/4000 system (Illumina Inc. San Diego, CA, USA), following the manufacturer's protocols, with a read setup of 1 × 150 bp.

treatment_protocol: The WT and Batf-deficient pDCs were left untreated or stimulated with 1µM CpG 2216 (Tib Molbiol, Nr. 930507l) complexed to transfection reagent DOTAP (Roche) for 2, 6 or 12 hours. RNA was isolated by using NucleoSpin II RNA mini kit (Macherey- Nagel) and subjected to RNA-Seq.

tag: tissue

value: bone marrow

tag: strain

tag: cell type

value: pDC

tag: condition

value: CpG 2h

tag: genotype

value: Batf-deficient


title: Excell_DMSO_rep2_amp3


title: Excell_SHAPE_rep2_amp2


title: Tcell, DddA-G1404_base-editing_panelDddA, biol. rep. 4

city: Richmond

first: Jessica

last: Davis

state: CA

address: 501 Canal Blvd

institute: Sangamo Therapeutics

description: IDT's rhAmpSeq Design Tool for CRISPR gene editing analysis was used to design multiplexed primer pools. Libraries were generated using each primer pool and IDT's rhAmpSeq CRISPR Library Kit along with rhAmpSeq Index Primers. Samples were run according to manufacturer’s instructions.  Forward and reverse reads were merged with SeqPrep. Reads were then demultiplexed followed by application of quality and amplicon filters. Amplicons within each sample were demultiplexed using an in-house script using the first 23 bp of reads. Processed data file contains the # of reads per amplicon and the frequency of bases per amplicon position across these reads. The percent of reads per amplicon that matched the expected hg38 amplicon sequence is indicated in the perc_non_indel column.

library_source: genomic

data_processing:
Basecalling: Illumina Real Time Analysis (RTA) v3
Demultiplexing: Illumina bcl2fastq v2.20.0.422, with parameters “--no-lane-splitting --barcode-mismatches 0”
Adaptor trim and read merging: SeqPrep v1.3.2, with parameters “-y I”
Sequence read quality filter: Custom script with minimum quality threshold of 14 over all bases
Indel detection and quantization: Custom script where reads are aligned to the intended hg38 amplicon using the Biopython v1.78 pairwise2.globalmd aligner with parameters match=8, mismatch=-5, gapopenA=-5, gapextendA=-0.1, gapopenB=-5, gapextendB=-0.1. Then indels are called based on alignment gaps. Bowtie v2 is run to remove sequences that map to an unintended locus. Then a position weight matrix is generated from the set of alignments using the “wildtype” sequences that had no indels.
Assembly: hg38
Supplementary files format and content: Excel sheet of all amplicons measured across all samples that lists reads measured per amplicon, percent matching the expected hg38 amplicon sequence, and frequency of bases per position.
Library strategy: Amplicon sequencing

molecule: genomic DNA

source_name: Peripheral Blood Leukopak

growth_protocol: Cells were grown in X-Vivo 15 Serum-free Hematopoietic Cell Media (Lonza) with 20 mM HEPES (Gibco), 2 mM GlutaMax (Gibco), 1 mM Sodium Pyruvate (Corning), 1% MEM Vitamins Solution (Gibco), 5% Human AB Serum Heat-Inactivated (Valley Biomedical, #HP1022HI), and 100 IU/mL ProLeukin, IL-2

extract_protocol:
Genomic DNA was isolated using QuickExtract to a final concentration of 1440 cells/µL
Potential base edited sites were amplified from genomic material isolated from transfected T cells using the rhAmpSeq™ CRISPR Library Kit (IDT). 6.4 µL of quick extract solution was used with 1 µL DMSO in the first rhAmpSeq™ PCR reaction, adjusting the total reaction volume to 25 µL. 10.2 µL of PCR 1 was used with 0.8 µL of DMSO in the second PCR reaction.

treatment_protocol: Cells were activated for 72 h using Dynabeads human T-activator CD3/CD28 (cells to beads ratio of 1:3; Life Technologies) and IL-2 (100 IU ml−1; Thermo Fisher) without antibiotics. BTX H-200 transfection system (voltage 250V, frequency 4ms, # pulse 1up to 12 depending on columns to be fed, set# of pulse at 1) was used to transfect mRNA for the ZF-base editors

value: Peripheral Blood Leukopak

value: Peripheral Blood CD4+/CD8+ T cells

tag: age

tag: Sex

value: male

tag: biomaterial provider

value: Stemcells Technologies


title: R9449

city: Singapore

first: Nicholas

last: Ang

address: 8a Biomedical Grove, Singapore 138648

country: Singapore

institute: Singapore Immunology Network (SIgN)

data_processing:
FASTQ files were mapped using STAR to GRCm38 genome build
Gene counts were obtained using featureCounts on GencodevM20 annotations
Assembly: GRCm38
Supplementary files format and content: gene_counts

source_name: PBMC

growth_protocol: 10% FBS in RPMI media supplemented with HEPES

extract_protocol:
Joint footpads were excised 6 days post-infection (dpi) and were digested in RPMI (Hyclone) with 10% heat-inactivated Fetal Bovine Serum (FBS; Biowest), supplemented with DNase I (50 mg/mL; Roche Applied Science), collagenase IV (20 mg/mL; Sigma-Aldrich), and dispase (2 U/mL; Invitrogen). The digestion was performed with slight agitation at 37°C for 3 hours before being filtered through a cell strainer (40 μm pore size). Red blood cells were subsequently lysed and cells were purified with Percoll solution (Sigma-Aldrich) diluted (35% vol/vol) in RPMI FBS. After the digestion and purification steps, joint-footpad cells were stained the LIVE/DEAD determination dye (Thermo Fisher Scientific) for 20 minutes. Thereafter, the cells were stained with the following antibodies: Rat anti-mouse CD45 (clone: 30-F11), Rat anti-mouse CD11b (Clone: M1/70), Rat anti-mouse Ly6C (clone: HK1.4), Rat anti-mouse Ly6G (clone: 1A8), Mouse anti-mouse CD64 (clone: X54-4/7.1) and Rat anti-mouse MHCII (clone: M5/114.15.2). All antibodies used for staining were purchased from BD Horizon, BioLegend or ThermoFisher Scientific. Stained cells were washed, resuspended in an appropriate buffer and the target cells of CD64+MHCII- and CD64+MHCII+ phenotype were sorted with FACS Aria III sorter (BD Biosciences).
Total RNA was extracted using the Arcturus PicoPure RNA Isolation kit (Thermo Fisher Scientific) according to the manufacturer's protocol. All mouse RNAs were analyzed on Agilent Bioanalyzer for quality assessment with RNA Integrity Number (RIN) ranging from 8.8 to 9.6 with a median of 9.5. cDNA libraries were prepared using 2 ng of total RNA and 1 µl of a 1:50,000 dilution of ERCC RNA Spike in Controls (Thermo Fisher Scientific) using the SMARTSeq v2 protocol 75 with the following modifications: 1. Addition of 20 µM template switching oligos (TSO); 2. Use of 200 pg cDNA with 1/5 reaction of Illumina Nextera XT kit (Illumina). The length distribution of the cDNA libraries was monitored using a DNA High Sensitivity Reagent Kit on the Labchip (Perkin Elmer). All samples were subjected to an indexed paired-end sequencing run of 2x151 cycles on an Illumina HiSeq 4000 system (~26 samples/lane).

treatment_protocol: Infected with DiD-labelled dengue virus

tag: mhcii


title: R9448


title: R9450


title: Tcell, DddA-G1404_base-editing_panelTDD14, biol. rep. 3


title: Excell_SHAPE_rep2_amp1


title: Excell_DMSO_rep2_amp2


title: Excell_DMSO_rep2_amp1


title: R9446


title: Tcell, DddA-G1404_base-editing_panelDddATDD14, biol. rep. 3


title: Excell_SHAPE_rep1_amp4


title: R9445


title: Excell_SHAPE_rep1_amp3


title: Excell_DMSO_rep1_amp4


title: Excell_DMSO_rep1_amp3


title: Tcell, DddA-G1404_base-editing_panelDddA, biol. rep. 3


title: R9444


title: Tcell, DddA-G1404_base-editing_panelDddATDD14, biol. rep. 4


title: R9447


title: Invitro_DMS_rep1


title: Tcell, DddA-G1404_base-editing_panelTDD14, biol. rep. 2


title: Excell_SHAPE_rep1_amp2


title: Excell_SHAPE_rep1_amp1


title: Tcell, DddA-G1404_base-editing_panelDddA, biol. rep. 2


title: Tcell, DddA-G1404_base-editing_panelDddATDD14, biol. rep. 2


title: Incell_DMSO_rep2_amp4


title: Incell_SHAPE_rep2_amp4


title: normal rats with electroacupuncture, No.29

city: Shanghai

first: Ming-Shu

last: Xu

address: No. 650 South Wanping Road, Xuhui District

department: Shanghai Research Institute of Acupuncture and Meridian

country: China

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
CLC Genomics Workbench v 11.0.1
mRNA-seq reads were trimmed from 3' end until the final base had a quality score > 20, using seqtk v1.0-r82-dirty, discarding reads left with < 25 bp
Trimmed sequence reads were mapped to Rnor_6.0 using Hisat2(version:2.0.4)
The number of Fragments of each gene after Hisat2 comparison was counted by Stringtie (version:1.3.0), and then normalized by the original mean of M Values (TMM) method. Finally, the FPKM value of each gene was calculated by Perl script.
Assembly: Rnor_6.0

organism: Rattus norvegicus

source_name: motor cortex

extract_protocol:
Total RNA was extracted following the manufacturer’s instructions and checked for a RIN number to inspect RNA integrity by an Agilent 4200 TapeStation (Agilent technologies, Santa Clara, CA, US). Qualified total RNA was further purified by RNAClean XP Kit (Cat A63987, Beckman Coulter, Inc. Kraemer Boulevard Brea, CA, USA) and RNase-Free DNase Set (Cat#79254, QIAGEN, GmBH, Germany).
According to the instructions of the experiment, the purified Total RNA was separated into mRNA, fragmented, first-strand cDNA synthesis, second-strand cDNA synthesis, end repair, adding A to the 3 'end, ligating connector, enrichment and other steps to complete the construction of sequencing sample library.

