title: MD6, H3K27ac, HiChIP

data_processing:
HiChIP sequencing reads were pre-processed, aligned and filtered using HiC-Pro (Servant et al., 2015).
We specified the genome assembly (hg19) and the restriction fragment coordinates file for the enzyme used in the processing of the samples (DpnII), while all the other parameters were kept with default values.
Filtered reads were then used as input to FitHiChIP (Bhattacharyya et al., 2019) for the identification of interacting regions.
Since ChIP-seq peaks were not available for these experiments, we used ATAC-seq ones as reference to improve accuracy of loop calling.
Loops were identified at different resolutions (bin sizes of 10 and 25 kb) and we used both peak to peak and peak to nonpeak loops for background modeling together with the coverage bias regression to assess the significance of identified interactions. Peaks with a q-value < 0.01 were considered significant.
Assembly: hg19
Supplementary files format and content: bedpe files showing interactions with a 10kb- and 25kb-resolution
Library strategy: HiChIP

extract_protocol:
HiChIP was performed as described (Mumbach et al., 2016) with some modifications. Briefly, ChIP protocol was replaced with the one reported in Crispatzu et al., 2021, using H3K27ac antibody (Abcam #ab4729), starting from 1*10 6 cells per condition. Digestion and ligation were performed overnight (NEB T4 Ligase, #M0202 instead of Invitrogen T4, 15224-041) and DNA was extracted with phenol-chlorophorm.
After biotin pull-down, beads were resuspended in 25 μL of 2X TD Buffer, 0.5uL of Tn5 (Illumina #1503861), and water to 50 μL. After transposition, beads were resuspended in 50 µL of Phusion HF 2× (New England Biosciences). Generally, 14 cycles were used for Tn5 Nextera PCR amplification (Illumina Nextera DNA UD Indexes Kit) with the following PCR program: 72 °C for 5 min, 98 °C for 1 min, then cycle at 98 °C for 15 s, 63 °C for 30 s, and 72 °C for 1 min. 50ul of PCR product were size-selected with 25ul Ampure XP Beads and separated on a magnet. The supernatant was incubated again with 90ul Ampure XP Beads. The supernatant was then discarded, beads were combined, washed with Ethanol and eluted in 30ul of Elution buffer. 1ul was loaded onto D1000 Screen Tape (TapeStation) for a second size check, where library size and molarities were extracted. Then, qPCR was performed with standard Illumina primers in order to quantify the libraries. Finally, samples were pooled with different Index/Adapter sequences and sequenced on a NovaSeq 6000

value: metastasis-derived cell line

tag: chip antibody

value: H3K27ac (ab4729, abcam)


title: Left bin of Sort-seq on YFP/RFP ratio with mutational librar, replicate-1

status: Public on Feb 02 2024

type: SRA

city: Berkeley

first: Joseph

middle: Heimlich

last: Lobel

state: CA

address: 1 Barker Hall # 3202

department: Molecular and Cell Biology

country: USA

institute: UC berkeley

library_source: transcriptomic

data_processing:
Adaptors were trimmed with Cutadapt (Martin 2011) and aligned to peptide library with bowtie2 (Langmead 2012).
Each amplicon count corresponding to a peptide was counted with SamTools (Li, 2009)
Assembly: Custom list of DNA sequences encoding 50 amino acid peptides
Supplementary files format and content: text file containing read counts for each peptide for each sample
Library strategy: Amplicon sequencing

molecule: total RNA

organism: Saccharomyces cerevisiae

source_name: yeast

growth_protocol: Yeast were grown in synthetic media minus uracil for 16 hour in a custom turbidostat before being flow sorted (McGeachy 2019)

extract_protocol:
After flow sorting, RNA was extract by phenol/choloroform followed by ethanol precipitation
Libraries were prepared by constructing cDNA from total cellular mRNA using dT priming. Peptide constucts were amplifeid from cDNA with oJL090 and oJL109, followed by 2nd step amplification with indexing primers for illumina sequencing

treatment_protocol: For yeast expressing degron tagged nucleases, cells were grown in synthetic media minus uracil + 0.5 mM indole-3-acetic acid (Sigma I3750)

tag: strain

tag: cell type

value: yeast

tag: genotype

value: citirine-boxB, mScarlet-pp7

tag: treatment


title: XD5, H3K27ac, HiChIP

city: Trento

first: CIBIO

last: Zippo

state: Not Applicable

address: via sommarive 9

department: Cellular, Computation and Integrative Biology (CIBIO)

country: Italy

institute: University of Trento

library_source: genomic

molecule: genomic DNA

organism: Homo sapiens

source_name: XD

tag: cell line

value: XD

value: xenograft-derived cell line


title: Right bin of Sort-seq on YFP/RFP ratio with mutational librar, replicate-1


title: Far Right bin of Sort-seq on YFP/RFP ratio with mutational librar, replicate-2


title: cr_myod_dtag43 (matr3.ko and yy1.wt) (for double ko comparison)

city: Boston

first: Stuart

last: Orkin

state: MA

address: 1 Blackfan Circle

department: Hematology and Oncology

institute: Boston Childrens Hospital

data_processing:
RNAseq, SLAMseq: RNA-seq experiments were processed by the HISAT pipeline (Kim et al 2019), which includes alignment, filtering, and gene quantification steps. Differential expression analysis was carried out using DESeq2 using default settings. We performed SLAM-seq at 4 hrs. post dTAG47 exposure and quantified nascent RNA transcription using the SlamDunk pipeline (Neumann et al., 2019, Harada, Taku et al., 2022). Differential analysis of SLAM-seq data was performed on the transcript read counts with thymine-to-cytosine (T>C) conversions following s4U metabolic labeling (newly synthesized RNA) and also on the total transcript read counts (total RNA). DESeq2 was again used for differential nascent transcript analysis.
CUT&RUN: We used CUT&RUNTools (Zhu et al., 2019) to process MyoD, YY1, CTCF, and Rad21 CUT&RUN experiments from raw fastq reads. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody). For experiments per group, we pooled all experiments’ BAM files and performed MACS2 (Zhang et al., 2008) peak calling to get merged peaks. Peak-flanking regions were obtained, and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor() (Love et al., 2014) was called on the matrix of peak-flanking region reads over all experiments to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file. A normalized bigwig file was generated for visualization.
ATACseq: ATAC-seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150bp instead of <120bp setting for TF CUT&RUN. For ATAC-seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN (see CUT&RUN section).
Chip-seq: We used a ChIP-seq data processing pipeline (Zhu et al, 2019) to perform reads trimming, alignment to the reference genome (mm10), and BAM file duplicate marking. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody), similar to the normalization procedure used in CUT&RUN data.
Assembly: mm10
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: SLAMseq TXT – Slamseq nascent gene expression matrix. Columns: Gene, CoverageOnTs in 3’UTR, ConversionOnTs in 3’UTR, Conversion rate, Total Reads with T>C conversion in 3’UTR, Total Reads with Ts in 3’ UTR, Conversion rate (Reads)
Library strategy: CUT&RUN

organism: Mus musculus

growth_protocol: C2C12 cells were grown following the standard protocol (Doynova et al., 2017). C2C12 myoblasts were propagated at 37°C, 5% CO2 in Dulbecco’s modified Eagle’s medium (Thermo Fisher Scientific) supplemented with 10% fetal bovine serum (Omega Scientific) and antibiotics (penicillin 100 U/ml, streptomycin 100μg/ml, Thermo Fisher Scientific).

extract_protocol:
CUT&RUN experiments were carried out as described (Janssens et al., 2019, Meers et al, 2019) with modifications. Briefly, ~0.5x106 cells were collected and incubated with primary antibody on a nutator at 4°C overnight. After washing away unbound antibody, protein A-MNase was added at 700ng/ml and incubated for 1h at 4°C. Samples were washed again and placed in a 0°C metal block. To activate protein A-MNase, CaCl2 was added to a final concentration of 2mM. The reaction was incubated at 0°C for and stopped by chelating Ca2+. The CUT&RUN fragments were released from the insoluble nuclear chromatin at 37°C for 30min. Digested chromatin in the supernatant were collected and then digested by proteinase K at 50°C for 1h. DNA was extracted by phenol chloroform extraction, ethanol precipitation. The antibodies used were: Matr3, Proteintech, 12202-2-AP; CTCF, Abcam, ab70303; Rad21, Abcam, ab992; YY1, santa cruz, sc-7341X; MyoD, Santa cruz, sc-32758 X; H3K27Ac, millipore, MABE647; H3K4me3, active motif, 39159; Rabbit Anti-Mouse IgG H&L, abcam, ab46540.
For transcription factors (TF), libraries were constructed using the library preparation manual of “NEBNext® Ultra™ II DNA Library Prep Kit for Illumina”, NEB E7645, with modification (Liu et al., 2018). Briefly, dA-tailing temperature was decreased to 50°C to avoid DNA melting, and the reaction time was increased to 1 hour to compensate for lower enzymatic activity. After adaptor ligation, 1.87x volume of AMPure XP beads was added to the reaction to ensure high recovery efficiency of short fragments. After 12 cycles of PCR amplification, the reaction was cleaned up with 1.2x volume of AMPure XP beads. For histone markers, libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina”, NEB E7645, per manufacturer’s instruction with modification. Briefly, after end repair and adapter ligation, 1.1x volume of AMPure XP beads was added to the reaction for DNA cleanup. After 12 cycles of PCR amplification, the reaction was cleaned up with 1.1x volume of AMPure XP beads. 16-24 barcoded libraries were quantified and mixed at equal molar ratio. Library was loaded to a NextSeq 500/550 High Output Kit v2 (75 cycles), and sequenced in the NextSeq 500 platform. To enable determination of fragment length, paired-end sequencing was performed (2x42 bp, 6 bp index)

treatment_protocol: As for acute depletion, dTag-Matr3 cells were treated with DMSO/dTAG47 (500nM) for indicated hours. As for steady state, Matr3KO cells and wildtype cells were used.

value: myoblast

value: dTag-Matr3 depleted, YY1wt

tag: time

tag: replicate

tag: antibody

value: MyoD


title: r4-MD6-contr

data_processing:
.Raw reads were quality controlled using FastQC and trimmed using Trimmomatic v0.31
Reads were aligned to the human genome hg19 using BowTie2.
SAM files were further processed and duplicates were removed using samtools v1.10
‘MultiBamSummary’ of Deeptools v3.1.2 was used to retrieve the counts per sample over the RefSeq-transcript model in bed format.
Counts transformed to FPKM values and spike-in normalized as described in Palozola et al., 2021)
Assembly: hg19
Supplementary files format and content: count table of spike-in normalized expression values [fpkm]
Supplementary files format and content: bigwig files of merged replicates per treatment

extract_protocol:
For the analysis of nascent RNA expression, cells were treated with RA as described above and pulse-labeled with 0.5 mM 5-ethynyluridine for 30 min at 37°C and 5% CO2. After pulse-labeling, total RNA was isolated using TRIzol and purified RNA was further processed using the Click-iTTM Nascent RNA Capture Kit (Invitrogen, C10365)
In brief, 5-EU incorporated RNA was biotinylated, purified and pulled down using Dynabeads™ MyOne™ Streptavidin T1 beads. Before the pulldown, biotinylated custom-made spike-in RNAs #1 (2.5e-5 ug) and #2 (2.5-e-4 ug) (expression vectors kindly provided by Kenneth Zaret, University of Pennsylvania) were added to 1 ug of biotinylated RNA. After washing the beads, cDNA was directly generated off the beads using the Universal Plus Total RNA-Seq with NuQuant kit (Tecan) as described by the manufacturer with the following modifications: fragmentation time was increased to 10 min and after second strand synthesis, beads were collected on a magnet and supernatant was transferred to a new tube for subsequent steps. Quality of the libraries was assessed using the 2100 Bioanalyzer (Agilent cat. #G2939BA) and the Qubit fluorometer (Thermo Fisher cat. #Q33226), pooled and sequenced on an Illumina NovaSeq6000 with 150 bp PE.

treatment_protocol: Cells were treated with  1µM atRA treatment (30min for the pulse samples), for 2h with 1µM atRA for the primed samples and for 2h with 1µM atRA (primed), followed by a short atRA treatment for 30min 36 hours after the priming to obtain the primed + pulse samples.

