title: mds 7 N14

first: Xiaoping

last: Su

address: 7300 Brompton St, Apt 5633

institute: MD Anderson Cancer Center

description:
mds 7
10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: MDS Bone marrow

extract_protocol:
Frozen BM cells stored in liquid nitrogen were retrieved right before sample processing. To maximize the cellular viability recovery, samples were processed in batches according to thawing protocol. Briefly, cells were gently thawed in water bath at 37 °C for 5 minutes until partially thawed and immediately placed on ice. Next, cells were gently transferred to 10 ml room temperature warm media (10 ml RPMI1640 supplemented with 20% FBS) and centrifuged (453 g for 5 min). After finishing centrifugation, supernatant was disposed, the cell pellet was carefully re-suspended in 10 ml thawing media (RPMI1640, supplemented with 20% FBS, containing 500 μl Heparin (stock 2 mg/ml, Cat# 9041-08-1; Sigma Aldrich), 20 μl DNase (stock 1 ug/ml, Cat# 89835, Thermo Fischer Scientific) and 200 μl MgSO4 (stock 200 mM, Sigma Aldrich) and incubate in 37 °C for 15 min to digest the DNA released from the dead cells. Following incubation, cells were centrifuged and gently washed twice in 2 ml of 0.04% BSA in PBS. Finally, to remove cell clumps, cells were filtered with 35μm mesh strainer directly to falcon tubes (BD Falcon® 5 ml Round-Bottom Tubes with Cell Strainer Cap, Corning, NY, USA). After transferring cells, 10 ul of cell suspension was stained with 10 ul of 0.4% Trypan blue, counted and assessed for viability using standard hemocytometer and light microscopy. To adjust the cell density, cells were eventually centrifuged again and re-suspended in desired amount of PBS with 0.04% BSA.
scRNA-seq libraries were generated using a 10x Genomics Chromium Controller instrument and Chromium Single-Cell 5′ V2 reagent kits (10x Genomics). In brief, cells were concentrated to 1,000 cells per μl and cells were loaded into each channel to generate single-cell Gel Bead-In-Emulsions (GEMs), resulting in mRNA barcoding of an expected 5,000 single cells for each sample. After the reverse transcription step, GEMs were broken, and single-strand cDNA was cleaned up with DynaBeads. The amplified barcoded cDNA was fragmented, A-tailed, ligated with adaptors and amplified by index PCR. cDNA and constructed libraries were assessed by High Sensitivity D5000 DNA Screen Tape analysis (Agilent Technologies) and Qubit dsDNA HS Assay Kit (Thermo Fisher Scientific). Sequencing was conducted on an Illumina NovaSeq sequencer with 2 × 100 bp paired reads to reach a depth of at least 50,000 read pairs per cell. The Chromium Single-Cell V(D)J Enrichment Kit was used to enrich immune repertoire, TCR or B-cell immunoglobulin (Ig) transcripts. The single-cell V(D)J enriched libraries were sequenced at 2 × 150 bp with a minimum depth of 5,000 read pairs per cell.

treatment_protocol: This Phase 1b/2 clinical trial (NCT03047993) was designed to assess the safety, tolerability, and efficacy of telaglenastat in combination with azacytidine for the treatment of advanced MDS.    The study was fully completed with twenty-eight patients enrolled from December 2017 to September 2020: six in the Phase 1b portion and twenty-two in the Phase 2. All patients received standard azacytidine 75 mg/m2 daily x 7 days by intravenous or subcutaneous injection, and telaglenastat was self-administered orally twice daily continuously, for 28 days per cycle.    The Phase 1b study portion was designed to enroll six patients, treated at the standard approved azacytidine dose, in combination with telaglenastat at a dose of 600mg BID. If < 1 DLT was observed at this combination, this level would be identified as the recommended phase 2 combination dose (RP2D) and the study would progress to the Phase 2 portion. If > 2 patients experienced a DLT, an additional six patients would be enrolled at the next lower dose level. The Phase 1b portion enrolled without reported DLTs and the study moved into the Phase 2 portion.  The Phase 2 portion opened after confirmation of the combination RP2D of 600mg BID. One interim analysis was designed after 16 patients enrolled, with a plan to continue total accrual if > 7 of the first 16 patients achieved response. The final efficacy analysis was designed such that if 15 or more of the 28 enrolled patients achieved response, treatment would be considered efficacious and worthy of further investigation.  Clinical response was evaluated using the modified IWG response criteria for MDS.38 The overall response rate included complete remission (CR), partial remission (PR), and marrow CR (mCR).