value: electroacupuncture

tag: time

value: 8 weeks

value: motor cortex

value: Sprague-Dawley


title: normal rats with electroacupuncture, No.53


title: Excell_DMSO_rep1_amp1


title: Incell_DMSO_rep2_amp3


title: normal rats with electroacupuncture, No.26


title: Incell_SHAPE_rep2_amp3


title: Tcell, DddA-G1404_base-editing_panelTDD14, biol. rep. 1


title: Incell_SHAPE_rep2_amp2


title: Tcell, DddA-G1404_base-editing_panelDddATDD14, biol. rep. 1


title: Excell_DMSO_rep1_amp2


title: cerebral ischemia and reperfusion with electroacupuncture group, No.33


title: Incell_DMSO_rep2_amp2


title: Incell_SHAPE_rep2_amp1


title: Incell_DMSO_rep2_amp1


title: R9443


title: Tcell, DddA-G1404_base-editing_panelDddA, biol. rep. 1


title: cerebral ischemia and reperfusion with electroacupuncture group, No.24-4


title: Incell_SHAPE_rep1_amp4


title: Tcell, DddA-G1397_base-editing-nicking_panelTDD14, biol. rep. 4


title: Tcell, DddA-G1404_base-editing_panelTDD14, biol. rep. 4


title: Incell_DMSO_rep1_amp4


title: Tcell, DddA-G1397_base-editing-nicking_panelDddATDD14, biol. rep. 4


title: Incell_SHAPE_rep1_amp3


title: cerebral ischemia and reperfusion with electroacupuncture group, No.12


title: Incell_SHAPE_rep1_amp2


title: Incell_DMSO_rep1_amp3


title: cerebral ischemia and reperfusion group, No.35

value: cerebral ischemia and reperfusion


title: Tcell, DddA-G1397_base-editing-nicking_panelDddATDD14, biol. rep. 3


title: Incell_DMSO_rep1_amp2


title: cerebral ischemia and reperfusion group, No.19


title: Incell_DMSO_rep1_amp1


title: cerebral ischemia and reperfusion group, No.70


title: fb-Col0-MNase

city: Los Angeles

first: Shuya

last: Wang

state: California

address: 610 Charles E Young Dr S

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
ChIP-seq: Quality control was initially run to filter out the low-quality reads. Trim Galore (Babraham Institute) was used to remove the Illumina adapters. Then the reads were aligned to the Arabidopsis reference genome (TAIR10) using the bowtie2, allowing only uniquely mapped reads with perfect matches. MarkDuplicates.jar (picard-tools suite, Broad Institute) was used to remove the PCR duplicates. Bigwig files were generated using deeptools (v 3.0.2) bamCoverage with the options -- normalizeUsing RPGC and --binSize 10. For correlation analysis between the ChIP-seq signal and mCG density, the samples were normalized to the no-FLAG control using bamCompare with the options --scaleFactorsMethod readCount, --binSize 10, and --operation log2. The normalized ChIP-seq signal and CG methylation percentages were summarized into 400 bp bins. We took a random subset covering 10% of all genomic regions for the correlation analysis. The data were plotted using the R package ggplot with the option geom_smooth. ChIP-seq peaks were called using MACS2 (v2.1.1) using an FDR cutoff of 0.05. The FLAG-associated hyperchipable regions, defined as peaks called in the anti-FLAG Col-0 controls, were removed from the peak files. Heterochromatin peaks were defined as peaks intersecting with TAIR10 pericentromeric regions using bedtools intersect55 function from deeptools (v 3.0.2).
Mnase-seq: The reads of low quality were fileterd out and the adaptors were trimmed with Trim Galore (Babraham Institute). Next the processed reads were aligned to TAIR10 using bowtie2 keeping reads smaller than 2000 bp and allowing only uniquely mapped reads with perfect matches. Then PCR duplicates were removes using MarkDuplicate (picard-tools suit, Broad Institute) and bigwig files were generated using bamCoverage.
RNA-seq: RNAs-seq reads were filtered according to quality score and were trimmed out Illumina adaptors using Trim Galore (Babraham Institute). Then the filtered reads were mapped to the Arabidopsis reference genome (TAIR10) using STAR. We allowed only uniquely mapped reads with less than 5% of mismatches. Bigwig files for genome browser visualization were generated using bamCoverage with the options -- normalizeUsing RPGC and --binSize 10. HTSeq was used to obtain the read counts for TE and our previously reannotated pollen transcripts. DESeq2 was used to perform the differential analysis with the cutoff padj < 0.05 and |log2FC| > 1. We used ggplot to generate all the related plots.
snRNA-seq: The analysis was performed following the published pipeline (Ichino et. al). In brief, Cell Ranger 6.1.1 was used to process the raw data following the published pollen transcriptome reannotations. With Cell Ranger results, SoupX and Seurat were used to remove the ambient RNA and filter out the cells detected with less than 200 genes. The data were normalized and scaled following the published settings. After the normalization, PCA analysis was performed (npc=20). DoubletFinder v3 was used to identify doublets and find.pK was used to obtain the ideal pK parameters for each sample. The percentage of doublets removed and the pK values were summarized in Table S1. Col-0 and mbd2 datasets were integrated with Seurat v4 FindIntegrationAnchors and IntegrateData using default settings. The data was scaled, and PCA analysis was performed (npcs=40). Then clustering analysis was done using FindNeighbors and FindClusters functions. The number of cells per cluster is summarized in Table S1. In addition, the markers for each cluster were obtained with FindAllMarker using the integrated dataset. Finally, DEG analysis was performed on individual clusters. We specifically focused on activated TEs using the cutoff padj < 0.05 & |avg_log2FC| > 0.25. In this analysis, the following clusters were groups: VN_bi and VN_late_bi, VN_tri and VAN_mature. The TE expression heatmap was generated using Seurat function AverageExpression.
WGBS: WGBS were filtered and removed with Illumina adaptors using Trim Galore (Babraham Institute). Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. Bismark51 was used to map the reads to the Arabidopsis reference genome (TAIR10) and obtain the methylation percentages for each cytosine. We used ViewBS to generate the plots showing the genome-wide methylation information across genotypes.
Assembly: TAIR10
Supplementary files format and content: bigwig: ChIP-seq, RNA-seq, and MNase-seq intensity
Supplementary files format and content: narrowPeak: peak file
Supplementary files format and content: tsv.gz and matrix.gz: tab-seprated values files and matrix files
Supplementary files format and content: bed and bedGraph for WGBS: methylation ratio

organism: Arabidopsis thaliana

source_name: floral tissue

growth_protocol: Arabidopsis thaliana plants in this study were Col-0 ecotype and were grown under long-day condition (16h light and 8h dark).

extract_protocol:
For ChIP-seq experiments, 1~2 g of unopen flower buds or 2~4 g rosette leaves from the T2 lines were collected. For RNA-seq, rosette leaf tissues from 4- to 5-week-old plants, 500 uL of open flowers, 1 inflorescence, or 3 individuals of 10-day-old seedlings were harvested. For WGBS, rosette leaf tissues from 4- to 5-week-old plants, 1000 uL of open flowers, or 5 individuals of 10-day-old seedlings were pooled as one biological replicate. For snRNA-seq, 5 mL of unopen flower buds and open flowers from the same inflorescence were harvested. For MNase-seq, 0.5 g of unopen flower buds were freshly harvested.
ChIP-seq and Mnase-seq libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN, 0344NB-A01) following the manufacturer’s instructions. Whole genome bisulfite sequencing libraries were prepared using the Nugen Ultralow Methyl Kit. RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina). SnRNA-seq libraries were prepared with 10x Genomics Chromium Single Cell 30 Reagent Kit v3.
ChIP-seq, RNA-seq, snRNA-seq, WGBS, and MNase-seq

treatment_protocol: For 5AZA treatment, 100mg of 5AZA (Sigma) was first dissolved in 10ml of DMSO. Then the 5AZA stock was added to MS agar plates to reach 100uM final concentration. Control plates were only added with the same volume of DMSO. Seedlings of the Col-0 and mbd2 CRISPR mutant were harvested after 10-day incubation under long-day conditions.

value: floral tissue

value: WT

tag: ecotype


title: Tcell, DddA-G1397_base-editing-nicking_panelDddA, biol. rep. 4


title: WGBS-mbd2CR-DMSO-rep2

source_name: seedling

value: seedling

value: mbd2 CRISPR mutant


title: Tcell, DddA-G1397_base-editing-nicking_panelDddA, biol. rep. 3


title: WGBS-mbd2CR-DMSO-rep1


title: Tcell, DddA-G1397_base-editing-nicking_panelDddATDD14, biol. rep. 2


title: Tcell, DddA-G1397_base-editing-nicking_panelTDD14, biol. rep. 2


title: WGBS-mbd2CR-5AZA-100uM-rep2


title: Tcell, DddA-G1397_base-editing-nicking_panelDddA, biol. rep. 2


title: Tcell, DddA-G1397_base-editing-nicking_panelTDD14, biol. rep. 3


title: Incell_SHAPE_rep1_amp1

value: LNCaP


title: WGBS-mbd2CR-5AZA-100uM-rep1


title: WGBS-Col0-DMSO-rep2


title: Tcell, DddA-G1397_base-editing-nicking_panelDddATDD14, biol. rep. 1


title: WGBS-Col0-DMSO-rep1


title: Tcell, DddA-G1397_base-editing-nicking_panelDddA, biol. rep. 1


title: Bladder cancer tissue 63

type: genomic

city: Beijing

first: HUANG

last: CHEN

address: Yinghuadongjie 2#, Chaoyang District, Beijing

department: Department of Etiology and Carcinogenesis

institute: China-Japan Friendship Hospital

description: Human Genomic DNA from Fresh-frozen tissue of bladder cancer

hyb_protocol: Differentially labeled patient and reference DNAs were combined and hybridized to Agilent Human Genome CGH 244A microarrays at 65℃ for 40 hr. Four washing steps were completed with Agilent Oligo CGH washes: Wash Buffer 1 at room temperature for 5 min, Wash Buffer 2 at 37℃ for 1 min, an acetonitrile rinse at room temperature for 1 min and a 30 sec wash at room temperature in Agilent’s Stabilization and Drying Solution.

scan_protocol: Arrays were scanned using an Agilent Technologies Scanner G2505B US22502629 (Agilent Technologies, Inc).

data_processing: Data were obtained using Agilent Feature Extraction Software and analyzed with Agilent Genomic Workbench 6.0 Software using the statistical algorithms z-score and common aberration detection method 2 (ADM-2) with sensitivity thresholds at 2.5 and 6.0, respectively, and a moving average window of 0.2 Mb.

source_name: bladder cancer tissue

label_protocol: Same amounts (1.5㎍) of patient DNA and gender-matched reference DNA were digested. The digested DNAs were labeled by random priming with Cy3-dUTP (reference DNA) and Cy5-dUTP (patient DNA) using Agilent Labeling KIT.

extract_protocol: Genomic DNAs from tumor tissue was extracted from the fresh tissue by manual microdissection, standard proteinase K digestion, using QIAamp DNA Micro Kit #56304 (Qiangen, Germany).

tag: ttumor stage

tag: gender

value: m

tag: age/y


title: Bladder cancer tissue 65


title: Bladder cancer tissue 60


title: Bladder cancer tissue 57


title: Tcell, DddA-G1397_base-editing_panelTDD14, biol. rep. 4


title: Bladder cancer tissue 55


title: Bladder cancer tissue 62


title: Bladder cancer tissue 52

value: f


title: Bladder cancer tissue 58

value: ta


title: Tcell, DddA-G1397_base-editing-nicking_panelTDD14, biol. rep. 1

value: Peripheral Blood Leukopak


title: Tcell, DddA-G1397_base-editing_panelDddATDD14, biol. rep. 4

value: Peripheral Blood CD4+/CD8+ T cells


title: WGBS-Col0-5AZA-100uM-rep1


title: Bladder cancer tissue 61


title: Tcell, DddA-G1397_base-editing_panelDddA, biol. rep. 4

value: male


title: WGBS-mbd2-CR-2

source_name: mature pollen

value: mature pollen


title: Bladder cancer tissue 53


title: Bladder cancer tissue 50


title: WGBS-mbd2-CR-1


title: WGBS-Col0-5AZA-100uM-rep2


title: Bladder cancer tissue 56


title: Tcell, DddA-G1397_base-editing_panelTDD14, biol. rep. 3

value: Stemcells Technologies


title: WGBS-Col0-2


title: Bladder cancer tissue 54


title: Bladder cancer tissue 51


title: Tcell, DddA-G1397_base-editing_panelDddA, biol. rep. 3


title: mbd2Shuya

description: 10x Genomics

source_name: floral tissue and mature pollen

value: floral tissue and mature pollen


title: WGBS-Col0-1


title: Bladder cancer tissue 47


title: Bladder cancer tissue 46


title: Bladder cancer tissue 49


title: Col0Shuya

description: 10x Genomics


title: pollen-col0-for-mbd2adcp1-rep3


title: Bladder cancer tissue 42


title: Bladder cancer tissue 59


title: Bladder cancer tissue 64


title: Tcell, DddA-G1397_base-editing_panelTDD14, biol. rep. 2


title: Bladder cancer tissue 43


title: Bladder cancer tissue 38


title: Tcell, DddA-G1397_base-editing_panelDddATDD14, biol. rep. 2


title: Bladder cancer tissue 45


title: Bladder cancer tissue 39


title: Tcell, DddA-G1397_base-editing_panelDddATDD14, biol. rep. 3


title: Bladder cancer tissue 41


title: Bladder cancer tissue 35


title: Bladder cancer tissue 40


title: Tcell, DddA-G1397_base-editing_panelTDD14, biol. rep. 1


title: Bladder cancer tissue 48


title: Tcell, DddA-G1397_base-editing_panelDddATDD14, biol. rep. 1


title: Tcell, DddA-G1397_base-editing_panelDddA, biol. rep. 2


title: Bladder cancer tissue 44


title: Bladder cancer tissue 37


title: Bladder cancer tissue 36


title: Bladder cancer tissue 34


title: Bladder cancer tissue 31


title: Bladder cancer tissue 32


title: pollen-col0-for-mbd2adcp1-rep2


title: Bladder cancer tissue 29


title: Bladder cancer tissue 30


title: pollen-col0-for-mbd2adcp1-rep1


title: forebrain_sd18_rep8

type: RNA

city: Lausanne

first: Leonore

last: Wigger

address: Amphipôle Building

country: Switzerland

institute: Swiss Institute of Bioinformatics

hyb_protocol: The labeled RNAs were hybridized to a Mouse miRNA Microarray (G4472B, Agilent Technologies) for 20h at 55°C with rotation. A total of 16 arrays (i.e., 8 SD and 8 control animals) were used.