value: control


title: 27_S27

city: CRETEIL

first: Cecile

last: LEFEBVRE

address: 51 Avenue du Maréchal de Lattre de Tassigny, Bât R+1 Eq16 U955

country: France

institute: INSERM

description: No

data_processing:
Transcript reads were aligned and quantified relative to the “Vero_WHO_p.1.0 Chlorocebus sabaeus (AGM) transcriptome reference from NCBI using Salmon v1.9.0. Quality control of the alignment was performed via MultiQC v1.1345. Finally, counts were filtered and normalized (cpm + 0,0001) using EdgeR v3.38 R package. Low expressed genes were excluded using filterByExpr function with default parameters. The conserved counts were normalized as counts per million, plus 0.0001 to avoid null values, then log2 transformed.
Differential gene expression analysis was performed with the dearseq v.1.8.4 package using a mixed model with variance component test to calculate the adjusted p values and with limma v3. package to obtain the fold-change in expression.
Assembly: Vero_WHO_p.1.0 Chlorocebus sabaeus (AGM) transcriptome reference from NCBI
Supplementary files format and content: normalized as counts per million (log2)

organism: Chlorocebus sabaeus

source_name: Blood

extract_protocol:
Whole blood was sampled in tempus buffer (ThermoFisher Scientific). Total RNA was purified from whole blood using the Tempus Spin RNA Isolation Kit (ThermoFisher Scientific). RNA samples were depleted of globin mRNA using the Globinclear Kit (Invitrogen)
mRNA library preparation using the NEB Kit (NEBNext Biolab). Libraries were sequenced on an Illumina HiSeq 2500 V4 system.

treatment_protocol: 9 African green monkeys (AGM) were vaccinated with CD40.NiV+Poly-ICLC  at D0 and D21

tag: subject

tag: timepoint

tag: Sex

value: M

tag: tissue

value: Blood

value: No


title: 26_S26

description: No


title: cr_myod_dtag41 (matr3.ko and yy1.wt) (for double ko comparison)


title: cr_myod_dtag42 (matr3.ko and yy1.wt) (for double ko comparison)


title: Far Right bin of Sort-seq on YFP/RFP ratio with mutational librar, replicate-1


title: tIMEC, H3K27ac, HiChIP

source_name: tIMEC

value: tIMEC

value: mammary epthelial cell-derived cell line


title: MD6_IgG

data_processing:
Raw reads were quality controlled using FastQC and trimmed using Trimmomatic v0.39
Reads were aligned to the human genome hg19 and to mouse genome mm10 (calibrator) using Bowtie2 and resulting SAM files were further processed and duplicates were removed using samtools v1.10
Resulting bam files were spike-in normalized and visualized using ‘bamCoverage’ of DeepTools v3.5
Raw counts of Cut&Run experiments identified  ATAC-seq peaks on differential ATAC-seq peaks were retrieved using HOMER v4.11
Assembly: hg19
Supplementary files format and content: bigwig filies of the processed and normlaized files
Library strategy: Cut&Run

growth_protocol: For each antibody, 250k cells were collected and mixed with 10k NIH 3T3 cells for the spike-in.

extract_protocol:
All cells required for one experiment were spun down for 3 min at 200 x g at RT, supernatant was removed and cell pellet was resuspended in 1.5 ml RT Wash Buffer (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, EDTA-free protease inhibitor) by gently pipetting, spun down and washed twice more. After the last wash, supernatant was removed, the pellet was resuspended in 1 ml RT Wash Buffer. ConcavalinA-coated magnetic beads were activated by washing once in binding buffer (20 mM HEPES pH 7.5, 10 mM KCl, 1 mM CaCl2 and 1 mM MnCl2) and added to the sample while gently vortexing at RT. Samples were incubated on a rotator for 10 min at RT. Sample was divided in aliquots (250k cells / ab) and placed on a magnet to remove the supernatant. 100 ul of antibody buffer + corresponding antibody (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.025% Digitonin, 4 mM EDTA and EDTA-free protease inhibitor) were pipetted along the sides of the tubes and pipetted up and down 10x. The following antibodies were used at a dilution 1:100: H3K27ac (ab4729, abcam), H3K4me1 (ab8895, abcam), MED1 (ab64965, abcam), H3K4me3 (07-473, Millipore), SOX9 (AB5535, Millipore) and IgG ( . The resuspended beads were rotated o/n at 4°C. The next day, tubes were quickly spun, put on a magnetic rack and supernatant was removed. 150 ul of Dig-wash buffer antibody (20 mM HEPES pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 0.025% Digitonin, and EDTA-free protease inhibitor) were added and tubes mixed by inversion for four times. Supernatant was removed and 150 ul Protein-A-MNase (700 ng/ml) were added along the tube sites, mixed by pipetting and incubated for 1 h at 4°C on the rotator. Supernatant was removed, samples were washed four times with 150 ul Dig-wash buffer, resuspended in 100 ul Dig-wash buffer and stored in wet ice (0°C) to chill down. 2 ul of 100 mM CaCl2 were added and digestion was incubated for 30 min. Digestion reaction was stopped by adding 100 ul 2x STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% Digitonin, 100 ug/ml RNAse A and 50 ug/ml Glycogen). After addition, samples were incubated at 37°C for 30 min for the release of soluble fragments to the supernatant, which was transferred to a new tube. Released DNA was purified by phenol-chloroform extraction.
Sequencing libraries were produced using the NEBNext® Ultra™ II DNA Library Prep Kit for Illumina® (E7645) as described by the manufacturer

value: IgG (PP64B, Millipore)


title: Right bin of Sort-seq on YFP/RFP ratio with mutational librar, replicate-2


title: 25_S25

description: No


title: cr_myod_dmso43 (matr3.wt and yy1.ko) (for double ko comparison)

value: dTag-Matr3, YY1ko

value: DMSO


title: MD6_SOX9

value: metastasis-derived cell line

value: SOX9 (AB5535, Millipore)


title: Far Left bin of Sort-seq on YFP/RFP ratio with mutational librar, replicate-2

value: yeast

value: citirine-boxB, mScarlet-pp7


title: 24_S24

value: F

value: Vaccin


title: 23_S23


title: Far Left bin of Sort-seq on YFP/RFP ratio with mutational library, replicate-1


title: cr_myod_dmso42 (matr3.wt and yy1.ko) (for double ko comparison)

value: myoblast


title: Unsorted reporter yeast expressing mutational scanning librry, replicate-2, sequencing-2, from irfp


title: MD6_H3K27ac

value: H3K27ac (ab4729, abcam)


title: MD6_MED1

value: MED1 (ab64965, abcam)


title: 22_S22


title: Unsorted reporter yeast expressing mutational scanning librry, replicate-2, sequencing-1, from irfp


title: Unsorted reporter yeast expressing mutational scanning librry, replicate-1, sequencing-2, from irfp


title: 18_S18


title: MD6_H3K4me1

value: H3K4me1 (ab8895, abcam)


title: MD6_H3K4me3

value: H3K4me3 (07-473, Millipore)


title: Unsorted reporter yeast expressing mutational scanning librry, replicate-1, sequencing-1, from irfp


title: cr_myod_dmso42 (matr3.wt and yy1.wt) (for double ko comparison)

value: dTag-Matr3, YY1wt

value: MyoD


title: XD5_IgG

value: primary tumor-derived cell line


title: 17_S17

value: Blood


title: Right bin of Sort-seq on iRFP/RFP ratio with mutational librar, replicate-2


title: 16_S16


title: cr_myod_dtag83

value: dTag-Matr3 depleted


title: cr_myod_dtag82


title: 12_S12


title: XD5_SOX9


title: XD5_MED1


title: 11_S11


title: Left bin of Sort-seq on iRFP/RFP ratio with mutational librar, replicate-2


title: Right bin of Sort-seq on iRFP/RFP ratio with mutational librar, replicate-1


title: cr_myod_dtag81


title: cr_myod_dmso41 (matr3.wt and yy1.ko) (for double ko comparison)

value: dTag-Matr3, YY1ko

value: DMSO


title: 10_S10


title: XD5_H3K27ac


title: Left bin of Sort-seq on iRFP/RFP ratio with mutational librar, replicate-1


title: cr_myod_dmso43 (matr3.wt and yy1.wt) (for double ko comparison)


title: cr_myod_dtag43


title: 6_S6

description: No

value: No


title: XD5_H3K4me1


title: cr_myod_dmso41 (matr3.wt and yy1.wt) (for double ko comparison)


title: Far Right bin of Sort-seq on iRFP/RFP ratio with mutational librar, replicate-2

value: yeast


title: XD5_H3K4me3


title: 5_S5

description: No


title: Far Right bin of Sort-seq on iRFP/RFP ratio with mutational librar, replicate-1

value: citirine-boxB, mScarlet-pp7


title: Far Left bin of Sort-seq on iRFP/RFP ratio with mutational library, replicate-1


title: aortic valve interstitial cells, circHIPK3 OE-4

city: Guanzghou

first: Gaopeng

last: Xian

state: Guangdong

address: No. 1838, Baiyun Avenue North

country: China

institute: Nanfang Hospital

data_processing:
cluster analysis,Expression Profiling,Differentially_Expressed_RNAs,RNA_GO Analysis Results
Assembly: hg38
Supplementary files format and content: xlsx, rna_expressio,rna_diff

source_name: Heart

growth_protocol: The AVICs were cultured in M199 growth medium containing penicillin G, streptomycin, amphotericin B and 10% fetal bovine serum, and the medium was changed every three days.

extract_protocol:
The total RNA was isolated from the tissue samples using TRIzol reagent (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions.
The RNA-seq libraries were constructed by using pretreated RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions

value: Heart

value: aortic valve interstitial cells

value: circHIPK6 OE


title: Far Left bin of Sort-seq on iRFP/RFP ratio with mutational librar, replicate-2


title: 4_S4

description: No

value: F


title: cr_myod_dmso83

value: myoblast


title: tIMEC_MED1

value: tIMEC

value: mammary epthelial cell-derived cell line

value: MED1 (ab64965, abcam)


title: tIMEC_SOX9

value: SOX9 (AB5535, Millipore)


title: cr_myod_dmso82

value: MyoD


title: mcm2-1 ago1Δ clr4W31G_230927

city: Bethesda

first: Shiv

last: Grewal

state: MD

address: 9000 Rockville Pike

department: National Cancer Institute

institute: National Institutes of Health

description: mcm2-1 ago1Δ clr4W31G_230927

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the Star aligner (Dobin et al. 2013) and RPM normalized bedgraphs were generated using the Star –outWigNorm option. RPM normalized bedgraphs for IPs were converted to wigs, normalized to DNA input by subtraction saved in bedgraph format using Deeptools (Ramirez et al. 2016). Values that were negative after input subtraction were set to zero in the final bedgraph.

organism: Schizosaccharomyces pombe

growth_protocol: Growth in EMM and YEA, 26°C and 36°C, 30°C

extract_protocol:
Cells were crosslinked using 3% PFA at room temperature for 30 min. Cells were spun at 2,000g for 10 min and pellets were lysed using glass beads and lysis buffer (50mM Hepes/KOH, 140mM NaCl, 1 mM EDTA, 1% Triton X100, 0.1% DOC plus protease inhibitors). Cell lysates were sheared using a Bioruptor-300 (Diagenode) to an approximate size of 300–600 bp.
Sequencing libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer’s protocol and analyzed using an Agilent 4200 TapeStation system (Agilent).