value: BM cells

value: MDS Bone marrow

value: post

value: NR


title: mds 6 N12

status: Public on Feb 12 2024

type: SRA

city: Houston

state: Texas

country: USA

description:
mds 6
10x Genomics

library_source: transcriptomic single cell

molecule: total RNA

organism: Homo sapiens

tag: cell type

tag: tissue

tag: time

tag: genotype

tag: disease state

value: mCR


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, POLR2A

city: Memphis

first: Jeffery

last: Klco

state: TN

address: 262 Danny Thomas Place

department: Pathology

institute: St Jude Children's Research Hospital

description: Figure 2B

library_source: genomic

data_processing:
To obtain quality reads, raw reads were processed and trimmed with Trim_galore (v0.4.4) from cutadapt (DOI: 10.14806ej.17.1.200) and FASTQC analysis. A default quality score cutoff of Q20 is used.  Quality trimmed reads were then mapped to "hg38+rDNA” (DOI: 10.1101/2022.11.10.514243) genome build by bwa (v0.7.12-r1039) and converted to a bam file by samtools (v1.2).
Duplicate reads were marked with biobambam2 (v2.0.87, DOI: 10.1186/175109473-9-13). Uniquely mapped and properly paired reads were then extracted with samtools (v1.2, "-F 1804 -q 1") and sorted by read name using biobambam2 (v2.0.87)
bedtools(v2.17.0, PMID: 20110278) were used to convert bam file to bedpe file as fragments. Fragments with size shorter than 2000bp were extracted and center 80bp of each fragment were used to generate bigwig track files by UCSC tools (v4) and visualized using IGV (v2.16.0).
Narrow peaks were called with MACS2 (v2.1.1.20160309, parameters "-q 0.05") and broad peaks were called by SICER (v1.1, parameters "hg38 1 200 fragmentsize 0.86 600 0.00001").
To perform statistical test between experimental groups (DMSO/dTAG), fragments for each reference peak were counted with intersect command from pybedtools (v0.9.1). Next, the number of raw reads mapping per peak were converted to FPKM unit (Fragments Per Kilo base per Million mapped reads), and TMM (trimmed mean of M-values) from edgeR package. Next, we used limma-voom approach to assess the significance of differential peak binding.  Significant peaks were defined by log2FC < -1 or > 1 and FDR < 0.05.
Assembly: hg38+ custom rDNA build from  DOI:  https://doi.org/10.1101/2022.11.10.514243
Supplementary files format and content: bw
Library strategy: CUT&RUN

molecule: genomic DNA

source_name: Human cord-blood CD34+ cells

growth_protocol: Cells were growin in SFEM II supplemented with pen-strep, I-glutamine, and recombinant human SCF, FLT-3, TPO and IL-6 (all 50ng/mL PeproTech), UM729 (#72332, STEMCELL Technologies) and SR-1 (1µmol/L, #72344, STEMCELL Technologies)

extract_protocol:
CUT&RUN was performed following the kit from EpiCypher (cat# 14-1048)
CUT&RUN DNA libraries were made following NEBNext Ultra II DNA Library Prep Kit for Illumina (cat# E7103), PCR amplification was done for 12 cycles

tag: expression vector

value: MPC-nHA-UBTF-TD

tag: treatment

value: Human cord-blood CD34+ cells

tag: chip antibody

value: POLR2A (EMD-Millipore, 05-623)


title: mds 4 N8

description:
mds 4
10x Genomics

value: pre


title: mds 5 N10

description:
mds 5
10x Genomics

value: mCR w/ HI


title: mds 2 N4

description:
mds 2
10x Genomics

value: CR


title: mds 5 N9

description:
mds 5
10x Genomics


title: CB-012 Lot 2 Rep 3 and pNK post-infusion

city: EMERYVILLE

first: Ryan

middle: Tevia

last: Davis

state: California

address: 2929 Seventh St

institute: Caribou Biosciences

description: 10x Genomics

data_processing:
The Cell Ranger Single-Cell Software Suite (version 7.0.1) was used to perform sample demultiplexing, barcode assignments, and gene alignments (10x Genomics). Raw base BCL files from the NextSeq 2000 were demultiplexed using the Cell Ranger mkfastq pipeline into sample-specific FASTQ files. FASTQ files were processed individually using the Cell Ranger count pipeline with pre-built GRCh38 human reference genome provided by Cell Ranger (10x Genomics). Aligned reads were filtered for valid cell barcodes and unique molecular identifiers (UMIs). For samples that contained CAR-T cells, an additional alignment to a custom build of GRCh38 containing the coding sequence of the BCMA-chimeric antigen receptor (CAR) was performed and the CAR status of individual cells was added to the metadata of the sample. For downstream analysis, gene expression levels were determined using the pre-built GRCh38 reference genome alignment.
Assembly: GRCh38
Supplementary files format and content: Tab-seperated value files and matrix files