scan_protocol: After hybridization and washing, the arrays were scanned with an Agilent microarray scanner using high dynamic range settings as specified by the manufacturer. Agilent Feature Extraction Software was used to extract the data.

data_processing: Agilent Genespring software, quantile normalization was used to normalize expression levels on 15 miRNA samples that passed QC.

source_name: forebrain, sleep deprived

label_protocol: Total RNA (100ng) was dephosphorylated with calf intestine alkaline phosphatase (GE Healthcare Europe GmbH), denaturated with dimethyl sulfoxide, and labeled with pCd-Cy3 using T4 RNA ligase (GE Healthcare Europe GmbH).

extract_protocol: Brain tissues dissected from SD and control mice were homogenized in QIAzol Lysis Reagent (Qiagen). RNA was extracted and purified using the QIAGEN miRNeasy mini kit 50 (Qiagen) according to the manufacturer instructions. All RNA sample amounts were measured with a NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific) and the quality of RNA samples was verified on Agilent 2100 bioanalyzer chips (Agilent technologies).

treatment_protocol: Half of the mice were submitted to a 6 hour SD performed by the so-called “gentle handling protocol”, starting at light onset (Zeitgeber Time 0). The other half was left undisturbed and used as control. At the end of the SD (ZT6), animals from both groups were sacrificed and forebrain was dissected and collected. For forebrain dissection, the cerebellum and brainstem were removed from whole brain, and the remaining part was considered as forebrain.

value: forebrain

value: sleep-deprived


title: forebrain_sd16_rep7


title: Bladder cancer tissue 28


title: Bladder cancer tissue 33


title: Bladder cancer tissue 26


title: pollen-mbd2-rep3

value: mbd2 T-DNA mutant


title: Bladder cancer tissue 27


title: pollen-mbd2adcp1-rep3

value: mbd2 adcp1 mutant


title: Bladder cancer tissue 25


title: Bladder cancer tissue 23


title: forebrain_sd14_rep6


title: pollen-mbd2adcp1-rep2


title: Bladder cancer tissue 22


title: Bladder cancer tissue 21


title: pollen-mbd2-rep1


title: pollen-mbd2adcp1-rep1


title: forebrain_sd10_rep5


title: Bladder cancer tissue 19


title: Bladder cancer tissue 18


title: pollen-adcp1-rep3

value: adcp1 CRISPR mutant


title: Bladder cancer tissue 17


title: Bladder cancer tissue 24


title: pollen-adcp1-rep2


title: pollen-mbd2-rep2


title: Bladder cancer tissue 16


title: forebrain_sd08_rep4


title: forebrain_sd06_rep3


title: pollen-adcp1-rep1


title: Bladder cancer tissue 14


title: forebrain_sd02_rep1


title: Bladder cancer tissue 15


title: Bladder cancer tissue 20


title: forebrain_ctl17_rep8

source_name: forebrain, control condition

value: control


title: fb-col0-for-mbd2adcp1-rep2

value: floral tissue

value: WT


title: forebrain_ctl15_rep7


title: fb-col0-for-mbd2adcp1-rep1


title: Bladder cancer tissue 12


title: Bladder cancer tissue 11

value: m


title: Bladder cancer tissue 10


title: Bladder cancer tissue 13


title: forebrain_ctl12_rep6


title: fb-col0-for-mbd2adcp1-rep3


title: Bladder cancer tissue 9

value: f


title: fb-mbd2adcp1-rep3


title: Bladder cancer tissue 7


title: Bladder cancer tissue 8


title: forebrain_ctl11_rep5


title: Bladder cancer tissue 6


title: fb-mbd2adcp1-rep2


title: forebrain_ctl09_rep4


title: IRF3ko_120x_r2

first: Stephen

last: Smale

state: Ca

address: 6-730 MRL 675 Charles E. Young Drive South

department: MIMG

institute: University of California Los Angeles

data_processing:
ATAC-seq libraries were sequenced on an Illumina HiSeq 2000.
Adapter sequences were removed with cutadapt -a CTGTCTCTTATA -m 23 and all fastq files were mapped using Bowtie2.
The reads were excluded from downstream analysis if unmapped to index genome, multiple alignments, in duplicate, aligned to mitochondrial genome. or contiguous sequences.
Genomic sites enriched with aligned reads were identified and called peaks by using MACS2. The called peaks from each sample were merged to generate a combined probe list using HOMER.
All the sorted bam files were imported into seqMonk for quantification. Raw reads among each combined probe site were converted to reads per kilobases of the probe and per million reads of total read counts (RPKM).
Assembly: mm9
Supplementary files format and content: bedGraph files for each sample were generated from sorted bam files using HOMER to represent the reads coverage genome-widely.

source_name: bone marrow-derived macrophages

growth_protocol: Bone marrow precursors were grown in CMG media containing FBS for 6 days prior to stimulation.

extract_protocol:
50,000 mature BMDM were centrifuged and washed with PBS once. The cell pellet was resuspended with cold hypotonic lysis buffer. The lysate was centrifuged and the supernatant was discarded. The crude nuclei were treated with transposition reaction mix (50ul) containing 2.5ul Tn5 transposase (Nextera) and incubated in a 37oC thermomixer with 1000RPM mixing for 30 minutes. The transposed DNA was then cleaned up with a Qiagen Minelute PCR Purification Kit.
The transposed DNA was amplified by a non-saturating PCR containing primer 1 and barcode primer 2 provided in the published protocols by Buenristro et al. The amplified DNA was size selected on the gel from 100bp to 1000bp and purified with a Qiagen QIAquick Gel Extraction Kit. The selected DNA library was quantified by Qubit and Agilent Bioanalyzer High-Sensitivity DNA Analysis Kit.

treatment_protocol: Bone-marrow derived macrophages from C57/B16 and Irf3-/- mice were stimulated with lipid-A for 0, 30, 60 or 120 minutes. Additionally, WT and Irf3-/- macrophages were preincubated with cycloheximide for 15 minutes and treated with lipid A for 120 minutes.

value: bone marrow-derived macrophages

tag: stimulus

value: lipidA + cycloheximide

tag: time (minutes)


title: IRF3ko_120x_r1


title: fb-mbd2adcp1-rep1


title: forebrain_ctl07_rep3

tag: treatment


title: Bladder cancer tissue 4


title: IRF3ko_120_r2

value: lipidA


title: Bladder cancer tissue 3


title: Bladder cancer tissue 5


title: Bladder cancer tissue 1


title: Bladder cancer tissue 2

value: ta


title: fb-mbd2-rep3

tag: tissue


title: Tcell, DddA-G1397_base-editing_panelDddA, biol. rep. 1

value: Peripheral Blood Leukopak

value: Peripheral Blood CD4+/CD8+ T cells

value: male


title: forebrain_ctl03_rep2

tag: strain

value: forebrain


title: fb-mbd2-rep2


title: BMDM_120x_r1

tag: cell type


title: IRF3ko_0_r2

value: unstimulated


title: IRF3ko_0_r1


title: BMDM_120x_r2


title: negative liver cells isolated from recovery mice

first: Zebin

last: Mao

state: Beijing

address: No. 38 Xueyuan Road, Haidian District, Beijing

department: Department of Biochemistry and Molecular Biology

institute: Peking University

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Raw reads were processed to generate gene expression profiles using an in-house pipeline. Briefly, after filtering all read one sequences lacking a poly T tail, cell barcodes, and UMI were extracted. Adapters and poly-A tails were trimmed (fastp V1) before aligning read two to GRCh38 with ensemble version 92 gene annotation (fastp 2.5.3a and feature Counts 1.6.2). Reads with the same cell barcode, UMI, and gene were grouped to calculate the number of UMIs per gene per cell. The UMI count tables of each cellular barcode were used for further analysis.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: liver

extract_protocol:
After perfusion with EGTA, Pronase (14 mg per mouse), and Collagenase (3.7 U per mouse), liver specimens were further digested by Pronase/Collagenase and purified via Nycodenz density gradient centrifugation.
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics)

value: liver

value: non-parenchymal cells

value: Col1a2-CreERT2; R29RtdTomato reporter mice


title: negative liver cells isolated from MCDHF-injury mice

description: 10x Genomics

value: Col1a2-CreERT2; R28RtdTomato reporter mice


title: forebrain_ctl01_rep1

value: control


title: fb-mbd2-rep1

value: floral tissue

value: mbd2 T-DNA mutant


title: BMDM_120_r5

value: wildtype


title: IRF3ko_120_r1

value: bone marrow-derived macrophages


title: fb-adcp1-rep3

value: adcp1 CRISPR mutant


title: BMDM_120_r4

value: lipidA


title: BMDM_120_r3


title: fb-adcp1-rep2


title: BMDM_120_r2


title: positive liver cells isolated from recovery mice

description: 10x Genomics

value: Col1a2-CreERT2; R27RtdTomato reporter mice


title: positive liver cells isolated from MCDHF-injury mice

description: 10x Genomics

value: Col1a2-CreERT2; R26RtdTomato reporter mice


title: fb-adcp1-rep1


title: BMDM_60_r2


title: ATAC-Seq KO2CpG2h

data_processing:
Reads were aligned using the BWA algorithm (mem mode; default settings). Duplicate reads were removed, only reads mapping as matched pairs and only uniquely mapped reads (mapping quality >= 1) were used for further analysis. Alignments were extended in silico at their 3’-ends to a length of 200 bp and assigned to 32-nt bins along the genome. The resulting histograms (genomic “signal maps”) were stored in bigWig files. Peaks were identified using the MACS 2.1.0 algorithm at a cut off of p-value 1e-7, without control file, and with the –nomodel option. Peaks that were on the ENCODE blacklist of known false ChIP-Seq peaks were removed. Signal maps and peak locations were used as input data to Active Motifs proprietary analysis program, which creates Excel tables containing detailed information on sample comparison, peak metrics, peak locations and gene annotations. For differential analysis, reads were counted in all merged peak regions (using Subread), and the replicates for each condition were compared using DESeq2.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include average values for each sample and one file containing the peak values and associated genes for each merged region.

extract_protocol:
For ATAC-Seq, BM-derived pDCs (CD3-CD19-CD11c+CD11blowB220+SiglecH+mPDCA1+) were FACS purified using FACS Aria III (BD).
Cells were harvested and frozen in culture media containing FBS and 5% DMSO. Cryopreserved cells were sent to Active Motif to perform the ATAC-seq assay. The cells were then thawed in a 37°C water bath, pelleted, washed with cold PBS, and tagmented as previously described (Buenrostro et al., 2013), with some modifications based on (Corces et al., 2017). Briefly, cell pellets were resuspended in lysis buffer, pelleted, and tagmented using the enzyme and buffer provided in the Nextera Library Prep Kit (Illumina). Tagmented DNA was then purified using the MinElute PCR purification kit (Qiagen), amplified with 10 cycles of PCR, and purified using Agencourt AMPure SPRI beads (Beckman Coulter). Resulting material was quantified using the KAPA Library Quantification Kit for Illumina platforms (KAPA Biosystems), and sequenced with PE42 sequencing on the NextSeq 500 sequencer (Illumina).

treatment_protocol: The pDCs were left untreated or stimulated with 1µM CpG 2216 (Tib Molbiol, Nr. 930507l) complexed to transfection reagent DOTAP (Roche) for 2 hours.

value: pDC

tag: condition

value: CpG 2h

value: Batf-deficient


title: BMDM_60_r1

tag: genotype


title: BMDM_30_r2


title: pollen-mbd56-3

value: mature pollen

value: mbd56 mutant


title: BMDM_30_r1


title: ATAC-Seq KO1CpG2h


title: pollen-mbd56-2


title: BMDM_0_r3


title: ATAC-Seq KO2

value: naïve


title: pollen-mbd56-1


title: BMDM_0_r2


title: BMDM_0_r1


title: BMDM_120_r1


title: pollen-mbd256-2

value: mbd256 mutant


title: Quintuple mutant source leaves biol. rep. 3

city: Wuerzburg

first: Christoph

last: Weiste

address: Julius-von-Sachs Platz 2

department: Julius-von-Sachs Institute

institute: Julius-Maximilians-Universitaet

data_processing:
Reads of each sample were mapped to the Arabidopsis genome as reference using salmon v0.7.2. In all samples, between 70 and 85 % of the reads could be unambiguously mapped. Only mapped reads were used to calculate the relative abundance in transcripts per million (TPM) units.
TPM values were used for downstream analyses with R software (www.cran.r-project.org, R version 3.5.1) and the GenomicRanges, rtracklayer , samtools 0.1.18, and edgeR packages. Differences in gene expression between WT and mutants were separately analyzed for each WT/mutant comparison using the DESeq2 package.
Assembly: Col-0 TAIR10 genome release
Supplementary files format and content: tab-delimited text file including raw counts for each sample

source_name: source leaf

growth_protocol: Plants were grown on soil under long-day regime (16 h light / 8h darkness) at a relative humidity of 60% and illuminated at 100 µmol m-2 s-1 until the onset of flowering of the primary inflorescence

extract_protocol:
Total RNA was extracted using the Trizol extraction method.
500 ng of total RNA was used for library preparation using oligo-dT capture beads for poly-A-mRNA enrichment using the TruSeq Stranded mRNA Library Preparation Kit Illumina

value: source leaf

value: quintuple mutant


title: Quintuple mutant sink leaves biol. rep. 3

source_name: sink leaf

value: sink leaf


title: Quintuple mutant sink leaves biol. rep. 1


title: Quintuple mutant sink leaves biol. rep. 2


title: WT2CpG2h ChIP-Seq

growth_protocol: BM-derived Flt3-L cultured cDCs and pDCs were generated as previously described (Scheu et al, PNAS 2008).