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18/-DS/E ago1::hphMx6 mcm2-1-GFP:kan FLAG-Clr4W31G

value: Abcam anti-H3K9me3 8904

tag: growth

value: Growth in YEA 30degreeC

tag: fixation

value: 3percent PFA


title: aortic valve interstitial cells, circHIPK3 OE-3

value: circHIPK5 OE


title: tIMEC_IgG

value: IgG (PP64B, Millipore)


title: tIMEC_H3K27ac

value: H3K27ac (ab4729, abcam)


title: cr_myod_dmso81

value: DMSO


title: aortic valve interstitial cells, circHIPK3 OE-2

value: Heart

value: aortic valve interstitial cells

value: circHIPK4 OE


title: Input_mcm2-1 ago1Δ clr4W31G_230927

description: Input_mcm2-1 ago1Δ clr4W31G_230927

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI:ura4+ leu1-32 ade6-M210 ura4-D18


title: cr_myod_dmso43

value: myoblast


title: aortic valve interstitial cells, circHIPK3 OE-1

value: circHIPK3 OE


title: tIMEC_H3K4me3

value: tIMEC

value: mammary epthelial cell-derived cell line

value: H3K4me3 (07-473, Millipore)


title: tIMEC_H3K4me1

value: H3K4me1 (ab8895, abcam)


title: cr_myod_dtag42

value: dTag-Matr3 depleted

value: MyoD


title: aortic valve interstitial cells, empty vector-4

value: empty vector


title: cr_myod_dmso42


title: mcm2-1 ago1Δ_230927

description: mcm2-1 ago1Δ_230927

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 ago1::hphMx6 mcm2-1-GFP:kan

value: Abcam anti-H3K9me3 8904

value: Growth in YEA 30degreeC

value: 3percent PFA


title: Input_mcm2-1 ago1Δ_230927

description: Input_mcm2-1 ago1Δ_230927


title: aortic valve interstitial cells, empty vector-3

value: Heart


title: mcm2-1_230927

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 mcm2-1-GFP:kan

value: Abcam anti-H3K9me3 8903


title: Spatial transcriptome of transplanted tissue of kidney

city: Changchun

first: Yang-He

last: Zhang

state: Jilin

address: 126 Xinmin street

institute: Jilin university

description: 10x Genomics

data_processing:
Raw FASTQ files and histology images were processed by sample with the Space Ranger (version spaceranger-1.2.0, 10X Genomics) software with default parameters.
The filtered gene-spots matrix and the fiducial-aligned low-resolution image was used for down-streaming data analyses (Seurat).
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Kidney

extract_protocol:
The Visium Spatial Tissue Optimization Slide & Reagent kit (10X Genomics) was used to optimize permeabilization conditions for the tissue according to Visium Spatial Tissue Optimization User Guide (CG000238, 10X Genomics).
The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to construct sequencing libraries according to the Visium Spatial Gene Expression User Guide (CG000239, 10X Genomics)

value: Kidney


title: cr_myod_dtag41

value: myoblast


title: cr_myod_dmso41

value: DMSO


title: cr_matr3_dtag42


title: Input_mcm2-1_230927


title: aortic valve interstitial cells, empty vector-2

value: aortic valve interstitial cells


title: GFP-negative cells, WTC11 line

city: La Jolla

first: Benjamin

middle: D

last: Gastfriend

address: 9500 Gilman Dr

institute: University of California, San Diego

data_processing:
Basecalling was performed by the Illumina NovaSeq 6000.
A DNA sequence from lentiviral transfer plasmid pWPI extending from the PacI site to the 3’ end of the WPRE (containing the IRES and eGFP CDS) was added to the reference genome (hg38) to permit quantification of transgene-derived transcripts.
RNA-seq FASTQ files were aligned to the resulting reference genome using STAR (version 2.5.3a).
Gene-level counts were generated using the featureCounts function from Subread (version 2.0.3). Transcripts per million (TPM) were calculated using gene lengths derived from featureCounts.
Assembly: hg38
Supplementary files format and content: An Excel spreadsheet containing raw counts and TPM values is provided.

molecule: polyA RNA

growth_protocol: Neural crest cells were differentiated from human pluripotent stem cells as previously described (PMID: 30891496) and maintained in E6-CSFD medium. Neural crest cells were transduced with N3ICD-GFP lentivirus when approximately 50% confluent. E6-CSFD medium was replaced every 2 days and cells analyzed 6 days after transduction.

extract_protocol:
RNA extraction was performed using the RNeasy Plus Micro Kit (Qiagen). Lysates were thawed on ice, processed through gDNA Eliminator spin columns, processed through RNeasy MinElute spin columns per manufacturer instructions, and eluted into RNase-free water.
RNA quality control, library preparation, and sequencing were performed by Novogene Corporation (Sacramento, CA). RNA quantity was assessed using a NanoDrop spectrophotometer; RNA quality was assessed using an Agilent 2100 Bioanalyzer. Poly(A) mRNA enrichment was performed using poly(T) oligo-conjugated magnetic beads, first-strand cDNA synthesis performed using random hexamer primers, second-strand cDNA synthesis performed, and libraries prepared using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs).

treatment_protocol: Neural crest cells were dissociated with Accutase for ~5 min. The Accutase/single cell suspension was transferred to 4× volume of DMEM/F12 medium and centrifuged for 5 min at 200×g, 4°C. Fluoresence-activated cell sorting was used to isolate GFP-negative and GFP-positive populations from cultures 6 days after transduction of neural crest with N3ICD-GFP lentivirus. Resulting suspensions were centrifuged for 5 min at 200×g, 4°C. Supernatants were aspirated and the resulting cell pellets immediately lysed with Buffer RLT Plus (Qiagen) supplemented with 1% β-mercaptoethanol and frozen at –80°C.

value: GFP-negative


title: GFP-positive cells, WTC11 line

value: GFP-positive (mural)


title: cr_matr3_dtag41


title: aortic valve interstitial cells, empty vector-1


title: aortic valve, CAVD-3

data_processing:
cluster analysis,Expression Profiling,Differentially_Expressed_circRNAs,circRNA_GO Analysis Results,circRNA_Visualization,circRNA-miRNA_Network
Assembly: hg38
Supplementary files format and content: xlsx, CircRNA Expression Profiling,Differentially Expressed circRNAs

extract_protocol:
The total RNA was isolated from the tissue samples using TRIzol reagent (Life Technologies, Carlsbad, CA) according to the manufacturer’s instructions. Before constructing the RNA-seq libraries, the Ribo-Zero rRNA Removal Kit (Illumina,San Diego, CA, USA) and the CircRNA Enrichment Kit (Cloud-seq,USA) were used to remove the rRNA and enrich the circRNAs.
The RNA-seq libraries were constructed by using pretreated RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions


title: Input_mcl1-4 ago1Δ_230927

description: Input_mcl1-4 ago1Δ_230927

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M216 ura4-D18 ago1::hphMx6 mcl1-3xFLAG:kanMX

value: Abcam anti-H3K9me3 8902


title: mcl1-4 ago1Δ_230927

description: mcl1-4 ago1Δ_230927


title: aortic valve, CAVD-2


title: cr_matr3_dmso43


title: Neural crest cells, WTC11 line

value: Neural crest


title: GFP-positive cells, IMR90-4 line


title: cr_matr3_dmso42


title: GFP-negative cells, IMR90-4 line


title: aortic valve, CAVD-1


title: cr_matr3_dmso41


title: Neural crest cells, IMR90-4 line


title: ago1Δ_230927

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 ago1::hphMx6

value: Abcam anti-H3K9me3 8900


title: cr_matr3_dtag43

value: dTag-Matr3 depleted


title: mcl1-4_230927

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI:ura4+ leu1-32 ade6-M216 ura4-D18 mcl1-3xFLAG:kanMX

value: Abcam anti-H3K9me3 8901

value: Growth in YEA 30degreeC


title: cr_h3k4me3_dtag42


title: Input_mcl1-4_230927

value: 3percent PFA


title: aortic valve, Non-CAVD-4

description: d-CA

value: Heart


title: cr_h3k4me3_dtag41


title: GFP-positive cells, H9 line


title: GFP-negative cells, H9 line


title: aortic valve, Non-CAVD-1

description: a-CA


title: cr_h3k4me3_dmso42


title: aortic valve, Non-CAVD-2

description: b-CA


title: Input_ago1Δ_230927


title: WT_230927

value: mat1M-smt0 mat2PDelta(Bg-Bs)-XbaI:ura4+ leu1-32 ade6-M210 ura4-D18

value: Abcam anti-H3K9me3 8899


title: Neural crest cells, H9 line


title: GFP-positive cells, DF19-9-11T line


title: mcm2-1_pob3Δ_230222

data_processing:
Single ended fastq format sequences derived from ChIP-seq data were quality-trimmed using fastp (Chen et al. 2018).
Trimmed fastqs were aligned to the S. pombe reference (Wood et al. 2002) using the BWA aligner (Li H. and Durbin R. 2009) and fold enrichment bedgraphs were generated using Macs2 (Zhang Y et al, 2008).

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M216 ura4/ura4-D18 pob3::kanMx4, mcm2-1-GFP:kanMx

value: Abcam anti-H3K9me3 8905


title: cr_h3k27ac_dtag42

value: myoblast


title: Pre-osteoclasts, OSS-Ift88 shRNA

city: Seoul

first: Jinman

last: Kim

address: 88, Olympic-ro 43-gil, Songpa-gu

country: South Korea

institute: Asan medical center

data_processing:
bcl2fastq v1.8.4 package was used for basecalling.
Sequenced reads were trimmed for adaptor sequence and masked for low-complexity or low-quality sequence with Trimmomatic 0.32.
To estimate expression levels, the RNA-Seq reads were mapped to the genome of Mus musculus using TopHat 2.0.13, which is capable of reporting split-read alignments across splice junctions and determined using Cufflinks 2.2.1 software in default options.
The reference genome sequence of Mus musculus (mm10) and annotation data were downloaded from UCSC. The transcript counts in isoform level were calculated, and the relative transcript abundances were measured in FPKM (Fragments Per Kilobase of exon per Million fragments mapped) using Cufflinks.
Raw data (the reads for each transcript) were normalized by FPKM (Fragments Per Kilobase of exon model per Millon mapped fragments).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

source_name: Bone

growth_protocol: Pre-osteoclast were cultured in MEMa medium containing 10% FBS, antibiotics, MCSF and RANKL in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRIzol reagent.
A library was prepared with 1ug of total RNA for each sample by Illumina TruSeq mRNA Sample Prep kit (Illumina, Inc., San Diego, CA, USA).

treatment_protocol: Osteoclast differentiation was induced by treatment of MCSF and RANKL in culture medium for 2 days. Orbital shear stress stimulation was applied to the differentiated cells for 24 hours, and then RNAs were extracted.

value: Bone

value: Primary cells

value: pre-osteoclasts

value: Ift88 knockdown

value: orbital shear stress


title: Pre-osteoclasts, OSS-con shRNA

value: WT


title: GFP-negative cells, DF19-9-11T line

value: GFP-negative


title: Input_230927

value: Abcam anti-H3K9me3 8898


title: Input_mcm2-1_pob3Δ_230222

value: Abcam anti-H3K9me3 8904


title: cr_h3k27ac_dtag41

value: dTag-Matr3 depleted


title: Pre-osteoclasts, CON-con shRNA


title: aortic valve, Non-CAVD-3

description: c-CA


title: CBAM-44728 derived PDX, IPI-549, biol rep 3

first: Jean

last: Zhao

address: 450 Brookline Ave

institute: Dana Farber Cancer Institute

description:
G18
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

data_processing:
Data processing was used the ampliSeqRNA plugin v5.12.0.1 available inside the Ion Torrent suite 5.12 for Ion torrent sequencing platform with default settings for all steps.
Assembly: Mouse: AmpliSeq_Mouse_Transcriptome_v1 (AmpliSeq_Mouse_Transcriptome_V1_Designed.bed);Human  hg19_AmpliSeq_Transcriptome_v1.1 (hg19_AmpliSeq_Transcriptome_21K_v1.bed)
Supplementary files format and content: xlsx: Tab-separated values and matrix file

source_name: CBAM-44728 derived PDX

extract_protocol:
Mouse MLL-AF9+ L-GMPs were sorted from primary transplantation recipients. Lin-CD34+CD38- PDX cells were sorted from PDX mouse models upon vehilce or IPI-549 treatment in vivo. Sorted L-GMP cells or  Lin-CD34+CD38- PDX cells were homogenized in 1 mL of TRIZOL reagent and 0.2 mL of chloroform was added to the samples. Samples were vortexed vigorously for 15 seconds and then incubated at 4℃ for 10 minutes. After centrifugation at 12, 000 g for 15 minutes at 4℃, upper aqueous phase of the samples was carefully removed to a new tube and the total RNA was purified by RNAeasy Mini Kit (QIAGEN) according to the manufacturer’s instruction.
RNA libraries were prepared using Ampliseq Library Prep Kit following manufacturer's protocols for targeted amplicon amplification.
Ion AmpliSeq Transcriptome Mouse Gene Expression Manual Chef-S5; Ion AmpliSeq Transcriptome Human Gene Expression Panel

treatment_protocol: NSG/NSG-SGM3 mice injected with PDX cells were treated once daily by oral gavage with vehicle (5% NMP and 95% PEG 400) and 15 mg/kg of IPI-549 24 hours post transplantation.

value: CBAM-44728 derived PDX

value: patient AML cells

value: Lin-CD34+CD38- AML cells

value: Wild-type


title: Neural crest cells, DF19-9-11T line

value: Neural crest


title: N3ICD-GFP-transduced cells, input, replicate C

data_processing:
Basecalling was performed by the Illumina NovaSeq 6000.
ChIP-seq FASTQ files were aligned to the genome using bowtie2 (version 2.2.1).
Unmapped reads, reads in blacklist regions, and reads from nonchromosomal assemblies were removed from resulting BAM files using sambamba (version 0.8.2), samtools (version 1.11), and bedtools (version 2.30.0).
bigWig (.bw) files were generated using the bamCoverage function in DeepTools (version 3.5.1).
Peaks were called and narrowPeak files generated using MACS3 (version 3.0.0a7) with P-value ≤ 0.0005
Assembly: hg38
Supplementary files format and content: bigWig (.bw) files are provided for all samples; narrowPeak files are provided for non-input samples

growth_protocol: Neural crest cells were differentiated from human pluripotent stem cells as previously described (PMID: 30891496) and maintained in E6-CSFD medium. Neural crest cells were transduced with GFP or N3ICD-GFP lentiviruses when approximately 50% confluent. E6-CSFD medium was replaced every 2 days and cells analyzed 6 days after transduction.

extract_protocol:
DNA was purified using spin columns and reagents provided in the SimpleChIP Enzymatic Chromatin IP kit (CST).
DNA quality control, library preparation, and sequencing were performed by Novogene Corporation (Sacramento, CA).

treatment_protocol: Cells were dissociated with Accutase for ~20 min. The Accutase/single cell suspensions were transferred to 2× volume of DMEM/F12 medium and 1% formaldehyde added to crosslink proteins to DNA. Nuclei preparation, chromatin digestion, chromatin immunoprecipitation, elution, and crosslink reversal were performed using the SimpleChIP Enzymatic Chromatin IP Kit with Magnetic Beads (Cell Signaling Technology, CST, Danvers, MA) and Notch3 antibody (CST #5276) per manufacturer instructions.

value: mural


title: mcm2-1_230222

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 mcm2-1-GFP:kan

value: Abcam anti-H3K9me3 8903

value: Growth in YEA 30degreeC

value: 3percent PFA


title: cr_h3k27ac_dmso41

value: myoblast

value: DMSO


title: CBAM-44728 derived PDX, IPI-549, biol rep 2

description:
G17
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx


title: N3ICD-GFP-transduced cells, input, replicate B


title: cr_ctcf_dtag43

value: CTCF


title: pob3Δ_230222

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 pob3::kanMx4

value: Abcam anti-H3K9me3 8901


title: N3ICD-GFP-transduced cells, input, replicate A


title: GFP-transduced cells, input, replicate C

value: neural crest


title: CBAM-44728 derived PDX, vehicle, biol rep 3

description:
G15
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: vehicle


title: cr_ctcf_dtag41

value: dTag-Matr3 depleted


title: GFP-transduced cells, input, replicate B


title: cr_ctcf_dtag42


title: CBAM-44728 derived PDX, IPI-549, biol rep 1

description:
G16
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: CBAM-44728 derived PDX

value: patient AML cells


title: WT_230222

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI:ura4+ leu1-32 ade6-M210 ura4-D18

value: Abcam anti-H3K9me3 8899


title: Input_pob3Δ_230222

value: Abcam anti-H3K9me3 8900


title: GFP-transduced cells, input, replicate A


title: cr_h3k27ac_dmso42


title: CBAM-44728 derived PDX, vehicle, biol rep 2

description:
G14
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: Lin-CD34+CD38- AML cells

value: Wild-type


title: DFAM-22359 derived PDX, IPI-549, biol rep 3

description:
G12
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

source_name: DFAM-22359 derived PDX

value: DFAM-22359 derived PDX


title: Input_mcm2-1_230222

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 mcm2-1-GFP:kan

value: Abcam anti-H3K9me3 8902

value: Growth in YEA 30degreeC

value: 3percent PFA


title: cr_h3k4me3_dmso41

value: myoblast

value: DMSO


title: cr_ctcf_dmso41

value: CTCF


title: CBAM-44728 derived PDX, vehicle, biol rep 1

description:
G13
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: vehicle


title: Input_WT_230222

value: Abcam anti-H3K9me3 8898


title: N3ICD-GFP-transduced cells, Notch3 ChIP, replicate B

value: mural

value: Notch3 (CST #5276)


title: atac_wt02

data_processing:
RNAseq, SLAMseq: RNA-seq experiments were processed by the HISAT pipeline (Kim et al 2019), which includes alignment, filtering, and gene quantification steps. Differential expression analysis was carried out using DESeq2 using default settings. We performed SLAM-seq at 4 hrs. post dTAG47 exposure and quantified nascent RNA transcription using the SlamDunk pipeline (Neumann et al., 2019, Harada, Taku et al., 2022). Differential analysis of SLAM-seq data was performed on the transcript read counts with thymine-to-cytosine (T>C) conversions following s4U metabolic labeling (newly synthesized RNA) and also on the total transcript read counts (total RNA). DESeq2 was again used for differential nascent transcript analysis.
CUT&RUN: We used CUT&RUNTools (Zhu et al., 2019) to process MyoD, YY1, CTCF, and Rad21 CUT&RUN experiments from raw fastq reads. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody). For experiments per group, we pooled all experiments’ BAM files and performed MACS2 (Zhang et al., 2008) peak calling to get merged peaks. Peak-flanking regions were obtained, and stored for the purpose of normalization. Bamliquidator was called to compute the number of reads in each peak-flanking region in each experiment. DESeq2’s estimateSizeFactor() (Love et al., 2014) was called on the matrix of peak-flanking region reads over all experiments to calculate a scale factor per experiment. With the scale factor computed, the original BAM file was subsampled at a rate equal to the scale factor to get a normalized BAM file. Finally, MACS2 was called to generate peaks from the normalized BAM file. A normalized bigwig file was generated for visualization.
ATACseq: ATAC-seq data were processed using a procedure similar to CUT&RUN described above, which included reads trimming, alignment to the reference genome, BAM duplicate marking, and fragment size filtering. A special note is that we kept paired-end fragments that are <150bp instead of <120bp setting for TF CUT&RUN. For ATAC-seq data normalization, we adopted the same background-based data normalization as used in CUT&RUN (see CUT&RUN section).
Chip-seq: We used a ChIP-seq data processing pipeline (Zhu et al, 2019) to perform reads trimming, alignment to the reference genome (mm10), and BAM file duplicate marking. Next, we performed background-based data normalization on the group of experiments to be normalized together (i.e. Matr3 dTAG47 & DMSO, or Matr3 WT & KO of a given antibody), similar to the normalization procedure used in CUT&RUN data.
Assembly: mm10
Supplementary files format and content: Bigwig - normalized bigwig files for visualization
Supplementary files format and content: TXT - gene expression matrix (counts)
Supplementary files format and content: SLAMseq TXT – Slamseq nascent gene expression matrix. Columns: Gene, CoverageOnTs in 3’UTR, ConversionOnTs in 3’UTR, Conversion rate, Total Reads with T>C conversion in 3’UTR, Total Reads with Ts in 3’ UTR, Conversion rate (Reads)

extract_protocol:
ATAC-seq was performed as described (Buenrostro et al., 2015). Total 50,000 cells were washed with cold PBS and lysed using cold lysis buffer (10mM Tris-HCl, pH 7.4, 10mM NaCl, 3mM MgCl2 and 0.1% IGEPAL CA-630). The pellet was then resuspended in the transposition reaction mix (25 μL 2× TD buffer, 2.5μLTn5 Transposes (Illumina) and 22.5μL nuclease-free water) and incubated at 37°C for 30min. Immediately following transposition incubation, DNA was purified using a Qiagen MinElute Kit.
ATAC-seq libraries were generated using Ad1_noMX and Ad2.1-2.4 barcoded primers (Buenrostro et al., 2013) and were amplified for 6-9 total cycles. All libraries were sequenced on Illumina NextSeq500 with pair-end reads (2X 42bp, 8bp index).

treatment_protocol: As for acute depletion, dTag-Matr3 cells were treated with DMSO/dTAG47 (500nM) for 4hrs, 8hrs. As for steady state, Matr3KO cells and wildtype cells were used.

value: wildtype

value: growth


title: DFAM-22359 derived PDX, IPI-549, biol rep 2

description:
G11
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: patient AML cells


title: Input_mcl1-4 pob3Δ_230426

description: Input_mcl1-4 pob3Δ_230426

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M216 ura4-D18 mcl1-3xFLAG:kanMX pob3::natMx6

value: Abcam anti-H3K9me3 8904


title: mcl1-4_230426

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI:ura4+ leu1-32 ade6-M216 ura4-D18 mcl1-3xFLAG:kanMX

value: Abcam anti-H3K9me3 8903


title: atac_wt01


title: N3ICD-GFP-transduced cells, Notch3 ChIP, replicate C


title: DFAM-22359 derived PDX, IPI-549, biol rep 1

description:
G10
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: DFAM-22359 derived PDX

value: Lin-CD34+CD38- AML cells

value: Wild-type


title: Input_mcl1-4_230426

value: Abcam anti-H3K9me3 8902

value: Growth in YEA 30degreeC

value: 3percent PFA


title: N3ICD-GFP-transduced cells, Notch3 ChIP, replicate A


title: atac_ko02

value: myoblast


title: cr_ctcf_dmso42

value: DMSO

value: CTCF


title: atac_ko01


title: pob3Δ_230426

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 pob3::kanMx4

value: Abcam anti-H3K9me3 8901


title: mcl1-4 pob3Δ_230426

description: mcl1-4 pob3Δ_230426

value: Abcam anti-H3K9me3 8905


title: GFP-transduced cells, Notch3 ChIP, replicate B

value: neural crest

value: Notch3 (CST #5276)


title: atac_dtag_82

value: dTag-Matr3 depleted


title: DFAM-22359 derived PDX, vehicle, biol rep 1

description:
G07
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: patient AML cells

value: vehicle


title: WT_230426

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI:ura4+ leu1-32 ade6-M210 ura4-D18

value: Abcam anti-H3K9me3 8899


title: atac_dtag_81


title: shACOX1_3

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for adaptor sequence,and masked for low-complexity or low-quality sequence, then mapped to mm8 whole genome using bowtie v0.12.2 with parameters.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol form Chepelev et al., Nucleic Acids Research, 2009.
Supplementary files format and content: mm8
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

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

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent .Illumina Truseq RNA sample Prep Kit (Cat#FC-122-1001) was used with 1ug of total RNA for the construction.
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: Kidney

value: epithelial cell

value: Knock down ACOX1


title: DFAM-22359 derived PDX, vehicle, biol rep 2

description:
G08
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: DFAM-22359 derived PDX

value: Lin-CD34+CD38- AML cells

value: Wild-type


title: GFP-transduced cells, Notch3 ChIP, replicate A


title: DFAM-68555 derived PDX, IPI-549, biol rep 3

description:
G06
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

source_name: DFAM-68555 derived PDX

value: DFAM-68555 derived PDX


title: Input_WT_230426

value: Abcam anti-H3K9me3 8898

value: Growth in YEA 30degreeC

value: 3percent PFA


title: shACOX1_2


title: atac_dtag_41

value: myoblast


title: Rix1 IRΔ3

description: Rix1 IRΔ3

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+  ade6-M210 ura4/ura4-D18/-DS/E leu1:GFP-rix1 IR-delta3

value: Abcam anti-GFP 291


title: shACOX1_1


title: DFAM-68555 derived PDX, IPI-549, biol rep 2

description:
G05
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: patient AML cells


title: DFAM-68555 derived PDX, IPI-549, biol rep 1

description:
G04
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx


title: GFP-transduced cells, Notch3 ChIP, replicate C

value: neural crest

value: Notch3 (CST #5276)


title: atac_dtag_42

value: dTag-Matr3 depleted


title: DFAM-22359 derived PDX, vehicle, biol rep 3

description:
G09
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: vehicle


title: Rix1 IRΔ2

description: Rix1 IRΔ2

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+  ade6-M210 ura4/ura4-D18/-DS/E leu1:GFP-rix1 IR-delta2

value: Abcam anti-GFP 290


title: DFAM-68555 derived PDX, vehicle, biol rep 3

description:
G03
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx


title: atac_dmso_81

value: DMSO


title: atac_dmso_82


title: shCtrl_3

value: Kidney

value: epithelial cell

value: Control


title: Input_pob3Δ_230426

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+ leu1-32 ade6-M210 ura4-D18 pob3::kanMx4

value: Abcam anti-H3K9me3 8900


title: shCtrl_2


title: Rix1

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+  ade6-M210 ura4-D18/-DS/E leu1:GFP-rix2

value: Growth in YEA 30degreeC

value: 3percent PFA


title: atac_dmso_42

value: myoblast


title: shCtrl_1


title: DFAM-68555 derived PDX, vehicle, biol rep 1

description:
G01
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: DFAM-68555 derived PDX

value: patient AML cells

value: Lin-CD34+CD38- AML cells

value: Wild-type


title: hen2-4, 57h light, rep2, sRNA-seq

status: Public on Feb 01 2024

city: Cerdanyola del Vallès

first: Julia

middle: I.