extract_protocol:
For ChIP-Seq, BM-derived pDCs (CD3-CD19-CD11c+CD11blowB220+SiglecH+mPDCA1+) were FACS purified using FACS Aria III (BD).
Cells were fixed with 1% formaldehyde for 15 min and quenched with 0.125 M glycine, and sent to Active Motif Services (Carlsbad, CA) to be processed for ChIP-Seq. In brief, chromatin was isolated by the addition of lysis buffer, followed by disruption with a Dounce homogenizer. Lysates were sonicated and the DNA sheared to an average length of 300-500 bp. Genomic DNA (Input) was prepared by treating aliquots of chromatin with RNase, proteinase K and heat for de-crosslinking, followed by ethanol precipitation. Pellets were resuspended and the resulting DNA was quantified on a NanoDrop spectrophotometer. Extrapolation to the original chromatin volume allowed quantitation of the total chromatin yield. An aliquot of chromatin (20 µg, spiked-in with 200 ng of Drosophila chromatin) was precleared with protein A agarose beads (Invitrogen). Genomic DNA regions of interest were isolated using 4 ug of antibody against BATF (CST, 8638BF). Antibody against H2Av (0.4 ug) was also present in the reaction to ensure efficient pull-down of the spike-in chromatin (Egan et al., 2016). Complexes were washed, eluted from the beads with SDS buffer, and subjected to RNase and proteinase K treatment. Crosslinks were reversed by incubation overnight at 65 °C, and ChIP DNA was purified by phenol-chloroform extraction and ethanol precipitation. Quantitative PCR (QPCR) reactions were carried out in triplicate on specific genomic regions using SYBR Green Supermix (Bio-Rad).  The resulting signals were normalized for primer efficiency by carrying out QPCR for each primer pair using Input DNA.

value: bone marrow

value: wild type


title: Quintuple mutant source leaves biol. rep. 2


title: WT1CpG2h ChIP-Seq


title: pollen-mbd256-1


title: pollen-mbd256-3


title: WT2 ChIP-Seq


title: pollen-mbd2-3

value: mbd2 CRISPR mutant


title: Quintuple mutant rosette buds biol. rep. 2

source_name: rosette bud

value: rosette bud


title: Quintuple mutant rosette buds biol. rep. 3


title: Quintuple mutant source leaves biol. rep. 1


title: pollen-mbd2-2


title: Quintuple mutant flowers biol. rep. 3

source_name: flower

value: flower


title: Quintuple mutant rosette buds biol. rep. 1


title: WT1 ChIP-Seq

source_name: bone marrow


title: Quintuple mutant flowers biol. rep. 1


title: pollen-mbd2-1


title: Quintuple mutant flowers biol. rep. 2


title: ATAC-Seq KO1


title: B6, pDC.DTR+ Exp 2 Sample 2

city: Berkeley

first: Dmitri

middle: I

last: Kotov

address: 415 Weill Hall

department: Molecular and Cell Biology

institute: University of California, Berkeley

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic v.0.36
Trimmed reads were mapped to the Mus musculus GRCm38 reference genome with STAR aligner v.2.5.2b
Analysis of raw counts was performed with DESeq2
Assembly: mm10
Supplementary files format and content: csv file of raw counts for each sample

source_name: lung

extract_protocol:
RNA was harvested with Trizol LS and chlorofrom and then purified using the Rneasy micro kit (Qiagen).
RNA libraries for RNA-seq were prepared using an Illumina Poly(A) selection kit following manufacturer's protocols.

value: lung

tag: batch

value: plus

value: Day 25


title: Triple mutant sink leaves biol. rep. 3

value: triple mutant


title: pollen-col0-for-mbd256-3

value: WT


title: Triple mutant sink leaves biol. rep. 2


title: Sp140 KO, pDC.DTR+ Exp 2 Sample 4

value: Sp140 KO


title: Triple mutant sink leaves biol. rep. 1


title: Triple mutant source leaves biol. rep. 2


title: Triple mutant rosette buds biol. rep. 3


title: pollen-col0-for-mbd256-1

value: mature pollen


title: pollen-col0-for-mbd256-2


title: B6, pDC.DTR– Exp 2 Sample 3

value: minus


title: Triple mutant rosette buds biol. rep. 2


title: B6, pDC.DTR– Exp 2 Sample 1


title: Triple mutant source leaves biol. rep. 3


title: Triple mutant source leaves biol. rep. 1


title: Triple mutant rosette buds biol. rep. 1


title: B6, pDC.DTR– Exp 2 Sample 2


title: RNA-mbd2CR-DMSO-rep3

value: seedling


title: RNA-mbd2CR-DMSO-rep1


title: Triple mutant flowers biol. rep. 1


title: Sp140 KO, pDC.DTR+ Exp 2 Sample 2


title: Sp140 KO, pDC.DTR+ Exp 2 Sample 3


title: RNA-mbd2CR-100uM-rep3


title: WT sink leaves biol. rep. 2

value: wildtype


title: Triple mutant flowers biol. rep. 3


title: Sp140 KO, pDC.DTR+ Exp 2 Sample 1


title: WT sink leaves biol. rep. 3


title: B6, pDC.DTR+ Exp 2 Sample 1


title: WT source leaves biol. rep. 3

value: source leaf


title: RNA-mbd2CR-100uM-rep2


title: WT source leaves biol. rep. 2


title: RNA-mbd2CR-DMSO-rep2


title: Triple mutant flowers biol. rep. 2


title: WT sink leaves biol. rep. 1

value: sink leaf


title: WT source leaves biol. rep. 1


title: Sp140 KO, pDC.DTR– Exp 2 Sample 3


title: RNA-WT-DMSO-rep3


title: Sp140 KO, pDC.DTR– Exp 2 Sample 1


title: Sp140 KO, pDC.DTR– Exp 2 Sample 2


title: RNA-WT-DMSO-rep2


title: WT rosette buds biol. rep. 2


title: WT rosette buds biol. rep. 1


title: WT flowers biol. rep. 2


title: WT flowers biol. rep. 1


title: B6, pDC.DTR– Exp 1 Sample 2


title: RNA-WT-DMSO-rep1


title: B6, pDC.DTR– Exp 1 Sample 1


title: HiC_Svb_Rep_2

city: Toulouse

first: Cedric

last: Polesello

address: 118 Route de Narbonne

country: France

institute: Centre de Biologie Intégrative de Toulouse

data_processing:
Raw data from different lanes (L2+L3) were merged before alignment.
alignment: Juicer version 1.6; BWA 0.7.17-r1188; openjdk version 1.8.0_302
Assembly: genome_version : dm6-r6.32
Supplementary files format and content: HiC contact matrix (.hic format)

organism: Drosophila melanogaster

source_name: Late embryonic derived S2 cells

growth_protocol: Schneider 2 (S2) Drosophila cells were cultured in Schneider Drosophila medium complemented with 10% heat-inactivated FBS and 1% pen-strep

extract_protocol:
ARIMA HiC Kit
KAPA hyperprep

treatment_protocol: S2 cells were stably transfected with the repressive or the activated isoform of Shavenbaby (Svb) to study the influence of theproteasone mediated cleavage of this transcription factor.  Exponentially growing cells were crosslinked and harvested as previously (Liang, Lacroix et al., Molecular Cell, 2014, Vol 53, 672-681).

tag: cell line

value: Late embryonic derived S2 cells

value: S2 (Schneider 2) cell line

value: Expression of Svb-REP


title: HiC_Svb_Act_1

value: Expression of Svb-ACT


title: RNA-WT-100uM-rep2


title: B6, pDC.DTR+ Exp 1 Sample 3


title: HiC_Svb_Rep_1


title: RNA-sequencing on GBM-infiltrating CD8 T cells (4 patients combined)

city: Heidelberg

first: Michael

last: Kilian

address: Im Neuenheimer Feld 280

institute: German Cancer Research Center (DKFZ)

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the 10x Genomics Cell Ranger software v6.0.0 followed by integration with published datasets integrated independently using Seurat V.4.3.0 and Harmony V.0.1.1.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: human glioblastoma

extract_protocol:
Human brain tumor samples were cut into pieces and mashed through a 100 µm and 70 µm strainer to obtain a single cell suspension. Myelin was removed using Myelin removal beads II (Miltenyi). Human samples were frozen in 90% FBS / 10% DMSO and thawed on the day of analysis. An Aria Fusion (BD Biosciences) with following lasers was used for cell sorting: 355, 405 nm; 488 nm; 561 nm; 640 nm. Brain tumor samples were stained with following antibodies: anti-CD3-BV510 (clone HIT3A), anti-CD45 APC-H7 (Clone 2D1), anti-CD56-FITC (clone HCD56), NCR3LG1/B7H6 rabbit anti-human polyclonal (Biotin) antibody (LSBio) followed by a TotalSeq-C-streptavidin antibody (Biolegend). Fixable-viability dye eFluor780 (Thermo Fisher) was used for exclusion of dead cells. Unbiased mRNA profiling was then performed by using the chromium single cell 5’ TCR/RNA sequencing kit with feature barcode technology (10x Genomics).
5' scRNA/TCR/CITE-seq: Library was performed according to the manufacter’s instructions (single cell 5’ v2 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: human glioblastoma

tag: cell subtype

value: T cells


title: RNA-WT-100uM-rep1


title: B6, pDC.DTR+ Exp 1 Sample 2

value: lung

value: plus


title: TotalSeq-C hashtag CITE-sequencing on GBM-infiltrating CD8 T cells (4 patients combined)


title: RNA-sequencing on GBM-infiltrating CD4 T cells (4 patients combined)


title: WT rosette buds biol. rep. 3

value: rosette bud


title: B6, pDC.DTR– Exp 1 Sample 3

value: Day 25


title: pollen-complementation-mbd2LD-3

value: mbd2 CRISPR mutant


title: B7H6 CITE-sequencing on GBM-infiltrating CD8 T cells (4 patients combined)


title: B6, pDC.DTR+ Exp 1 Sample 1


title: WT flowers biol. rep. 3

value: flower


title: pollen-complementation-mbd2LD-2

value: mature pollen


title: B7H6 CITE-sequencing on GBM-infiltrating CD4 T cells (4 patients combined)


title: Sp140 KO, pDC.DTR+ Exp 1 Sample 3

value: Sp140 KO


title: HiC_Svb_Act_2


title: RNA-WT-100uM-rep3

value: seedling

value: WT


title: pollen-complementation-mbd2LD-1


title: MUTZ3 4xPLDLS - Input - Untreated

city: Rotterdam

first: Ruud

last: Delwel

address: Dr. Molewaterplein 40

country: Netherlands

institute: Erasmus MC

data_processing:
Base calling was conducted with bcl2fastq v1.8.4 for runs sequenced on the Hiseq 2500 and v2.20.422 for runs sequenced on the Novaseq 6000
ChIP-seq reads were aligned to the human reference genome build hg19 with either BBMap (v34.92) or bowtie (v1.1.1)
Peak calling was performed with MACS2 (v 2.1.2) using the default settings, using input sequencing data as controls.
Bigwig files were generated for visualization with deepTools bamCoverage (v3.5.1) and the options  --normalizeUsing RPKM --smoothLength 100 --binSize 20
Assembly: hg19
Supplementary files format and content: narrowPeak (except for Input samples)
Supplementary files format and content: bigwig