last: Qüesta

state: Barcelona

address: Carrer de la Vall Moronta

country: Spain

institute: Centre for Research in Agricultural Genomics

description:
hen2_2_input
hen2.sRNAseq.plus.bedGraph.gz
hen2.sRNAseq.minus.bedGraph.gz

data_processing:
*library strategy: Capped-small RNA sequencing (csRNA-seq)
Reads were trimmed for the csRNA-seq and sRNA-seq using HOMER v4.11.1 with the following command: homerTools trim -3 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -mis 2 -minMatchLength 4 -min 20. Trimmed reads for all samples were mapped to the TAIR10 genome sequence using STAR v2.7.9a with the following options: –outSAMstrandField intronMotif –outMultimapperOrder Random –outSAMmultNmax 1 –outFilterMultimapNmax 10000 –limitOutSAMoneReadBytes 10000000. The resulting csRNA-seq and sRNA-seq BAM files were filtered using samtools v1.14 and custom AWK scripts to exclude reads with more than 1 mismatch, a MAPQ score of less than 10, gaps, soft-clipping or a length outside of the range of 20-70 nucleotides. HOMER format tag directories were created using the makeTagDirectory program with the options -genome tair10 -checkGC.
The findcsRNATSS.pl program from HOMER v4.11.1 was used to identify TSS peaks from the csRNA-seq samples with the following options: -includeSingleExons -genome tair10 -ntagThreshold 1 -noFilterRNA -minDistDiff 0.01 -L 1.5. The corresponding sRNA-seq and total RNA-seq BAM files for each sample were also included in the command via the -i and -rna options, respectively. Only TSS peaks present in both replicates were kept, and a final merged TSS peak set was created using the mergePeaks program from HOMER78. TSSs were annotated as belonging to an existing Araport11 transcript30 if they were present either within the 5′ region of the transcript or 500 bp upstream to 200 bp downstream of a TSS, or were within the first 25% of the transcript length using R v4.3.1 and base Bioconductor packages.
TMM-normalized counts per million (CPM) from all csRNA-seq samples were obtained by first reading the counts into R v4.3.1, then normalizing them using the calcNormFactors and cpm functions from the edgeR package.
Coverage tracks in bedGraph format were generated from the csRNA-seq and sRNA-seq tag directories using the makeUCSCfile program from HOMER v4.11.1. The csRNA-seq files were further converted to bigWig using R v4.3.1 with the edgeR package to TMM-normalize the signal density.
Assembly: TAIR10
Supplementary files format and content: Transcription start site (TSS) tab-separated quantification tables contain a column of TSS names and columns of counts for each csRNA-seq sample.
Supplementary files format and content: csRNA-seq read pileups per strandare provided in bigWig format.
Supplementary files format and content: sRNA-seq (input) read pileups per strand are provided in bedGraph format.

organism: Arabidopsis thaliana

source_name: Seedlings

growth_protocol: Arabidopsis thaliana seeds were surface-sterilized using the gas product of 100 mL of bleach mixed with 3 mL hydrochloric acid for 1 h, followed by stratification in water in the dark at 4 ˚C. Seeds were grown in 50 mL liquid ½ MS in 125 mL Erlenmeyer flasks, shaking at 180 RPM, in continuous light at 22 ˚C.

extract_protocol:
50 mg of sample (or 25 mg for dry seeds) was flash-frozen in liquid nitrogen and ground to a powder with a mortar and pestle. 1.5 mL of extraction buffer (EB; 100 mM Tris-HCl pH 9.5, 150 mM NaCl, 5 mM EDTA pH 8, 1% sarkosyl) was prepared per sample, and 7.5 µL beta-mercaptoethanol was added to each EB aliquot and briefly vortexed. After addition of the EB to the frozen ground tissue powder, the homogenate was mixed vigorously and left on ice for 10 min, with intermittent vortexing. This was followed by a 10 min max-speed centrifugation at 4 ˚C in a benchtop centrifuge. 1 mL of supernatant (avoiding the starchy upper-most layer) was transferred to a new tube and mixed with 1 mL chloroform. Following a 15 s vortexing step, the mixture was centrifuged as before and 900 µL of the upper phase transferred to a new tube. To this was added 90 µL 3 M NaOAc and 1 mL Tris-buffered phenol-chloroform, followed by vortexing for 15 s and another centrifugation as before. As much clear supernatant as possible was moved to a new tube and gently mixed by inversion with an equal volume isopropanol and incubated at 4 ˚C for 1 h. The precipitated RNA was pelleted by a 20 min max-speed centrifugation at 4 ˚C. The supernatant was discarded and the pellet washed with 800 µL ice-cold 75% ethanol, followed by a 5 min centrifugation at 7,500 x g at 4 ˚C. The supernatant was discarded, further removed with a pipette after pulse-spinning, and left inverted to dry for 2 min. The pellet was dissolved in 100 µL nuclease-free water, to which 10 µL DNaseI buffer (ThermoFisher Scientific), 5 µL DNaseI (ThermoFisher Scientific), and 1 µL RiboLock (ThermoFisher Scientific) was added and left to incubate at 37 ˚C for 30 min. The resulting DNA-free RNA was isolated using a modified RNA purification protocol. Briefly, 240 µL nuclease-free water was added to the DNaseI reaction alongside 40 µL solubilization buffer (200 mM Tris-HCl pH 7.5, 10 mM EDTA pH 8, 5% SDS) and vortexed. Afterwards 40 µL 3 M NaOAc and 800 µL Tris-buffered phenol-chloroform was added and again vortexed for 15 s, followed by a max-speed centrifugation for 5 min at 4 ˚C. The supernatant was transferred to a new tube containing 800 µL chloroform and vortexed for 15 s, followed by another centrifugation as before. The supernatant was again transferred to a new tube, this time to one containing 1 mL ice-cold ethanol, gently mixed by inversion, and left at -80 ˚C overnight. The following day the tube was centrifuged as before for 20 min. The supernatant was discarded and the pellet was washed with 800 µL 75% ethanol, followed by a 5 min centrifugation at 7,500 x g at 4 ˚C. The supernatant was removed, and again removed using a pipette after pulse spinning. After leaving the tubes to dry inverted for 2 min, the pellet was dissolved in 27 µL nuclease-free water (of which 1.5 µL was used for quantification with a NanoDrop (ThermoFisher Scientific)) and stored at -80 ˚C. RNA integrity was assessed by running 1 µg RNA in a denaturing RNA gel and 100 ng RNA with a Bioanalyzer RNA analysis chip (Agilent). 15 µg of RNA in 15 µL TET buffer (10 mM Tris-HCl pH 7.5, 0.1 mM EDTA, 0.05% Tween-20) was mixed with 15 µL FLB solution (95% formamide, 0.005 % bromophenol blue, 0.005% xylene cyanol, 1 mM EDTA) and incubated at 75 ˚C for 5 min before cooling on ice. This was then run at 200 V for 40 min in a 6 mL 15% urea gel (2.88 g urea, 3 mL 30% acrylamide, 600 µL 10X TBE, 60 µL 10% APS, 2.4 µL TEMED, up to 6 mL with water) which had been pre-run for 30 min in 1X TBE. The gel was incubated in 0.5 µg/mL ethidium bromide (in 1X TBE) for 2 min in the dark with gentle rocking. Using a scalpel and a UV imager, the gel was cut from beneath the lowest visible band to the one-third point from the bottom marker to the top marker for each lane. The gel piece was placed in a 0.5 mL LoBind tube (Eppendorf) with three holes poked out at the bottom using 22 gauge hypodermic needles (Terumo), which itself was placed in a 2 mL LoBind tube (Eppendorf) and centrifuged at maximum speed in a benchtop centrifuge for 2 min. To the resulting slurry 500 µL GEB solution (0.4 M NaOAc pH 5.5, 10 mM Tris pH 7.5, 1 mM EDTA, 0.05% Tween-20) was added and incubated for 2 h in the dark with gentle shaking. This was then transferred to a PVDF 0.45 µm filter column (Merck) held in a 2 mL LoBind tube (Eppendorf) and centrifuged for 2 min at 1000 x g. The column was removed, 1.5 µL GlycoBlue (ThermoFisher Scientific) and 1.5 mL ice-cold ethanol added, and following mixing by inversion the tube was incubated overnight at -80 ˚C. The following morning the RNA was centrifuged at maximum speed in a cooled benchtop centrifuge (4 ˚C) for 30 min. The supernatant was removed and the pellet washed with 1 mL ice-cold 75% ethanol, followed by a final centrifugation at 7,500 x g for 5 min. The pellet was air-dried for 2 min and resuspended in 6 µL nuclease-free water containing 0.05% Tween-20.
Small RNA samples were incubated at 75 ˚C for 2 min before cooling on ice. For the sRNA-seq, 0.6 µL of the sample was transferred to a new tube containing 1 µL nuclease-free water containing 0.05% Tween-20 and set aside. 14 µL Terminator mastermix (10.75 µL nuclease-free water containing 0.05% Tween-20, 2 µL Terminator Buffer A (Lucigen), 0.25 µL RiboLock (ThermoFisher Scientific), 1 µL Ter51020 (Lucigen)) was added to the sample and incubated for 1 h at 30 ˚C. 30 µL CIP mastermix (24 µL nuclease-free water containing 0.05% Tween-20, 5 µL CutSmart buffer (New England Biolabs), 1 µL CIP (New England Biolabs)) was then mixed in and incubated for 45 min at 37 ˚C. Following this, 50 µL RNAClean XP beads (Beckman Coulter) were added and the solution mixed. 100 µL isopropanol was then added, the tube mixed, and incubated on ice for 10 min. The tube was placed in a magnetic rack for 5 min. The supernatant was removed and the beads were washed twice using 200 µL 80% ethanol containing 0.05% Tween-20. The beads were then air-dried and resuspended in 25 µL nuclease-free water containing 0.05% Tween-20. The tube was incubated at 75 ˚C for 3 min before cooling on ice. 25 µL CIP mastermix (18.5 µL nuclease-free water containing 0.05% Tween-20, 5 µL CutSmart buffer [New England Biolabs], 0.5 µL RiboLock (ThermoFisher Scientific), 1 µL CIP (New England Biolabs)) was added, the tube mixed, and the reaction incubated at 37 ˚C for 45 min. An additional 100 µL nuclease-free water containing 0.05% Tween-20 was added and the tube was placed in a magnetic rack for 5 min. The supernatant was transferred to a new 1.5 mL microcentrifuge tube. 500 µL TRIzol solution (Merck) was added and the tube was vortexed. 140 µL chloroform was added and again vortexed. The tube was centrifuged for 10 min in a benchtop centrifuge. The supernatant was transferred to a new 1.5 mL microcentrifuge tube, to which was added 1/10th volume 3 M NaOAc and 0.5 µL GlycoBlue (ThermoFisher Scientific) and vortexed. An equal volume of isopropanol was added and mixed by inversion, and left to incubate on ice for 20 min. The tube was centrifuged at max speed for 30 in in a cooled benchtop centrifuge (4 ˚C). The supernatant was discarded and the pellet washed with 400 µL 75% ethanol. A small volume containing the pellet was transferred to a PCR tube and spun down before discarding the ethanol wash and leaving to air-dry. The pellet was then dissolved in 3 µL nuclease-free water containing 0.05% Tween-20. This and the previously set aside sample for the sRNA-seq were incubated at 75 ˚C for 90 s before cooling on ice. To each were added 5 µL decapping mastermix (0.8 µL T4 RNA Ligase buffer (New England Biolabs), 3 µL PEG 8000 (New England Biolabs), 0.3 µL RiboLock (ThermoFisher Scientific), 1 µL RppH (New England Biolabs)) and incubated for 1 h at 37 ˚C after thorough mixing. The samples were then cooled on ice. sRNA-seq and csRNA-seq libraries were then prepared using the NEBNext Small RNA library kit (New England Biolabs) following the manufacturers protocol.

value: Seedlings

value: hen2-4, 57h light

tag: molecule type

value: Input RNA


title: rrp4-2, 57h light, rep1, sRNA-seq

description:
rrp4_1_input
rrp4.sRNAseq.plus.bedGraph.gz
rrp4.sRNAseq.minus.bedGraph.gz

value: rrp4-2, 57h light


title: Rix1 input

description: Rix1 input

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+  ade6-M210 ura4-D18/-DS/E leu1:GFP-rix1

value: Abcam anti-GFP 290


title: atac_dmso_41

value: DMSO


title: rrp4-2, 57h light, rep2, sRNA-seq

description:
rrp4_2_input
rrp4.sRNAseq.plus.bedGraph.gz
rrp4.sRNAseq.minus.bedGraph.gz


title: hen2-4, 57h light, rep1, sRNA-seq

description:
hen2_1_input
hen2.sRNAseq.plus.bedGraph.gz
hen2.sRNAseq.minus.bedGraph.gz


title: Seedling, 57h light, rep2, sRNA-seq

description:
L57_2_input
L57.sRNAseq.plus.bedGraph.gz
L57.sRNAseq.minus.bedGraph.gz

value: Seedling, 57h light


title: slc_3

city: Guangzhou

first: Ke

last: Song

address: No.1023,South Shatai Road, Baiyun District

institute: Southern Medical University

data_processing:
All reads were processed with cutadapt v1.9.1 to remove adaptors and poly-A sequences, and the sequenced fragments were mapped to the mouse genome and assembled using CLC Main Workbench
The DESeq package was used to calculate expression levels for normalized counts. Genes with counts greater than one were included in further analyses
Assembly: mm10
Supplementary files format and content: text file

source_name: SLC

growth_protocol: The testes were dissected from 7-day-old C57BL/6 mice, and the tunica albuginea was carefully removed, after which the testes were minced into small pieces. Interstitial cells were dissociated from seminiferous tubules using 1 mg/mL collagenase type IV (Gibco, 17104-019) in Dulbecco’s modified Eagle’s medium (DMEM)/F12 (Gibco, 11320033) at 37°C for 15 min. After the addition of DMEM/F12 containing 10% fetal bovine serum (VISTECH, SE100-011) to stop collagenase activity, the samples were centrifuged at 1500 × g for 3 min at room temperature. The pellets were resuspended in PBS and filtered through a 70 µm filter. The CD51+ cells were enriched by FACS using an Influx Cell Sorter (Becton Dickinson), after which they were seeded in SLC culture medium. The medium consisted of DMEM/F12 supplemented with 1 nM dexamethasone (Sigma, D4902), 1 ng/mL LIF (Sigma, LIF2005), 5 μg/L insulin-transferrin-sodium selenite (Gibco, 41400045), 5% chicken embryo extract (US Biologicals, C3999), 0.1 mM β-mercaptoethanol (Gibco, 21985023), 1% nonessential amino acids (Gibco, 11140050), 1% N2 (Gibco, 17502001) and 2% B27 (Gibco, 17504044) supplements, 20 ng/mL basic fibroblast growth factor (Invitrogen, RFGFB50), epidermal growth factor (PeproTech, 31509), platelet-derived growth factor (PeproTech, 31518), and oncostatin M (PeproTech, 30010). To isolate BMSCs, 7-day-old C57BL/6 mice were sacrificed, and both sides of their femurs and tibias were removed and temporarily stored in DMEM (GIBCO, C11885500BT) containing 1× penicillin/streptomycin (Gibco, 15140122) on ice. Subsequently, the majority of the muscles and connective tissues were scraped, and the ends of the femurs and tibias were cut using scissors to expose the bone marrow. The bone marrow was sucked using a syringe and flushed into fresh medium. A single-cell suspension was obtained by filtering the above flush fluid through a 70 μm cell strainer, followed by centrifugation and resuspension. The cell suspension was transferred into a T25 culture flask and cultured in DMEM supplemented with 10% FBS and 1 × penicillin/streptomycin. The purified BMSCs were obtained by gradually replacing the medium with fresh medium to remove nonadherent cells at different time points and subculturing the cells for 3 weeks.

extract_protocol:
Total RNA was isolated with TRIzol
NEBNext Ultra RNA Library Prep Kit for Illumina

value: SLC


title: slc_2


title: Germinating seed, 26h light, rep1, sRNA-seq

description:
L26_1_input
L26.sRNAseq.plus.bedGraph.gz
L26.sRNAseq.minus.bedGraph.gz

source_name: Seeds

value: Seeds

value: Germinating seed, 26h light


title: Rix1 IRΔ1

description: Rix1 IRΔ1

value: mat1M-smt0 mat2Pdelta(Bg-Bs)-XbaI::ura4+  ade6-M210 ura4/ura4-D18/-DS/E leu1:GFP-rix1 IR-delta1

value: Growth in YEA 30degreeC

value: 3percent PFA


title: bmsc_3

source_name: BMSC

value: BMSC


title: Seedling, 57h light, rep1, sRNA-seq

description:
L57_1_input
L57.sRNAseq.plus.bedGraph.gz
L57.sRNAseq.minus.bedGraph.gz


title: slc_1


title: bmsc_1


title: bmsc_2


title: Germinating seed, 6h light, rep2, sRNA-seq

description:
L6_2_input
L6.sRNAseq.plus.bedGraph.gz
L6.sRNAseq.minus.bedGraph.gz

value: Germinating seed, 6h light


title: Germinating seed, 6h light, rep1, sRNA-seq

description:
L6_1_input
L6.sRNAseq.plus.bedGraph.gz
L6.sRNAseq.minus.bedGraph.gz


title: CD45- EAE Brain, C3 negative

city: Baltimore

first: Matthew

last: Smith

address: 600 N Wolfe Street

department: Neurology

institute: Johns Hopkins University

library_source: transcriptomic single cell

data_processing:
Raw fastq files were processed with cellranger (v6.1.2) with "Include introns" set to false
Assembly: Reference used for cellranger was a custom reference built using Ensembl GRCm39.104 transcriptome with the sequence for tdTomato added (gene called "TDT")
Supplementary files format and content: Filtered tab seperated and matrix files generated by cellranger for each sample

source_name: Brain

growth_protocol: Mice were maintained in temperature-controlled animal facility at Johns Hopkins University School of Medicine with 12 h/12 h light/dark cycles and fed 18% autoclaved feed and water ad libitum

extract_protocol:
Mice were euthanized with isoflurane followed by perfusion with chilled HBSS. Brains were extracted, chopped into small pieces, then digested with 20U/mL Papain and 100U/mL DNAse I in digestion buffer (EBSS with 22.5mM D(+)-glucose, 26mM NaHCO3, 0.5mM EDTA, and 1mM L-cysteine at pH 7.4) under slow rotation at 37c  for 45 minutes with manual trituration steps every 15 minutes. After filtering, myelin debris was removed with 30% percoll solution. Cells from 7 animals (3 male, 4 female) were pooled and stained for viability (L/D Fixable NIR) and CD45 (anti-CD45 Pacific Blue) then two populations were sorted: viable;CD45-;C3-tdTomato+ and CD45-;C3-tdTomato-. Following sorting, cells were washed, counted, and loaded onto 2 seperate lanes (Pos cells in 1 lane, Neg cells in the other) of a 10X Chromium Chip G then partitioned into GEMs on a Chromium Controller following manufacturer's recommended protocol.
Libraries were constructed and sequenced using 10X 3' 3.1 chemistry according to manufacturer's recommendations

treatment_protocol: Mice were immunized with MOG35-55 emulsion (150μl of emulsion containing 150μg MOG35-55 peptide, 600μg Mtb) subcutaneously. On day of immunization and 2 days later, mice were also injected with 250ng pertussis toxin intraperitoneally. Mice were monitored for onset of EAE symptoms (all mice reached score greater than 1.0 - total tail tone loss) until 19 days post-immunizaiton.

value: Brain

value: 3 males, 4 females pooled into 1 sample

value: CD45- brain cells

value: C3-tdTomato Reporter homozygous

value: EAE 19 days


title: Germinating seed, 72h stratification, rep2, sRNA-seq

description:
S72_2_input
S72.sRNAseq.plus.bedGraph.gz
S72.sRNAseq.minus.bedGraph.gz

value: Germinating seed, 72h stratification

value: Input RNA


title: Germinating seed, 24h stratification, rep2, sRNA-seq

description:
S24_2_input
S24.sRNAseq.plus.bedGraph.gz
S24.sRNAseq.minus.bedGraph.gz

value: Germinating seed, 24h stratification


title: Germinating seed, 72h stratification, rep1, sRNA-seq

description:
S72_1_input
S72.sRNAseq.plus.bedGraph.gz
S72.sRNAseq.minus.bedGraph.gz


title: DFAM-68555 derived PDX, vehicle, biol rep 2

description:
G02
Column names: Genes, G01, G02, G03, G04, G05, G06, G07, G08, G09, G10,G11, G12, G13, G14, G15, G16, G17, G18
HG_PIK3CG_PDX_transcriptome.xlsx

value: DFAM-68555 derived PDX

value: patient AML cells

value: Lin-CD34+CD38- AML cells

value: Wild-type

value: vehicle


title: Germinating seed, 24h stratification, rep1, sRNA-seq

description:
S24_1_input
S24.sRNAseq.plus.bedGraph.gz
S24.sRNAseq.minus.bedGraph.gz

value: Seeds


title: Germinating seed, 26h light, rep2, sRNA-seq

description:
L26_2_input
L26.sRNAseq.plus.bedGraph.gz
L26.sRNAseq.minus.bedGraph.gz

value: Germinating seed, 26h light


title: rrp4-2, 57h light, rep1, csRNA-seq

description:
rrp4_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
rrp4.csRNAseq.plus.bw
rrp4.csRNAseq.minus.bw

value: Seedlings

value: rrp4-2, 57h light

value: Capped-small enriched RNA


title: rrp4-2, 57h light, rep2, csRNA-seq

description:
rrp4_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
rrp4.csRNAseq.plus.bw
rrp4.csRNAseq.minus.bw


title: 3LL_Vehicle_Mouse4_Tumour1

city: London

first: Miriam

last: Molina-Arcas

address: 1 Midland Road

country: United Kingdom

institute: The Francis Crick Institute

data_processing:
Mapped using nfcore/rnaseq pipeline with STAR and RSEM
The R package DESeq2 was used to perform differential analysis between treatment groups
Gene set enrichment analysis was carried out with the R package fgsea using a ranked list of Wald statistic values calculated by DESeq2 for each comparison.
Genes were taken from the Hallmark set available at MSigDB using the R package msigdbr.
Assembly: mouse GRCm38 genome
Supplementary files format and content: tab separated rsem output with raw counts
Supplementary files format and content: tab separated DESEQ2 output  vst normalised expression

source_name: Lung tumour

growth_protocol: Lung tumours were induced by intravenous injections of 1 million 3LL-ΔNRAS cells and scaned by microCT scan after 2weeks and 3 days.