source_name: Bone marrow

growth_protocol: The MOLM-1 cell line was cultured in RPMI with 10% FCS. The MUTZ3 cell lines were cultured in αMEM with 20% FCS and 20% conditioned 5637 medium

extract_protocol:
Nuclear lysates were sonicated and pulled down with antibody according to one of three different protocols: the Upstate histone protocol, with a single formaldehyde crosslink, or with a double DSG crosslink (see methods)
ChIP samples were processed according to the Illumina TruSeq ChIP Sample Preparation Protocol (Illumina) or Diagenode Library V3 preparation protocol (Diagenode) and either sequenced single-end (1 × 50 bp) on the HiSeq 2500 platform (Illumina) or paired-end (2 × 100 bp) on the Novaseq 6000 platform (Illumina)

value: Bone marrow

value: acute myelomonocytic leukemia

tag: timepoint

value: Untreated

tag: replicate

tag: antibody

tag: protocol

value: Double-crosslink DSG


title: MUTZ3 4xPLDLS - EVI1 ChIP-seq - Untreated Rep2

value: Cell Signaling, cat 2593


title: MUTZ3 4xPLDLS - Input - Dox

value: Dox


title: MUTZ3 4xPLDLS - EVI1 ChIP-seq - Untreated Rep1


title: MUTZ3 4xPLDLS - CTBP2 ChIP-seq - Untreated Rep2


title: Sp140 KO, pDC.DTR+ Exp 1 Sample 1

tag: time


title: Sp140 KO, pDC.DTR– Exp 1 Sample 3

value: minus


title: pollen-complementation-col0-3

tag: ecotype


title: MUTZ3 4xPLDLS - CTBP2 ChIP-seq - Untreated Rep1


title: pollen-complementation-col0-2


title: pollen-complementation-col0-1


title: TotalSeq-C hashtag CITE-sequencing on GBM-infiltrating CD4 T cells (4 patients combined)

value: human glioblastoma

value: T cells


title: MUTZ3 4xPLDLS - EVI1 ChIP-seq - Dox Rep1


title: Sp140 KO, pDC.DTR– Exp 1 Sample 2

value: lung


title: MUTZ3 4xPLDLS - CTBP2 ChIP-seq - Dox Rep2


title: MUTZ3 4xPLDLS - EVI1 ChIP-seq - Dox Rep2


title: pollen-9myc-MBD2-in-mbd2LD-3


title: MUTZ3 4xPLDLS - CTBP2 ChIP-seq - Dox Rep1


title: Sp140 KO, pDC.DTR– Exp 1 Sample 1

value: Day 25


title: pollen-9myc-MBD2-in-mbd2LD-2

value: mbd2 CRISPR mutant


title: Sp140 KO, pDC.DTR+ Exp 1 Sample 2

value: plus


title: Untreated BMDM 3

source_name: primary bone marrow-derived macrophages

growth_protocol: Bone marrow-derived macrophages were differentiated from bone marrow and maintained in  DMEM supplemented with 10% FBS, PenStrep, Glutamin, HEPES, and M-CSF in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Cells were lysed with TRK lysis buffer (Omega Bio-Tek) and 2-mercaptoethanol followed by total RNA isolation using the E.Z.N.A Total RNA Kit I (Omega Bio-Tek)
RNA libraries for RNA-seq were prepared using an Illumina Poly(A) selection kit following manufacturer's protocols.

treatment_protocol: BMDM were left untreated or stimulated with 10 ng / mL of IFN-b, IFN-g, TNF, or transforming growth factor-b for 6 hours.

value: primary bone marrow-derived macrophages


title: Untreated BMDM 2


title: PID21_miNs_DAPT_2

city: St Louis

first: Kyle

last: Burbach

state: MO

address: 660 S Euclid Ave

department: Developmental Biology

institute: Washington University in St Louis School of Medicine

data_processing:
Basecalling: Illumina's bcl2fastq
Custom python demultiplexing
Alignment: STAR version 2.5.1a
Gene counts: Subread:featureCount 1.4.6-p5
Sequencing performance assessment: RSeQC 2.6.2
Assembly: hg38
Supplementary files format and content: TSV containing ensembl ID, entrezgene ID, gene name, type, source of name, transcript count, description, and CPM for each sample per gene.

extract_protocol:
RNA was isolated using Qiashredder columns into Qiagen Rneasy plus mini.
Samples were prepared according to library kit manufacturer’s protocol

value: Fibroblast

value: DAPT


title: PID21_miNs_DAPT_1

value: WT


title: PID21_miNs_SAHM1_1


title: PID21_miNs_SAHM1_2


title: pollen-3F-MBD2-in-mbd2LD-2

value: mature pollen


title: pollen-9myc-MBD2-in-mbd2LD-1


title: pollen-3F-MBD2-in-mbd2LD-3


title: PID21_miNs_DMSO_1

value: DMSO


title: Untreated BMDM 1

value: Untreated


title: PID7_miNs_NICD_2

value: DMSO NICD

tag: biomaterial provider


title: PID7_miNs_NICD_1


title: PID7_miNs_SAHM1_2

value: SAHM1 LacZ


title: pollen-3F-MBD2-in-mbd2LD-1


title: TNF stimulated BMDM 2

value: TNF


title: PID7_miNs_SAHM1_1


title: TNF stimulated BMDM 1


title: PID7_miNs_DMSO_2

value: DMSO LacZ


title: PID7_miNs_DMSO_1


title: pollen-sant1234-2

value: sant1234 mutant


title: pollen-sant1234-3


title: Library_4_Multiplexing_Capture [37-2]

city: Alexandroupolis

first: Athanasios

last: Tasis

address: University Hospital of Alexandroupolis

country: Greece

institute: Democritus University of Thrace

description: Cell Multiplexing Oligo

data_processing:
The constructed libraries were sequenced on an NovaSeq 6000 sequencer with a paired-end reads sequencing mode.
The 10X Genomics Cell Ranger multi v7.1.0 pipeline, run under default parameters with specifying the r1-lengths and r2-lengths for gene expression and feature libraries to 28+90 respectively, was used to map the sequencing reads to the human genome (GRCh38) and generate the gene expression and feature barcode matrices.
Assembly: GRCh38
Supplementary files format and content: Cell Ranger multi count output files: raw_feature_bc_matrix -> barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz
Supplementary files format and content: Cell Ranger multi multiplexing_analysis: assignment_confidence_table.csv

extract_protocol:
Sorted CD8+ T cells were FACS isolated, counted, resuspended in PBS + 10% FBS at a concentration of 1600 cells/ uL, combined by three per well of the Chromium Next GEM Chip G (10X Genomics) and loaded onto the Chromium Controller (10X Genomics).
scRNA-seq with Cell Multiplexing; Samples were processed for single-cell encapsulation, cDNA and cell multiplexing library generation using the Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index) (10X Genomics).

value: bone marrow

value: Sorted Bone marrow CD8+ T cells

value: multiplexed sample (MDS, AML)


title: PID21_miNs_DMSO_2


title: Library_3_Multiplexing_Capture [36-2]

description: Cell Multiplexing Oligo


title: Pooled CD3+ T Cells, scRNAseq

city: KOLKATA

first: Puspendu

last: Ghosh

state: WEST BENGAL

address: CNO6,SECTOR V, BIDHANNAGAR

department: CBID

country: India

institute: CSIR-IICB

description:
BD-Rhapsody
polyA RNA, and protein

data_processing:
Basecalling was carried out using bcl2fastq version 2.20.0.422. The resulting .FASTQ files from sequencing were processed using the BD Rhapsody WTA Analysis Pipeline, specifically the Targeted Multiplex Rhapsody Pipeline v1.0 with default settings. Quality-filtered R1 reads were analyzed to detect sequences including the cell label sequence (CL), Molecular Identifier sequence (UMI), and poly-dT tail sequence. The processed R2 reads were examined according to the guidelines outlined in the pipeline. These reads contain information about the bioproducts. The information from putative cells, combined with RSEC-adjusted molecules, was utilized to construct a single-cell expression matrix. Subsequently, the raw gene expression matrices were individually imported into R (version ) and transformed into Seurat objects utilizing the Seurat R package (4.3.0).
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and every single cell

source_name: Blood

extract_protocol:
The microwell-seq barcoding technology (BD Rhapsody platform) was utilized for single cell transcriptomics analysis. Cell viability was determined using trypan blue on the ThermoFisher Scientific, Countess® II FL Automated Cell Counter. Approximately, 0.1X106 T cells were labelled using BD™ Single-Cell Multiplexing Kit-Human with unique tags for each sample and BD™ AbSeq Ab-Oligos as per the manufacturer’s guideline (Doc ID: 214419 Rev. 2.0). Subsequently, 20,000 cells (>90% viability) were loaded onto primed microwells of BD Rhapsody cartridge on BD Rhapsody express single-cell analysis system and oligonucleotide barcoded beads were added as per manufacturer’s instructions (Doc ID: 210967 Rev. 1.0). Following cell and bead pairing in the microwells, cells were lysed and cDNA was prepared by reverse transcription from poly-adenylated RNA, captured on the beads.
The cDNA of mRNA and AbSeq targets was first encoded on BD Rhapsody™ Cell Capture Beads, as described in the instrument user guides. At the same time, the barcode information from BD Rhapsody Cell Capture Beads was also added to AbOligos during reverse transcription, which enables amplification of the AbOligos and Sample Tags in solution. To generate the AbSeq and Sample Tag sequencing libraries, the extended AbOligos and Sample Tags were first denatured from the BD Rhapsody Cell Capture Beads, which were later amplified separately through a series of PCR steps. Meanwhile, the whole transcriptome amplification library was generated directly from the BD Rhapsody Cell Capture Beads using a random priming approach, followed by an index PCR step. The whole transcriptome mRNA, AbSeq, and Sample Tag libraries was combined together for sequencing on Illumina Novaseq 6000 instrument to generate 150bp paired-end reads.

value: Blood

value: CD3+ T Cells


title: TGF-b stimulated BMDM 3

value: primary bone marrow-derived macrophages

value: TGF-b


title: TGF-b stimulated BMDM 2


title: Library_4_Gene_Expression [37-1]

description: mRNA


title: pollen-sant1234-1

source_name: mature pollen


title: pollen-mbd2LD-3

value: mbd2 CRISPR mutant


title: Library_1_Multiplexing_Capture [32-2]

description: Cell Multiplexing Oligo


title: Library_3_Gene_Expression [36-1]

description: mRNA


title: TGF-b stimulated BMDM 1


title: SAT_84

first: Marcus

last: Alvarez

address: 695 Charles E Young Dr South, Gonda 6335

department: Human Genetics

institute: UCLA

description: 10X Genomics 3' v3.1

data_processing:
Reads were aligned to the GRCh38 primary human genome with Gencode v24 gene annotations. STARSolo v2.7.3a was used for alignment with the --soloFeatures GeneFull argument to include intronic regions for UMI counting. Demuxlet, implemented in the popscle v0.1-beta software package, was used for assigning droplets to the one of the 4 pooled donors for each library.
Assembly: GRCh38
Supplementary files format and content: Matrix market format for gene counts.
Supplementary files format and content: Tab-separated text file for meta data, barcodes (column names), and gene names (row names).

source_name: Subcutaneous adipose

extract_protocol:
Frozen tissue biopsies from 4 donors were combined prior to isolation. The tissue was minced over dry ice and incubated in ice-cold lysis buffer consisting of 0.1% IGEPAL, 10 mM Tris-HCl, 10 mM NaCl, and 3 mM MgCl2. After a 10-min incubation, the lysate was filtered through a MACS 30-um smart strainer (Miltenyi Biotec #130-110-915). Nuclei were centrifuged at 500 x g for 5 minutes at 4C, and gently re-suspended in 1 mL of wash buffer consisting of 1X PBS, 1.0% BSA, and 0.2 U/ul RNase inhibitor (Sigma #3335402001). Nuclei were filtered again through a 40 um flowmi tip strainer (Sigma Aldrich # BAH136800040). Finally, nuclei were centrifuged at 500 x g for 5 minutes at 4C, re-suspended, and submitted for library preparation.
Libraries were prepared using the 10X Single Cell 3' v3.1 protocol and the 10X Chromium platform. The 21 resulting libraries were sequenced using an Illumina NovaSeq S4 targeting 200 million reads per sample.

value: Subcutaneous adipose


title: IFN-g stimulated BMDM 3

value: IFN-g


title: TNF stimulated BMDM 3


title: pollen-mbd2LD-2

extract_protocol:
For ChIP-seq experiments, 1~2 g of unopen flower buds or 2~4 g rosette leaves from the T2 lines were collected. For RNA-seq, rosette leaf tissues from 4- to 5-week-old plants, 500 uL of open flowers, 1 inflorescence, or 3 individuals of 10-day-old seedlings were harvested. For WGBS, rosette leaf tissues from 4- to 5-week-old plants, 1000 uL of open flowers, or 5 individuals of 10-day-old seedlings were pooled as one biological replicate. For snRNA-seq, 5 mL of unopen flower buds and open flowers from the same inflorescence were harvested. For MNase-seq, 0.5 g of unopen flower buds were freshly harvested.
ChIP-seq and Mnase-seq libraries were prepared using the Ovation Ultra Low System V2 1-16 kit (NuGEN, 0344NB-A01) following the manufacturer’s instructions. Whole genome bisulfite sequencing libraries were prepared using the Nugen Ultralow Methyl Kit. RNA-seq libraries were prepared using TruSeq Stranded mRNA kit (Illumina). SnRNA-seq libraries were prepared with 10x Genomics Chromium Single Cell 30 Reagent Kit v3.
ChIP-seq, RNA-seq, snRNA-seq, WGBS, and MNase-seq

value: mature pollen


title: SAT_83

description: 10X Genomics 3' v3.1


title: SAT_82

description: 10X Genomics 3' v3.1


title: SAT_81

description: 10X Genomics 3' v3.1


title: IFN-g stimulated BMDM 2


title: pollen-mbd2LD-1


title: SAT_80

description: 10X Genomics 3' v3.1


title: SAT_79

description: 10X Genomics 3' v3.1


title: IFN-g stimulated BMDM 1


title: pollen-mbd2GK-2

value: mbd2 T-DNA mutant


title: IFN-b stimulated BMDM 3

value: IFN-b


title: SAT_78

description: 10X Genomics 3' v3.1


title: SAT_77

description: 10X Genomics 3' v3.1


title: SAT_76

description: 10X Genomics 3' v3.1


title: SAT_74

description: 10X Genomics 3' v3.1


title: SAT_75

description: 10X Genomics 3' v3.1


title: pollen-hda6salk-3

value: hda6 T-DNA mutant


title: IFN-b stimulated BMDM 1


title: pollen-mbd2GK-1


title: IFN-b stimulated BMDM 2


title: SAT_73

description: 10X Genomics 3' v3.1


title: pollen-hda6salk-2


title: SAT_71

description: 10X Genomics 3' v3.1


title: SAT_70

description: 10X Genomics 3' v3.1


title: Library_1_Gene_Expression [32-1]

description: mRNA


title: SAT_69

description: 10X Genomics 3' v3.1


title: SAT_68

description: 10X Genomics 3' v3.1


title: s28A, scrambled, batch 1

data_processing:
Data cleaning: Purity-filtered reads were adapters and quality trimmed with Cutadapt (v. 1.8). Reads matching to ribosomal RNA sequences were removed with fastq_screen (v. 0.11.1). Remaining reads were further filtered for low complexity with reaper (v. 15-065).
Alignment: Reads were aligned against Mus musculus.GRCm38.86 genome using STAR (v. 2.5.3a).
Obtaining raw read counts: The number of read counts per gene locus was summarized with htseq-count (v. 0.9.1, Anders et al. 2014) using Mus musculus.GRCm38.86 gene annotation.
Gene filtering: Before normalization, genes with low counts were filtered out. Only genes with at least 1 count per million (cpm) reads in at least one sample were retained.
Normalization: Library sizes were scaled using TMM normalization and log-transformed into counts per million or CPM (EdgeR package, version 3.20.7).
Genome_build: Mus musculus.GRCm38.86
Supplementary_files_format_and_content: Tab-separated .txt files with raw gene-level read counts for each sample
Supplementary_files_format_and_content: Matrix table with normalized counts

source_name: cortical neuronal cultures from C57BL6/J mice

growth_protocol: Dissociated cortical primary cultures were prepared from C57BL/6J mouse brains at embryonic day 17–18 (E17 –E18; of either sex) as detailed in (83, 84). In brief, pregnant mice (12-14 weeks old) were sacrificed by cervical dislocation, and embryos were removed and decapitated in phosphate-buffered saline at 4°C. Both cortices from 5 embryos were dissected in a solution of phosphate buffer containing HEPES, 33 mM glucose, and 40 mM sucrose. The isolated cortices were digested with a solution containing 50 U of Papain (Sigma) for 30 min at 37°C. Digestion was stopped by the addition of trypsin inhibitor (Sigma) for 10 min also at 37°C. Cells were dissociated mechanically by pipetting in Neurobasal medium (NBM) supplemented with 2% B-27 (Invitrogen), 0.5mM Glutamax (Invitrogen), and 1% penicillin/streptomycin. After 4 triturations, the cells in suspension were transferred to a separate tube. Dissociated cells were centrifuged during 4 min at 150g and resuspended in 2 ml of complete NBM, then plated (at 1.5x106 cells) in 3 mL of NBM on 35 mm dishes, precoated with 0.1 mg/ml poly-L-lysine. Cultures were maintained in a humidified CO2 incubator (5% CO2, 37°C) for 3 days.

extract_protocol:
Following treatment, RNA from primary cortical cells (DIV5) was extracted and purified using the RNeasy Mini Kit 50 (Qiagen), according to the manufacturer instructions for cells grown in a monolayer. All RNA sample amounts were measured with a NanoDrop ND-1000 spectrophotometer (ThermoFisher Scientific). RNA quality was assessed on a Fragment Analyzer (Advanced Analytical Technologies) and all RNAs had a RQN between 8.8 and 9.5.
RNA-seq libraries were prepared using 1000 ng of total RNA and the Illumina TruSeq Stranded mRNA reagents (Illumina). Cluster generation was performed with the resulting libraries using the Illumina TruSeq SR Cluster Kit v4 reagents and sequenced on the Illumina HiSeq 2500 using TruSeq SBS Kit v4 reagents.

treatment_protocol: After 3 days in vitro (DIV3), half of the medium was removed and kept at 37oC. Subsequently, primary cortical cells were treated for 12 hours with 2μl of Lipofectamine® 2000 (Invitrogen) transfection reagent, and 2μl of either specific miR-709 inhibitors (i-miR-709; 40nM final conc. ; n=6), scrambled (scr; 40 nM final conc.; n=6) or ddH2O (ctrl, n=6; for the exact constructs see Methods, In vivo miR-709 inhibition), diluted in a total of 100μL Gibco™ Opti-MEM™ Reduced Serum Media (ThermoFisher Scientific), according to the manufacturer’s protocol. Forty-eight hours post-transfection, cells were lysed for RNA extraction.

value: scrambled control

tag: experiment number

value: experimental batch 2

value: cortical neuronal culture


title: SAT_67

description: 10X Genomics 3' v3.1


title: pollen-hda6salk-1


title: pollen-mbd2GK-3


title: pollen-col0-for-mbd2hda6sant1234-2

value: WT


title: SAT_66

description: 10X Genomics 3' v3.1


title: s15B, scrambled, batch 6

tag: treatment

value: experimental batch 6


title: SAT_64

description: 10X Genomics 3' v3.1

tag: tissue


title: SAT_65

description: 10X Genomics 3' v3.1


title: pollen-col0-for-mbd2hda6sant1234-1


title: s01B, scrambled, batch 4

tag: strain

value: experimental batch 4


title: SAT_62

description: 10X Genomics 3' v3.1


title: SAT_63

description: 10X Genomics 3' v3.1


title: pollen-mbd2-CR3


title: s28B, scrambled, batch 2

value: experimental batch 1

tag: cell type


title: SAT_72

description: 10X Genomics 3' v3.1


title: s01A, scrambled, batch 3

value: experimental batch 3


title: SAT_61

description: 10X Genomics 3' v3.1


title: pollen-mbd2-CR2


title: SAT_59

description: 10X Genomics 3' v3.1


title: SAT_60

description: 10X Genomics 3' v3.1


title: SAT_58

description: 10X Genomics 3' v3.1


title: m28B, inhibited, batch 2

value: miR-709 inhibition


title: SAT_56

description: 10X Genomics 3' v3.1


title: pollen-col0-for-mbd2-3


title: m28A, inhibited, batch 1


title: pollen-col0-for-mbd2hda6sant1234-3


title: m15B, inhibited, batch 6


title: SAT_57

description: 10X Genomics 3' v3.1


title: s15A, scrambled, batch 5

value: experimental batch 5


title: SAT_54

description: 10X Genomics 3' v3.1


title: pollen-col0-for-mbd2-2


title: SAT_53

description: 10X Genomics 3' v3.1


title: m15A, inhibited, batch 5


title: RNA-mbd2CR-100uM-rep1

source_name: seedling

value: seedling

value: mbd2 CRISPR mutant


title: SAT_52

description: 10X Genomics 3' v3.1

value: Subcutaneous adipose


title: pollen-col0-for-mbd2-1

value: mature pollen


title: SAT_51

description: 10X Genomics 3' v3.1


title: pollen-mbd14-3

value: mbd14 T-DNA mutant


title: SAT_47

description: 10X Genomics 3' v3.1


title: c28B, control, batch 2

value: ddH2O control


title: SAT_49

description: 10X Genomics 3' v3.1


title: pollen-mbd14-1


title: SAT_48

description: 10X Genomics 3' v3.1


title: pollen-mbd14-2


title: SAT_46

description: 10X Genomics 3' v3.1


title: SAT_55

description: 10X Genomics 3' v3.1


title: c28A, control, batch 1


title: SAT_44

description: 10X Genomics 3' v3.1


title: SAT_45

description: 10X Genomics 3' v3.1


title: c15B, control, batch 6


title: pollen-mbd124-3

value: mbd124 T-DNA mutant


title: c15A, control, batch 5


title: SAT_43

description: 10X Genomics 3' v3.1


title: SAT_41

description: 10X Genomics 3' v3.1


title: pollen-mbd124-1


title: SAT_39

description: 10X Genomics 3' v3.1


title: m01B, inhibited, batch 4


title: c01B, control, batch 4


title: m01A, inhibited, batch 3


title: SAT_50

description: 10X Genomics 3' v3.1


title: SAT_38

description: 10X Genomics 3' v3.1


title: c01A, control, batch 3


title: SAT_36

description: 10X Genomics 3' v3.1


title: SAT_35

description: 10X Genomics 3' v3.1


title: SAT_34

description: 10X Genomics 3' v3.1


title: pollen-mbd1-1

value: mbd1 T-DNA mutant


title: pollen-mbd1-2


title: Granzyme B Non-Secreting T cell scRNAseq Barcode

first: Dino

last: Di Carlo

address: 420 Westwood plaza

description:
scRNA-seq
Negative_feature_bc_matrix.tar_GEX.gz

data_processing:
SEC-seq libraries proceeded via normal workflow
Data was demultiplexed and output as FASTQ in Basespace using library indexes
FASTQs were mapped to their respective genomes using the Cellranger utility to construct a gene by cell matrix for each sample
Data was analyzed using 10X Cell Ranger and Loupe browsers.
Assembly: GRCh38 (human)
Supplementary files format and content: Data was filtered based on Cell Ranger Multi analysis.

growth_protocol: PBMCs isolated from healthy donors came from commercially available sources. PBMCs were cultured for 10-14 days with 1mg/ml peptides of interest and 25U/ml IL-2. TCRPMI media (RPMI 1640 + 10%FBS + 1%Glutamax, 1XSodium Pyruvate, 10mM HEPES, 1X non-essential amino acids, 50uM beta-mercaptoethanol and 1X Penicillin-Streptomycin.

extract_protocol:
Nanovials were loaded directly into the cell mix in the 10x Chromium workflow.
Libraries were constructed as described in the Chromium Single Cell 5' Reagent Kits User Guide
scRNAseq libraries were constructed as typically described in the guide above.

treatment_protocol: PBMCs were cultured and loaded onto pMHC monomer and cytokine capture antibody coated nanovials for 2 hours before straining excess cells. Cells were bound and allowed to secrete for a 3 hour incubation. Nanovials are then collected and incubated with anti-granzyme B APC antibody, calcein AM viability dye, anti-CD3 and anti-CD8 antibody for 30 minutes. Nanovials containing single cells were isolated by FACS using calcein stain and anti-granzyme B fluorescent signal as positive and negative secretors. Cell-loaded nanovials were then stained with anti-APC oligo-barcoded antibody for 30 minutes, washed and added directly to the single cell RNA-seq workflow.