extract_protocol:
RNA was extracted via a column-based method (QIAGEN)
NEBNext Ultra II Directional PolyA mRNA (New England Biolabs)

treatment_protocol: Mice were treated daily for a week

value: Lung tumour

value: Mixed

value: Vehicle


title: SP_TMDI_memory_biol_rep2

city: Geneva

first: Liqing

last: Cheng

address: 1 rue Michel-Servet 1

country: Switzerland

institute: University of Geneva

description:
SP_rep2
Raw_counts containing spleen memory T.tsv

data_processing:
Read were mapped to the UCSC mm10 mouse genome with STAR v.2.7.4.
The biological QC was performed with picard tools
Table of counts was prepared with HTseq v0.9.1.
After normalization, the differential expression analysis was performed with the package edgeR (v1.34.1) in R.
PCA were obtained using Deseq2
Assembly: UCSC mm10 mouse genome
Supplementary files format and content: tsv file containing raw counts of each sample (naïve, mLN, LILP, SP memory)

source_name: spleen

extract_protocol:
RNA was harvested using Rneasy micro plus kit (Qiagen).
Nextera Smarter following manufacture's protocol

value: spleen

value: transferred CD8+ OTI T cells sorted at day30 from spleen

value: WT

tag: infection

value: Lm-OVA infection in recipient mice


title: SP_TMDI_memory_biol_rep3

description:
SP_rep3
Raw_counts containing spleen memory T.tsv


title: SP_TMDI_memory_biol_rep1

description:
SP_rep1
Raw_counts containing spleen memory T.tsv


title: 3LL_Vehicle_Mouse4_Tumour4


title: 3LL_Vehicle_Mouse3_Tumour1


title: hen2-4, 57h light, rep2, csRNA-seq

description:
hen2_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
hen2.csRNAseq.plus.bw
hen2.csRNAseq.minus.bw

value: hen2-4, 57h light


title: Seedling, 57h light, rep2, csRNA-seq

description:
L57_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
L57.csRNAseq.plus.bw
L57.csRNAseq.minus.bw

value: Seedling, 57h light


title: CD45- EAE Brain, C3 positive

value: Brain

value: 3 males, 4 females pooled into 1 sample

value: CD45- brain cells

value: C3-tdTomato Reporter homozygous

value: EAE 19 days


title: hen2-4, 57h light, rep1, csRNA-seq

description:
hen2_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
hen2.csRNAseq.plus.bw
hen2.csRNAseq.minus.bw

value: Seedlings


title: Germinating seed, 26h light, rep2, csRNA-seq

description:
L26_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
L26.csRNAseq.plus.bw
L26.csRNAseq.minus.bw

value: Seeds

value: Germinating seed, 26h light


title: Germinating seed, 26h light, rep1, csRNA-seq

description:
L26_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
L26.csRNAseq.plus.bw
L26.csRNAseq.minus.bw

value: Capped-small enriched RNA


title: 3LL_Vehicle_Mouse2_Tumour1

value: Lung tumour

value: Mixed


title: 3LL_Vehicle_Mouse1_Tumour2

value: Vehicle


title: Seedling, 57h light, rep1, csRNA-seq

description:
L57_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
L57.csRNAseq.plus.bw
L57.csRNAseq.minus.bw


title: 3LL_RMC-4550_Mouse8_Tumour2


title: 3LL_Vehicle_Mouse1_Tumour1


title: Germinating seed, 6h light, rep1, csRNA-seq

description:
L6_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
L6.csRNAseq.plus.bw
L6.csRNAseq.minus.bw

value: Germinating seed, 6h light


title: Germinating seed, 6h light, rep2, csRNA-seq

description:
L6_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
L6.csRNAseq.plus.bw
L6.csRNAseq.minus.bw


title: 3LL_RMC-4550_Mouse8_Tumour1


title: Germinating seed, 72h stratification, rep2, csRNA-seq

description:
S72_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
S72.csRNAseq.plus.bw
S72.csRNAseq.minus.bw

value: Germinating seed, 72h stratification


title: Dry seed, rep2, sRNA-seq

description:
DS_2_input
DS.sRNAseq.plus.bedGraph.gz
DS.sRNAseq.minus.bedGraph.gz

value: Dry seed

value: Input RNA


title: Dry seed, rep1, sRNA-seq

description:
DS_1_input
DS.sRNAseq.plus.bedGraph.gz
DS.sRNAseq.minus.bedGraph.gz


title: 3LL_RMC-4550_Mouse7_Tumour1


title: Germinating seed, 72h stratification, rep1, csRNA-seq

description:
S72_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
S72.csRNAseq.plus.bw
S72.csRNAseq.minus.bw


title: 3LL_Vehicle_Mouse3_Tumour2


title: 3LL_RMC-4550_Mouse6_Tumour1


title: 3LL_Vehicle_Mouse2_Tumour2


title: Germinating seed, 24h stratification, rep2, csRNA-seq

description:
S24_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
S24.csRNAseq.plus.bw
S24.csRNAseq.minus.bw

value: Germinating seed, 24h stratification


title: Dry seed, rep1, csRNA-seq

description:
DS_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
DS.csRNAseq.plus.bw
DS.csRNAseq.minus.bw


title: Germinating seed, 24h stratification, rep1, csRNA-seq

description:
S24_1_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
S24.csRNAseq.plus.bw
S24.csRNAseq.minus.bw


title: 3LL_RMC-4550_Mouse6_Tumour2


title: 3LL_RMC-4550_Mouse5_Tumour2


title: Dry seed, rep2, csRNA-seq

description:
DS_2_csRNA
tss.csRNAseq.bed
counts.cpm.csRNAseq.tsv
counts.raw.csRNAseq.tsv
DS.csRNAseq.plus.bw
DS.csRNAseq.minus.bw


title: peripheral blood, P2

city: Bunkyo-ku

first: Yoshitaka

last: Shirasaki

state: Tokyo

address: Hongo 7-3-1

department: Graduate School of Pharmaceutical Science

country: Japan

institute: The University of Tokyo

data_processing:
The obtained sequence data were mapped to the reference genome (GRCh38.87) using Bowtie2 (version 2.3.1), and the number of transcripts was counted using the RSEM software package (1.3.0).
Assembly: hg38
Supplementary files format and content: Comma-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
Peripheral blood was obtained from healthy volunteers. Mononuclear cells were obtained using Lymphoprep (Serumwerk, Berunburg, Germany), according to the manufacturer’s protocols. Lineage-negative (CD3, CD14, CD16, CD19, CD20 and CD56) and CD45-, CD127-, CRTH2- and CD161-positive cells were sorted using a MoFlo XDP flow cytometer (Beckman Coulter, Brea, CA, USA) as ILC2s.
We obtained cDNA from poly(A) RNA of each sample using a SMART-Seq v4 Ultra Low Input RNA Kit for Sequencing (Takara Bio Inc., Shiga, Japan), following the manufacturer’s instructions. The pre-amplified cDNA was obtained after reverse transcription (90 min at 42 °C, 10 min at 70 °C) and pre-amplification (24 cycles (N1–N4) or 18 cycles (P1–P3): 1 min at 95 °C, 10 s at 98 °C, 30 s at 65 °C, and 3 min at 68 °C). After the purification of the amplified cDNA using Agencourt AMPure XP beads (A63881, Beckman Coulter), cDNA sequences were analyzed using Illumina HiSeq with an entrusted analysis service (50 bp single-read, Medical & Biological Laboratories Co., Ltd. Japan).

value: peripheral blood

tag: phenotype

value: hyperactive

value: incubated with IL-2/IL-33/TSLP


title: peripheral blood, P3


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse20_Tumour1


title: 3LL_RMC-4550_Mouse5_Tumour1


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse18_Tumour2


title: peripheral blood, P1


title: 3LL_RMC-4550_Mouse7_Tumour2


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse19_Tumour2


title: HCC38 siGRHL2 ATAC

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

institute: Japanese Foundation for Cancer Research

data_processing:
Fastq files were generated by RTA in Illumina MiSeq or NextSeq 550.
Adaptor sequence were trimmed by Skewer
Reads were mapped to hg38 genome by bowtie2
PCR de-duplicate was performed by Picard
Peak call was performed by MACS2
Assembly: hg38
Supplementary files format and content: peak summit data

source_name: cell line

extract_protocol:
Briefly, 50,000 cells were lysed to release the nuclei and subjected to a transposition reaction using Tn5 transposase (Illumina). Transposed fragments underwent preamplification, quantification via real-time polymerase chain reaction, and subsequent amplification.
Libraries were prepared with the Omni-ATAC protocol.

value: cell line

value: breast cancer


title: peripheral blood, N2

value: silent


title: peripheral blood, N1


title: 3LL_RMC-4998_RMC-4550_Mouse16_Tumour2


title: peripheral blood, N4


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse20_Tumour2


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse17_Tumour1


title: peripheral blood, N3


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse19_Tumour1


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse18_Tumour1


title: 3LL_RMC-4998_RMC-4550_αPD1_Mouse17_Tumour2


title: HCC38 siCtrl ATAC

value: siCtrl


title: 3LL_RMC-4998_RMC-4550_Mouse15_Tumour2


title: 3LL_RMC-4998_RMC-4550_Mouse16_Tumour1


title: 3LL_RMC-4998_RMC-4550_Mouse15_Tumour1


title: MDA-MB-157 ATAC


title: 3LL_RMC-4998_RMC-4550_Mouse14_Tumour1


title: MDA-MB-436 ATAC


title: 3LL_RMC-4998_RMC-4550_Mouse13_Tumour2


title: MDA-MB-468 ATAC


title: HCC1937 ATAC


title: 3LL_RMC-4998_RMC-4550_Mouse14_Tumour2


title: Hs578T ATAC


title: 3LL_RMC-4998_Mouse9_Tumour1


title: BT20 ATAC


title: 3LL_RMC-4998_RMC-4550_Mouse13_Tumour1


title: 3LL_RMC-4998_Mouse9_Tumour2


title: MDA-MB-453 ATAC


title: 3LL_RMC-4998_Mouse12_Tumour2


title: 3LL_RMC-4998_Mouse12_Tumour1


title: 3LL_RMC-4998_Mouse11_Tumour1


title: HCC1395 ATAC


title: HCC1143 ATAC


title: 3LL_RMC-4998_Mouse11_Tumour2


title: MDA-MB-231 ATAC


title: HCC38 siFOXA1 ATAC


title: DU4475 ATAC


title: HCC70 ATAC


title: HCC38 ATAC


title: HCC1806 ATAC


title: 3LL_RMC-4998_Mouse10_Tumour2


title: MDA-MB-361 ATAC


title: CsA_2

city: Shanghai

first: Debao

last: Li

address: No. 1678 Dongfang Road, Tangqiao Street

institute: Shanghai Children's Medical Center

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
The mapped reads of each sample were assembled by StringTie (v1.3.3b) (Mihaela Pertea.et al. 2015) in a reference-based approach.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene. And then FPKM of each gene was calculated based on the length of the gene and reads count mapped to this gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).Gene Ontology (GO) enrichment analysis of differentially expressed genes was implemented by the clusterProfiler R package, in which gene length bias wascorrected.We used clusterProfiler R package to test the statistical enrichment of differential expression genes in KEGG pathways.GATK2 (v3.7) software was used to perform SNP calling. Raw vcf files were filtered with GATK standard filter method and other parameters (cluster:3; WindowSize:35; QD < 2.0 o; FS > 30.0; DP < 10 and SnpEff software was used to annotation for the Variablesite).
Assembly: GRCm38(mm10)
Supplementary files format and content: FPKM

source_name: right ventricular myocardium

growth_protocol: The suckling mice were breastfed by the mother mice and were housed in groups of 4-6 per cage, fed under the same conditions with free access to food and water, maintained in the 12h: 12h day: night cycle.

extract_protocol:
right ventricular tissue  was rapidly removed from executed mice and flash frozen in -80℃ refrigerator , RNA was harvested using Trizol reagent.
A total amount of 1 μg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.

treatment_protocol: P7 mice were anesthetized by isoflurane. The operation was performed under the stereomicroscope in the supine position,VO operation was constructed  and Cyclosporin A (CSA) was injected in CSA group. After the surgery was completed, the mice were placed on a heat plate of 37℃ to warm and wake up. The pups were not put back to their moms until they were absolutely conscious.

value: right ventricular myocardium

tag: strain

tag: developmental stage

value: Postnatal day 7

value: Wild type

value: fistula surgery+CsA injection


title: HCC1187 ATAC

tag: cell type


title: 3LL_RMC-4998_Mouse10_Tumour1

value: Lung tumour

value: Mixed

tag: genotype

tag: treatment


title: CsA_1


title: T47D ATAC

tag: cell line


title: Sham_3

value: Sham operated


title: SK-BR-3 ATAC


title: VO_3

value: fistula surgery


title: Sham_2


title: HCC1954 ATAC


title: BT549 ATAC


title: Sham_1


title: BT474  ATAC


title: YMB-1  ATAC


title: CsA_3


title: NC

first: Yang

last: Zeng

address: 360 Longwood Avenue

data_processing:
Sequence reads were trimmed to remove possible adapter sequences and nucleotides with poor quality using Trimmomatic v.0.36.
The trimmed reads were mapped to the Mouse GRCm38 genome using the STAR aligner v.2.5.2b.
Unique gene hit counts were calculated by using feature Counts from the Subread package v.1.5.2 followed by differential expression analysis using DESeq2.
Assembly: Mouse GRCm38 reference
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: Bone marrow

extract_protocol:
The samples were send to Genewiz for Processing. RNA was extracted by the CRO company using the Qiagen Rnease mini kit.
RNA sequencing (RNA-seq) was carried out by Genewiz using an ultra-low input RNA-seq package that includes polyA selection. Sequencing was performed with an Illumina HiSeq with 150-bp pair-ended reads.

treatment_protocol: The immature BMDCs were treated with different vaccines as mentioned above for 1 day and collected by TRIzol (Invitrogen).