value: Blood

value: PBMC

value: T cell


title: SAT_33

description: 10X Genomics 3' v3.1


title: SAT_42

description: 10X Genomics 3' v3.1


title: SAT_32

description: 10X Genomics 3' v3.1


title: SAT_40

description: 10X Genomics 3' v3.1


title: pollen-col0-for-mbd124-3

data_processing:
ChIP-seq: Quality control was initially run to filter out the low-quality reads. Trim Galore (Babraham Institute) was used to remove the Illumina adapters. Then the reads were aligned to the Arabidopsis reference genome (TAIR10) using the bowtie2, allowing only uniquely mapped reads with perfect matches. MarkDuplicates.jar (picard-tools suite, Broad Institute) was used to remove the PCR duplicates. Bigwig files were generated using deeptools (v 3.0.2) bamCoverage with the options -- normalizeUsing RPGC and --binSize 10. For correlation analysis between the ChIP-seq signal and mCG density, the samples were normalized to the no-FLAG control using bamCompare with the options --scaleFactorsMethod readCount, --binSize 10, and --operation log2. The normalized ChIP-seq signal and CG methylation percentages were summarized into 400 bp bins. We took a random subset covering 10% of all genomic regions for the correlation analysis. The data were plotted using the R package ggplot with the option geom_smooth. ChIP-seq peaks were called using MACS2 (v2.1.1) using an FDR cutoff of 0.05. The FLAG-associated hyperchipable regions, defined as peaks called in the anti-FLAG Col-0 controls, were removed from the peak files. Heterochromatin peaks were defined as peaks intersecting with TAIR10 pericentromeric regions using bedtools intersect55 function from deeptools (v 3.0.2).
Mnase-seq: The reads of low quality were fileterd out and the adaptors were trimmed with Trim Galore (Babraham Institute). Next the processed reads were aligned to TAIR10 using bowtie2 keeping reads smaller than 2000 bp and allowing only uniquely mapped reads with perfect matches. Then PCR duplicates were removes using MarkDuplicate (picard-tools suit, Broad Institute) and bigwig files were generated using bamCoverage.
RNA-seq: RNAs-seq reads were filtered according to quality score and were trimmed out Illumina adaptors using Trim Galore (Babraham Institute). Then the filtered reads were mapped to the Arabidopsis reference genome (TAIR10) using STAR. We allowed only uniquely mapped reads with less than 5% of mismatches. Bigwig files for genome browser visualization were generated using bamCoverage with the options -- normalizeUsing RPGC and --binSize 10. HTSeq was used to obtain the read counts for TE and our previously reannotated pollen transcripts. DESeq2 was used to perform the differential analysis with the cutoff padj < 0.05 and |log2FC| > 1. We used ggplot to generate all the related plots.
snRNA-seq: The analysis was performed following the published pipeline (Ichino et. al). In brief, Cell Ranger 6.1.1 was used to process the raw data following the published pollen transcriptome reannotations. With Cell Ranger results, SoupX and Seurat were used to remove the ambient RNA and filter out the cells detected with less than 200 genes. The data were normalized and scaled following the published settings. After the normalization, PCA analysis was performed (npc=20). DoubletFinder v3 was used to identify doublets and find.pK was used to obtain the ideal pK parameters for each sample. The percentage of doublets removed and the pK values were summarized in Table S1. Col-0 and mbd2 datasets were integrated with Seurat v4 FindIntegrationAnchors and IntegrateData using default settings. The data was scaled, and PCA analysis was performed (npcs=40). Then clustering analysis was done using FindNeighbors and FindClusters functions. The number of cells per cluster is summarized in Table S1. In addition, the markers for each cluster were obtained with FindAllMarker using the integrated dataset. Finally, DEG analysis was performed on individual clusters. We specifically focused on activated TEs using the cutoff padj < 0.05 & |avg_log2FC| > 0.25. In this analysis, the following clusters were groups: VN_bi and VN_late_bi, VN_tri and VAN_mature. The TE expression heatmap was generated using Seurat function AverageExpression.
WGBS: WGBS were filtered and removed with Illumina adaptors using Trim Galore (Babraham Institute). Reads with three or more consecutively methylated CHH sites were considered as non-converted reads and removed from the analyses. Bismark51 was used to map the reads to the Arabidopsis reference genome (TAIR10) and obtain the methylation percentages for each cytosine. We used ViewBS to generate the plots showing the genome-wide methylation information across genotypes.
Assembly: TAIR10
Supplementary files format and content: bigwig: ChIP-seq, RNA-seq, and MNase-seq intensity
Supplementary files format and content: narrowPeak: peak file
Supplementary files format and content: tsv.gz and matrix.gz: tab-seprated values files and matrix files
Supplementary files format and content: bed and bedGraph for WGBS: methylation ratio

value: WT


title: pollen-mbd124-2


title: SAT_30

description: 10X Genomics 3' v3.1


title: SAT_31

description: 10X Genomics 3' v3.1


title: Granzyme B Secreting T cell scRNAseq

description:
scRNA-seq
Positive_feature_bc_matrix.tar_GEX.gz


title: Granzyme B Non-Secreting T cell scRNAseq


title: pollen-mbd1-3


title: pollen-col0-for-mbd124-2


title: SAT_29

description: 10X Genomics 3' v3.1


title: pollen-col0-for-mbd124-1


title: MBD2-Flag-sant3

source_name: floral tissue

value: floral tissue

tag: chip antibody

value: Anti-FLAG M2 (Sigma, F1804)

value: sant3 T-DNA mutant


title: SAT_27

description: 10X Genomics 3' v3.1


title: SAT_28

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 9 T1

city: Orbassano

first: Giulio

last: Ferrero

state: TO

address: Regione Gonzole, 10

department: Dept. Clinical and Biological Sciences

country: Italy

institute: University of Turin

data_processing:
Reads were trimmed from the adapter sequences using Cutadapt v1.10 by imposing a maximum error rate in terms of mismatches, insertions, and deletions equal to 0.15. Reads shorter than 14 nt were removed.
Trimmed reads were mapped against a miRNA reference based on miRBase v22 annotations using the small RNA-Seq module of Docker4Seq. The alignment was performed using BWA algorithm v0.7.127 with the default settings
The human miRNAs were annotated and quantified using two methods called the "knowledge-based" and "position-based". miRNAs whose assigned arms were derived from the "position-based" methodology were indicated in italics
The results generated by the annotation and quantification methods were merged into a unique mature miRNA count matrix. In the case of mature miRNAs processed from different precursors but characterized by the same mature sequence, the read counts were summed.
Assembly: hg38
Supplementary files format and content: Matrix table with the raw mature miRNA read counts for each sample

source_name: Stool

extract_protocol:
Stool RNA was extracted from 200µl aliquots using stool total RNA purification kit (Norgen Biotek Corp.) following manufacturer’s protocol. RNA quality and quantity were verified following the MIQE guidelines (http://miqe.gene-quantification.info/). The RNA concentration was quantified with the Qubit microRNA assay kit (Invitrogen). The DNA was extracted with the DNeasy PowerSoil Pro Kit (Qiagen) following manufacturer's instructions with a higher final elution buffer volume (50µl) to increase DNA concentration which was quantified with Qubit DNA high sensitivity assay kit (Invitrogen).
Small RNA (sRNA) transcripts were converted into barcoded cDNA libraries. Library preparation was performed with the NEBNext Multiplex Small RNA Library Prep Set for Illumina (Protocol E7330, New England BioLabs Inc., USA).

value: Stool

tag: age

tag: Sex

value: M

value: Time 1


title: SAT_37

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 9 T2

value: Time 2


title: SAT_26

description: 10X Genomics 3' v3.1

value: Subcutaneous adipose


title: SAT_25

description: 10X Genomics 3' v3.1


title: SAT_24

description: 10X Genomics 3' v3.1


title: Col0-Flag-for-MBD2-sant3

tag: genotype


title: Granzyme B Secreting T cell scRNAseq Barcode

tag: cell line


title: Stool sRNA-Seq - Patient 9 T0

value: Time 0


title: pollen-mbd2-CR1

value: mature pollen

value: mbd2 CRISPR mutant


title: SAT_23

description: 10X Genomics 3' v3.1


title: HDA6-Flag-sant1234

value: sant1234 mutant


title: SAT_21

description: 10X Genomics 3' v3.1


title: SAT_22

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 8 T2


title: SAT_20

description: 10X Genomics 3' v3.1


title: HDA6-Flag-mbd2CR


title: SAT_18

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 8 T1


title: HDA6-Flag-Col0


title: Col0-Flag-for-HDA6


title: SAT_19

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 8 T0


title: SAT_17

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 7 T2

value: F


title: SAT_14

description: 10X Genomics 3' v3.1


title: SAT_15

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 7 T1


title: SAT_12

description: 10X Genomics 3' v3.1


title: SAT_13

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 7 T0


title: MBD4-RR-Flag

value: mbd4 T-DNA mutant


title: SAT_11

description: 10X Genomics 3' v3.1


title: SAT_10

description: 10X Genomics 3' v3.1


title: Stool sRNA-Seq - Patient 6 T2


title: Col0-Flag-for-MBD4-rep2


title: SAT_9

description: 10X Genomics 3' v3.1


title: SAT_8

description: 10X Genomics 3' v3.1


title: MBD4-123A-Flag


title: MBD4-FL-Flag


title: Stool sRNA-Seq - Patient 6 T1


title: MBD4-104A-Flag


title: Stool sRNA-Seq - Patient 6 T0


title: SAT_7

description: 10X Genomics 3' v3.1


title: SAT_16

description: 10X Genomics 3' v3.1


title: SAT_6

description: 10X Genomics 3' v3.1


title: hypothalamus_control_day14_rep6

city: Copenhagen

first: Lars

middle: Roed

last: Ingerslev

address: Blegdamsvej 3B

department: NNF Center for Basic Metabolic Research

country: Denmark

institute: Copenhagen University

data_processing:
The STAR aligner12 v. 2.7.3a was used to align RNA-seq read against the mm10 mouse genome assembly and GENCODE vM22 mouse transcripts
The software program featureCounts v. 1.6.4 was used to summarize reads onto genes
Assembly: mm10
Supplementary files format and content: csv file with read counts

source_name: hypothalamus

extract_protocol:
Total RNA was extracted from frozen mouse hypothalamic (n=6) of 4 experimental groups (n=6: control d14, ExpOF d14, control d14+3, ExpOF d14+3) using RNeasy mini kit (Qiagen) according to the manufacturers' protocol.
Messenger RNA sequencing libraries were prepared using the Illumina TruSeq Stranded mRNA protocol (Illumina). Poly-A containing mRNAs were purified by poly-T attached magnetic beads, fragmented, and cDNA was synthesized using SuperScript III Reverse Transcriptase (Thermo Fisher Scientific). To prime for adapter ligation cDNA was adenylated and after a clean-up using AMPure beads (Beckman coulter), the DNA fragments were amplified using PCR followed by a final clean-up. Libraries were quality-controlled using a Bioanalyzer instrument (Agilent Technologies) and subjected to 51-bp paired-end sequencing on a NovaSeq 6000 (Illumina). A total of 2.74 billion reads were generated.

treatment_protocol: On day 0, mice in the overfeeding group (ExpOF mice) were infused with a commercial liquid diet (584421, Nutridrink Vanilla, Nutricia, Netherlands) that was supplemented with 20% (w/v) sucrose (S0389, Sigma-Aldrich, USA). The addition of sucrose increased the caloric content of the liquid diet from 1.5 kcal/mL to 2.3 kcal/mL (fats 23 E%, Carbohydrates 67 E%, protein 10E%). To calculate the flow rate of diet infusion, the daily food intake of the chow (3.389 kcal/g) during the baseline period was averaged for all the mice and divided by the caloric density of the diet (2.3 kcal/mL) (macronutrient composition stated in Supplementary table 1). The flow rate was increased gradually until reaching 150% of energy infusion on day 9 (Supplementary table 1). The mice were automatically infused and remained connected to pumps 23 hr/day (Extended Data Fig. 1A). Specific flow rates, daily volume infused, and daily caloric infusion are indicated in supplementary table 1. Control mice were infused with sterile water using the same flow rates. Syringes were replaced with fresh liquid diet daily. Mice, water bottles and chow pellets were weighed every day. Mice were flushed with sterile water for 1 hr (flow: 1 mL/hr) to avoid clogging of the tubing and for additional hydration. All tubes and cages were changed on day 7 during overfeeding. On day 14, the overfeeding was terminated, and the gastric infusion was set to 100 μL/hr with sterile water for the overfed mice and control mice, until the mice in the overfeeding group had stabilized their food intake and body weight, to prevent any change in feeding behavior due to stress. Food intake, water intake, and body weights were monitored daily until the end of the study. In case surgery recovery was incomplete, the animals were not included in the overfeeding infusion. If the diet clogged in the internal tubing or if mice got tangled in the spring-tubing system, they were excluded from the study.

value: hypothalamus

tag: diet

value: Control

tag: timepoint

value: day 14

tag: date euthanized

tag: rna extraction_pool

tag: rin

value: male


title: Col0-Flag-for-MBD1-rep1

first: Shuya

last: Wang

address: 610 Charles E Young Dr S

value: floral tissue

value: Anti-FLAG M2 (Sigma, F1804)

value: WT

tag: ecotype


title: hypothalamus_control_day17_rep6

value: day 17


title: SAT_5

description: 10X Genomics 3' v3.1


title: MBD1-Flag-rep1

value: mbd1 T-DNA mutant


title: Stool sRNA-Seq - Patient 4 T1

value: Stool

tag: time

value: Time 1


title: hypothalamus_overfeeding_day17_rep6

value: Overfeeding


title: Stool sRNA-Seq - Patient 4 T2

value: Time 2


title: hypothalamus_overfeeding_day14_rep6


title: SAT_3

description: 10X Genomics 3' v3.1

value: Subcutaneous adipose


title: MBD4-Flag-Rep1


title: MBD1-Flag-Rep2


title: SAT_2

description: 10X Genomics 3' v3.1


title: hypothalamus_overfeeding_day17_rep5


title: Stool sRNA-Seq - Patient 33 T2

value: M


title: Col0-Flag-for-MBD1-Rep2


title: hypothalamus_control_day14_rep5


title: Col0-Flag-for-MBD4-Rep1


title: Stool sRNA-Seq - Patient 4 T0

value: F

value: Time 0


title: Stool sRNA-Seq - Patient 33 T1


title: SANT3-Flag-rep2


title: hypothalamus_control_day17_rep5

value: hypothalamus


title: Stool sRNA-Seq - Patient 33 T0


title: hypothalamus_control_day14_rep4

value: Control


title: Stool sRNA-Seq - Patient 32 T2


title: hypothalamus_overfeeding_day14_rep5

value: day 14


title: SAT_1

description: 10X Genomics 3' v3.1


title: SANT3-Flag-rep1


title: SAT_4

description: 10X Genomics 3' v3.1


title: MBD2-RR-Flag-rep2

value: mbd2 T-DNA mutant


title: hypothalamus_control_day17_rep4

value: male


title: Stool sRNA-Seq - Patient 32 T0


title: hypothalamus_overfeeding_day14_rep4


title: MBD2-RR-Flag-rep1

value: floral tissue

value: Anti-FLAG M2 (Sigma, F1804)


title: hypothalamus_overfeeding_day17_rep4

value: day 17


title: MBD2-Flag-rep2


title: Stool sRNA-Seq - Patient 31 T1


title: Stool sRNA-Seq - Patient 31 T2


title: Stool sRNA-Seq - Patient 31 T0


title: hypothalamus_overfeeding_day14_rep3


title: MBD2-Flag-rep1


title: hypothalamus_overfeeding_day14_rep2


title: MBD2-160A-Flag-rep2


title: Stool sRNA-Seq - Patient 30 T2


title: MBD2-160A-Flag-rep1


title: Stool sRNA-Seq - Patient 30 T0


title: Stool sRNA-Seq - Patient 30 T1


title: Stool sRNA-Seq - Patient 32 T1


title: MBD2-139A-Flag-rep2


title: hypothalamus_control_day17_rep3


title: hypothalamus_control_day14_rep3


title: MBD2-139A-Flag-rep1


title: Stool sRNA-Seq - Patient 2 T2


title: Stool sRNA-Seq - Patient 2 T1


title: hypothalamus_control_day17_rep2


title: Col0-Flag-for-MBD2SANT3-rep2

value: WT


title: Stool sRNA-Seq - Patient 2 T0

value: Stool


title: hypothalamus_overfeeding_day17_rep3


title: hypothalamus_control_day17_rep1


title: Col0-Flag-for-MBD2SANT3-rep1


title: phHep-derived iCCA-UDC_1

city: San Francisco

first: Cindy

middle: K

last: Pino

address: 400 Parnassus Ave.

institute: University of California, San Francisco

data_processing:
Sequencing reads were separated into human and mouse FASTQ files using xengsort v1.0.2 (https://gitlab.com/genomeinformatics/xengsort)
Ensembl Homo_sapiens.GRCh38.96 and Mus_musculus.GRCm38.96 were used as reference genomes
Mouse reads were discarded without further processing.
Human reads from tumors forming in mice and reads from patient-derived tumors were aligned to GRCh38.96 and reads per gene matrix were counted with the latest Ensembl annotation build using STAR_2.7.2b.
Read counts per gene were used as input to DESeq2
Assembly: Homo sapiens.GRCh38.96
Supplementary files format and content: tab-delimited text files include raw count matrix  for each Sample

source_name: Liver tumor

extract_protocol:
Quick-RNA FFPE Miniprep Kit (Zymo Research)
RNA sequencing was performed by BGI using a workflow optimized for FFPE samples

treatment_protocol: phHep-derived tumors were generated using different combinations of lentiviral vectors expressing simian virus 40 large T and small t antigens (SV40Tt), Harvey rat sarcoma viral oncogene homolog (HRAS) and human telomerase catalytic subunit (TERT). Because SV40T inhibits RB and TP53, patient-derived iCCAs with CDKN2A mutations or MDM2 amplifications were selected, including some with additional KRAS or NRAS mutations, and HCCs with TP53 mutations. All samples were fixed in formalin and embedded in paraffin (FFPE). Some mice were fed fed 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC) diet to induce cholestasis.

value: Liver tumor

value: HRAS, SV40Tt, TERT


title: Stool sRNA-Seq - Patient 29 T2

value: Time 2


title: hypothalamus_control_day14_rep2


title: Stool sRNA-Seq - Patient 29 T1

value: Time 1


title: phHep-derived iCCA-UDC_2


title: phHep-derived iCCA-UDC_3


title: Patient-derived iCCA_A

value: KRAS, MDM2


title: hypothalamus_overfeeding_day17_rep2

value: Overfeeding


title: hypothalamus_overfeeding_day14_rep1


title: hypothalamus_control_day14_rep1


title: Stool sRNA-Seq - Patient 28 T2

value: M


title: Patient-derived iCCA_C

value: KRAS, CDKN2A, TP53


title: hypothalamus_overfeeding_day17_rep1

value: hypothalamus


title: Stool sRNA-Seq - Patient 26 T2


title: phHep-derived iCCA_4


title: phHep-derived iCCA_6


title: Stool sRNA-Seq - Patient 28 T0

value: Time 0


title: phHep-derived iCCA_5


title: Stool sRNA-Seq - Patient 26 T1


title: Stool sRNA-Seq - Patient 29 T0

value: F


title: Stool sRNA-Seq - Patient 26 T0


title: Stool sRNA-Seq - Patient 25 T2


title: DLD1 E545K only vehicle 4

city: cleveland heights

first: ZHENGHE

last: WANG

state: Ohio

address: 2103 CORNELL Road, WRB 3203

institute: CASE WESTERN RESERVE UNIVERSITY

data_processing:
Quality control was performed using FastQC
Read alignment was performed using HISAT2 (default parameters), mapping to the GRCh38/hg38 reference
Transcript Assembly and Abundance Quantification were performed using Stringtie (default parameteres)
FPKM Normalization was performed using Ballgown
Assembly: hg38
Supplementary files format and content: GTF files include raw counts for each Sample
Supplementary files format and content: comma-delimited text file includes FPKM values for all Sample

source_name: colon

growth_protocol: DLD1 isogenic cells were maintained in DMEM/F12(1:1) with 10% FBS and antibiotic in 5% CO2 incubator

extract_protocol:
total RNA were extracted by Rnaesy mini kit (Qiagen)
RNA library were prepared using SMARTER mRNAseq

treatment_protocol: cells in 6 well plates treated with either DMSO or drug combination (5 μM CB839 plus 5 μM 5FU) for 16 hour

value: colon

value: colon cancer cells

value: PIK3CA E545K

value: DMSO


title: DLD1 WT only drug combination 4

value: PIK3CA WT

value: 5 μM CB839 plus 5 μM 5FU


title: Patient-derived iCCA_B

value: Liver tumor

value: KRAS, CDKN2A, BRCA1


title: Patient-derived HCC_D


title: Stool sRNA-Seq - Patient 28 T1

value: Stool


title: Ldlr-/-#3

city: Würzburg

first: Alexander

middle: M.

last: Leipold

address: Josef-Schneider-Str. 2

institute: Helmholtz Institute for RNA-based Infection Research

description: 3' mRNA library: read1 file contains cell barcode and UMI; read2 file contains transcript

data_processing:
Sequencing data was demultiplexed and mapped with Cell Ranger software v7.0.1 (10x Genomics). Mouse mm10 (Ensembl 98) reference was used for the alignment and counting steps with intronic reads included
Cell Ranger outputs (filtered_feature_bc_matrix) were loaded in R (version 4.3.1), pre-processed and analyzed using Seurat v4.3.0.1 and DoubletFinder v2.0.3. Each sample was pre-filtered as follows: nuclei with >3% mitochondrial transcripts were excluded, and clustering analysis was performed in Seurat using 20 principal components and a 0.2 resolution. Doublets were excluded using DoubletFinder v2.0.3, inputting a predicted doublet rate of 15%. The six resulting Seurat objects (one for each sample) were pooled. As all the samples were processed simultaneously (same 10x Genomics Chromium chip, sequencing in the same flow cell) and had similar quality control characteristics (number of nuclei recovered, reads per nuclei, UMI per nuclei etc…), the data presented in the manuscript were pooled in Seurat without applying batch correction (replicating the analysis using the batch correction tool Harmony yielded consistent results, not shown). Clustering analysis of all aortic nuclei was performed using 20 principal components and a 0.1 resolution to identify vascular cell lineages. Cells corresponding to mononuclear phagocytes (monocytes, macrophages, dendritic cells) were identified and separately reclustered using 20 principal components and a 0.3 clustering resolution. Cluster markers were identified using ‘FindAllMarkers’ in Seurat.
Assembly: Mouse mm10 (Ensembl 98)
Supplementary files format and content: 10x Genomics output files: barcodes.tsv.gz, features.tsv.gz, matrix.mtx.gz

source_name: Aorta

extract_protocol:
Aortas from Ldlr-/- and Ldlr-/-Trem2-/- mice fed a high fat diet for 10 weeks were snap frozen in liquid nitrogen and cryoconserved at -80°C. Nuclei from n=3 mice per group were isolated using Chromium Nuclei Isolation Kits (10x Genomics) according to the manufacturer’s instruction. For counting, nuclei were labelled with DAPI and counted using a fluorescence microscope and a Neubauer counting chamber (concentration range: 1,400-2,300 nuclei/µl). Nuclei from each sample were loaded onto separate lanes of the 10x Genomics Chromium with the aim to recover 10,000 nuclei per sample, using loading volumes recommended by the manufacturer. We employed Chromium Next GEM Single Cell 3’ Kit v3.1 (10x Genomics). Libraries were generated according to the manufacturer’s instructions.  All libraries were quantified by QubitTM 3.0 Fluometer (ThermoFisher) and quality was checked using 2100 Bioanalyzer with High Sensitivity DNA kit (Agilent). Sequencing was performed using a S1 flowcell with Novaseq 6000 platform (Illumina) targeting 26,500 reads per nucleus.
Single nuclei were encapsulated into droplets with the Chromium™ Controller (10x Genomics). Transcripts captured in all cells encapsulated with a bead were uniquely barcoded using a combination of a 16 bp 10x Barcode and a 12 bp unique molecular identifier (UMI). cDNA libraries were generated using the Chromium™ Single Cell 3’ Library & Gel Bead Kit v3 (10x Genomics) following the detailed protocol provided by the manufacturer.

value: Aorta

value: nuclei; various lineages

value: Ldlr-/-


title: Ldlr-/-#2


title: Stool sRNA-Seq - Patient 25 T1

value: Time 1


title: Ldlr-/-Trem2-/-#2


title: Ldlr-/-#1


title: Ldlr-/-Trem2-/-#3


title: Ldlr-/-Trem2-/-#1


title: Patient-derived HCC_E

value: CDKN2A, TP53, ARID2


title: DLD1 E545K only drug combination 4


title: Patient-derived HCC_F