value: Bone marrow

value: Dendritic cells

value: Primary cells

value: Negative Control


title: CpG2-SQB + free OVA

value: vaccine stimulation


title: VO_1


title: Spinal cord endothelial cells, Ctrl 3

city: Hospitalet de Llobregat

first: Victor

last: Arribas

address: Carrer de la Feixa Llarga, s/n

institute: Universitat de Barcelona

data_processing:
RNA-seq reads were mapped against the Mus musculus reference genome (GRCm39) with STAR/2.7.8a57 using ENCODE parametres. Annotated genes (gencode.M30) were quantified with RSEM/1.3.058 using default options.
Assembly: GRCm39
Supplementary files format and content: A tab-separated values (.tsv) file contains the raw counts of each sample

source_name: Spinal cord

extract_protocol:
To isolate endothelial cells cells from P16 mice spinal cord, we followed the previously published protocol by Crouch and Doetsch (2018). Briefly, spinal cord tissue was dissected, minced and digested with collagenase (1mg/mL) for 30 min at 37ªC with rotation, triturated in 2% FBS in 1x HBSS, and centrifuged through 22% Percoll (Sigma, P1644) to remove debris. The samples were blocked with HBSS/BSA/glucose buffer and incubated for 20 min with fluorescently conjugated antibodies at 4ºC. After washing, samples were resuspended in HBSS buffer with DAPI to exclude dead cells. Cells were sorted using FACS Aria III (BD Biosciences), and data were analysed using FACSDiva software (BD Biosciences). All FACS gates were set using unlabeled cells, single-color and isotype controls from mice spinal cord samples. RNA was isolated from sorted endothelial cells using RNeasy Micro Kit (Qiagen) and following the manufacturer’s protocol.
RNA sequencing libraries were prepared following the SMARTseq2 protocol with some modifications. Briefly, RNA was quantified using the Qubit RNA HS Assay Kit (Thermo Fisher Scientific) and the RNA integrity was estimated with Agilent RNA 6000 Pico Kit. Reverse transcription of the total RNA input material of 1.8 µl (0.2-3.1 ng, in function of the sample availability) was performed using SuperScrpit II (Invitrogen) in a presence of oligo-dT30VN (1µM; 5′ AAGCAGTGGTATCAACGCAGAGTACT30VN-3′), template-switching oligonucleotides (1µM) and betaine (1M). The cDNA was amplified using the KAPA Hifi Hotstart ReadyMix (Roche) with 100 nM IS PCR primer (5′-AAGCAGTGGTATCAACGCAGAGT-3′) by 15 or 20 cycles of single primer cDNA amplification. Following purification with Agencourt Ampure XP beads (1:1 ratio; Beckmann Coulter), product size distribution and quantity were assessed on a Bioanalyzer High Sensitivity DNA Kit (Agilent). The amplified cDNA (200 ng) was fragmented for 10 min at 55 ºC using Nextera XT (Illumina) and amplified for 12 cycles with indexed Nextera PCR primers. The library was purified twice using Agencourt Ampure XP beads (0.8:1 ratio) and quantified on a Bioanalyzer using a High Sensitivity DNA Kit. The libraries were sequenced on NovaSeq 6000 (Illumina) in paired-end with a read length of 2x51bp according to the manufacturer’s protocol for dual indexing. Image analysis, base calling and quality scoring of the run are processed using the manufacturer’s software Real Time Analysis (RTA 3.4.4) and followed by generation of FASTQ sequence files.

value: Spinal cord

value: Endothelial cells

value: Tardbpflox

value: Tamoxifen (1mg/mL) at P5-P7


title: Spinal cord endothelial cells, KO 2


title: Spinal cord endothelial cells, KO 3


title: Spinal cord endothelial cells, KO 1


title: free CpG + free OVA


title: MCF7 ATAC

value: cell line

value: breast cancer


title: CpG4-OVA-SQB


title: CpG1-OVA-SQB


title: Spinal cord endothelial cells, Ctrl 2


title: CpG3-OVA-SQB


title: Spinal cord endothelial cells, Ctrl 1


title: Wt_M_H2O_Pris_D431_CD4_RNA

city: Stanford

first: Diana

middle: Remy

last: Dou

address: 269 Campus Drive, CCSR 2130

institute: Stanford University

data_processing:
RNA-seq data was aligned to mm10 using STAR
RSEM was used to generate gene expression read counts.
DESeq2 was used to normalize and analyze RNA-seq read counts
Assembly: mm10
Supplementary files format and content: RSEM generated matrix of RNA-seq raw readCounts

source_name: CD4+ spleen

extract_protocol:
At 52 weeks post-injection, spleens were harvested and mechanically dissociated. CD4+ cells were isolated from freshly dissociated mouse spleen using the EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, 19852).
Freshly isolated CD4+ cells were prepared using the stranded mRNA Library Prep (Illumina, 20020594) to generate polyA-selected RNA-sequencing libraries. Cleanup performed on magnets with AMPure XP beads (Beckman Coulter, A63880).

treatment_protocol: 12-14 week old C57BL6/J mice of inidcated genotypes were injected with 0.5 mL pristane or PBS (control mock injection) and continuously fed water with or without doxycycline for 52 weeks post-injection

value: CD4+ spleen

tag: post-treatment (wks)

value: Male

value: Wt

value: Pristane


title: CpG0-OVA-SQB

city: Boston


title: Wt_M_H2O_Pris_D413_CD4_RNA


title: Wt_M_H2O_Pris_D414_CD4_RNA


title: VO_2

value: right ventricular myocardium

value: Postnatal day 7

value: Wild type


title: Wt_M_H2O_PBS_D429_CD4_RNA

value: PBS


title: Wt_M_H2O_PBS_D418_CD4_RNA


title: Wt_M_H2O_PBS_D416_CD4_RNA


title: Day 28

city: Ann Arbor

first: Jintao

last: Xu

state: MI

address: 2215 Fuller Rd

institute: University of Michigan Hospital

description: 10x Genomics

data_processing:
Data analyzed using Cell Ranger from 10x Genomics
Assembly: mm10
Supplementary files format and content: Standard Cell Ranger output

source_name: brain

extract_protocol:
Mouse brain digest and CD45+ cell enriched
10x Genomics library construction kit protocol

value: brain

value: immune cells

tag: time

value: Day 28


title: Day 14

description: 10x Genomics

value: Day 14


title: Day 7

description: 10x Genomics

value: Day 7


title: Tg_M_H2O_Pris_D54_CD4_RNA

value: tgXist/-


title: Tg_M_Dox_Pris_D55_CD4_RNA

value: Dox+Pristane


title: Tg_M_Dox_Pris_D35_CD4_RNA


title: Day 0

description: 10x Genomics

value: Day 0


title: Tg_M_Dox_Pris_D40_CD4_RNA


title: MTAL of WT mice (MTAL_WT_17)

city: PARIS

first: Caroline

last: Prot-Bertoye

address: 15 rue Ecole de Médecine

institute: CNRS EMR8228, INSERM UMRS 1138

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.10.11) was used for mapping on mm10 reference genome and quantification with gencode v25 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Supplementary files format and content: mm10
Supplementary files format and content: tab-delimited text files including expecting counts and TPM

source_name: Kidney

extract_protocol:
MTAL and CTAL were microdissected from liberase-treated kidneys as previously described. All media were prepared and used in RNA-free environment. After dissection pools of 150-200 strutures from a single mouse were thoroughly rinsed and stored at -80°C on Lysis Buffer (Quiagen, RNeasy micro kit). RNAs were extracted according to the manufactured protocol.
RNA library preparation was realized following manufacturer’s recommendations

value: Kidney

tag: tissue region

value: MTAL

value: WT


title: Tg_M_H2O_Pris_D37_CD4_RNA

value: CD4+ spleen

value: Male


title: MTAL of WT mice (MTAL_WT_19)


title: Tg_M_Dox_Pris_D41_CD4_RNA


title: Tg_M_Dox_Pris_D47_CD4_RNA


title: MTAL of WT mice (MTAL_WT_15)


title: Tg_F_H2O_Pris_D45_CD4_RNA

value: Female

value: Pristane


title: Wt_M_H2O_Pris_D411_CD4_RNA

value: Wt


title: Tg_F_H2O_Pris_D56_CD4_RNA


title: MTAL of WT mice (MTAL_WT_13)


title: Day 21

description: 10x Genomics

value: Day 21


title: MTAL of WT mice (MTAL_WT_11)


title: Tg_M_Dox_Pris_D33_CD4_RNA


title: Tg_F_H2O_Pris_D221_CD4_RNA


title: MTAL of Cldn10 KO mice (MTAL_KO_20)

value: Cldn10 KO


title: Wt_M_H2O_Pris_D413-1_CD4_ATAC

data_processing:
The adaptor of paired-end ATAC-seq data were first trimmed by an in-house software, and then aligned to mm10 genome using bowtie2.
The mitochondrial reads and reads with low alignment score (<10) were removed.
The aligned sam files were converted to bam files and sorted by Samtools.
Picard was used to remove duplicate reads and MACS2 was used to call peaks.
Bedtools was used to generate readCounts from called peaks
Each ATAC-seq peak was annotated by its nearby genes using GREAT under the basal plus extension default setting
Raw bulk ATAC-seq read counts normalized and analyzed using DESeq2
Assembly: mm10
Supplementary files format and content: Bedtools generated matrix of ATAC readCounts from called peaks
Supplementary files format and content: ATAC readCounts file

extract_protocol:
At 52 weeks post-injection, spleens were harvested and mechanically dissociated. CD4+ cells were isolated from freshly dissociated mouse spleen using the EasySep Mouse CD4+ T cell Isolation Kit (STEMCELL Technologies, 19852).
Freshly isolated CD4+ cells were prepared using the Omni-ATAC protocol to generate ATAC-seq libraries.

value: transposed genomic DNA


title: Wt_M_H2O_Pris_D414-1_CD4_ATAC


title: Wt_M_H2O_Pris_D411-2_CD4_ATAC


title: MTAL of Cldn10 KO mice (MTAL_KO_18)


title: Wt_M_H2O_Pris_D411-1_CD4_ATAC


title: MTAL of Cldn10 KO mice (MTAL_KO_16)


title: Wt_M_H2O_PBS_D419-2_CD4_ATAC

value: PBS


title: Wt_M_H2O_PBS_D419-1_CD4_ATAC


title: Wt_M_H2O_PBS_D418-2_CD4_ATAC


title: Wt_M_H2O_PBS_D418-1_CD4_ATAC


title: Wt_M_H2O_PBS_D416-1_CD4_ATAC


title: Wt_M_H2O_PBS_D416-2_CD4_ATAC


title: CTAL of WT mice (CTAL_WT_3)

value: CTAL


title: Tg_M_H2O_Pris_D54-1_CD4_ATAC


title: Tg_M_H2O_Pris_D54-2_CD4_ATAC


title: CTAL of WT mice (CTAL_WT_22)


title: CTAL of Cldn10 KO mice (CTAL_WT_1)


title: Tg_F_H2O_Pris_D222_CD4_RNA


title: Tg_M_H2O_Pris_D37-2_CD4_ATAC


title: Tg_F_H2O_Pris_D223_CD4_RNA


title: Tg_M_Dox_Pris_D55-1_CD4_ATAC


title: CTAL of WT mice (CTAL_WT_10)


title: Tg_M_Dox_Pris_D55-2_CD4_ATAC


title: Tg_M_H2O_Pris_D37-1_CD4_ATAC


title: Tg_M_Dox_Pris_D47-2_CD4_ATAC


title: Tg_M_Dox_Pris_D47-1_CD4_ATAC


title: CTAL of Cldn10 KO mice (CTAL_KO_9)


title: Tg_M_Dox_Pris_D41-2_CD4_ATAC


title: CTAL of Cldn10 KO mice (CTAL_KO_4)


title: Tg_M_Dox_Pris_D41-1_CD4_ATAC


title: CTAL of Cldn10 KO mice (CTAL_KO_7)


title: CTAL of WT mice (CTAL_WT_8)


title: Tg_M_Dox_Pris_D40-1_CD4_ATAC


title: Tg_M_Dox_Pris_D40-2_CD4_ATAC


title: CTAL of Cldn10 KO mice (CTAL_KO_2)


title: Tg_M_Dox_Pris_D33-2_CD4_ATAC


title: CTAL of Cldn10 KO mice (CTAL_KO_21)


title: Tg_M_Dox_Pris_D35_CD4_ATAC


title: Tg_M_Dox_Pris_D33-1_CD4_ATAC


title: Tg_F_H2O_Pris_D223-2_CD4_ATAC


title: Tg_F_H2O_Pris_D45-2_CD4_ATAC


title: Tg_F_H2O_Pris_D45-1_CD4_ATAC


title: Tg_F_H2O_Pris_D223-1_CD4_ATAC


title: Tg_F_H2O_Pris_D222-1_CD4_ATAC