source_name: spleen

extract_protocol:
For profiling of NK and T cells following infusion in vivo, 6 different cohorts were established in NOG-Tg (Hu-IL15) mice according to the protocol described above: (i) 2 cohorts of CB-011 cells without pNK cells (CB-011 only, n = 2 mice/cohort), (ii) 2 cohorts of CB-011 cells with NK cells (CB-011+NK, n = 3 mice/cohort), (iii) 1 cohort of B2M KO CAR-T cells without NK cells (B2M KO only, n = 2 mice), and (iv) 1 cohort of B2M KO CAR-T cells with NK cells (B2M KO+NK, n = 3 mice). Additionally, NK and CB-011 cells were isolated for single-cell RNA sequencing (scRNA-Seq; NK IP and CB-011 IP, n = 1/group) prior to infusion. NK and CAR-T cells from either the CB-011 or the CAR KI B2M KO cohorts were isolated from the spleens of NOG-Tg (Hu-IL15 mice) mice 4 days post CAR-T cell infusion by FACS using a human CD45-specific antibody. Cells were resuspended in PBS + 0.4% BSA at a concentration of 1x106 cells/mL and single-cell RNA sequencing libraries were generated (Supplemental methods).
Construction of single-cell RNA sequencing (scRNA-Seq) libraries was performed using the Chromium Next GEM Single Cell 5’ HT Reagent Kit v2 (10x Genomics). For each sample, 10,000 cells were targeted for capture based on a loading concentration of 1000 cells/µL. Following gene expression library construction, the samples were multiplexed on the same lane of a NextSeq 2000 platform (Illumina) and sequenced to a target depth of 20,000 to 30,000 reads/cell.

value: spleen

value: Mixed

value: post-infusion


title: mds 4 N7

description:
mds 4
10x Genomics


title: HepG2, coumarin 100 μM, rep2

city: Beijing

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

department: Post-translational modification

country: China

institute: Beijing Proteome Research Center

library_source: transcriptomic

data_processing:
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
For RNAseq data, a stringent pre-filtering criterion of median counts over all samples < 5 was carried out. The normalization and analysis of differentially expressed genes (DEGs) were conducted by using DESeq2
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts and fpkm for every gene and every sample

growth_protocol: About 5×10^7 HepG2 cells were treated in triplicates using 6 concentrations of coumarin and a control for 24 h.

extract_protocol:
After the culture medium with coumarin was removed, the cells were harvested by digestion of trypsin-EDTA solution and washed with ice-cold PBS twice and then centrifuged at 12,000 g for 15 min at 4 °C. RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.

treatment_protocol: Coumarin was dissolved in DMEM (100 mM stock solutions). Further dilutions were made with serum-free DMEM. At the time of coumarin exposure, after the FBS-DMEM culture medium was removed, HepG2 cells were washed with PBS once and were finally treated in the fresh serum-free DMEM culture medium containing different concentrations of coumarin (0-100 μM) for 24 h.

tag: cell line

value: 100 μM coumarin for 24 h


title: mds 1 N2

description:
mds 1
10x Genomics


title: mds 2  N3

description:
mds 2
10x Genomics


title: mds 1 N1

description:
mds 1
10x Genomics


title: HepG2, coumarin 10 μM, rep3

value: 10 μM coumarin for 24 h


title: RNA-seq of bone marrow cells from UBTF-TD PDX model treated with Veh, R17

description:
RNASeq_SNDX-Veh_log2CPM.txt
SJAML015373_R17- HMP_18_PDX_FMZVC_S04_bm_Veh

data_processing:
RNA-Seq reads were mapped to GRCh38/hg38 human genome assembly using STAR v2.7.9a
Gene expression count matrix was generated using RSEM (v1.3.0)
The count data were transformed to log2-counts per million (log2CPM) using Voom method available from R package Limma (v3.50.3). Limma was also used to perform differential expression analysis between DMSO and dTAG-13 treated samples.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text file for log2-counts per million (log2CPM) , one gene per row and one sample per column.

source_name: human blasts from UBTF-TD PDX Model

extract_protocol:
RNA was harvested using Quikc-RNA Miniprep Kit (Zymo Research R1055)). RNA was then quantified using the Quant-iT RiboGreen RNA assay (ThermoFisher) and quality checked by the 2100 Bioanalyzer RNA 6000 Nano assay (Agilent) or 4200 TapeStation High Sensitivity RNA ScreenTape assay (Agilent) prior to library generation.
Libraries were prepared from total RNA with the TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer’s instructions (Illumina, PN 20020599). Libraries were analyzed for insert size distribution using the 2100 BioAnalyzer High Sensitivity kit (Agilent), 4200 TapeStation D1000 ScreenTape assay (Agilent), or 5300 Fragment Analyzer NGS fragment kit (Agilent). Libraries were quantified using the Quant-iT PicoGreen ds DNA assay (ThermoFisher) or by low pass sequencing with a MiSeq nano kit (Illumina).
Paired end 100 cycle sequencing was performed on a NovaSeq 6000 (Illumina).

value: human blasts from UBTF-TD PDX Model

value: UBTF-TD PDX model treated with Veh


title: CB-012 Lot 2 Rep 2 and pNK post-infusion

description: 10x Genomics


title: HepG2, coumarin 100 μM, rep1


title: CB-012 Lot 2 Rep 1 cells post-infusion

description: 10x Genomics

value: T cells


title: cord-blood CD34+ cells, MPC-nHA-UBTF-TD, IgG

description: Figure 2B, Supplemental Figure 2A

value: IgG (EpiCypher, 13-0042)


title: HepG2, coumarin 10 μM, rep2


title: RNA-seq in FKBP12 tagged UBTF-TD54 cbCD34+ cells treated with DMSO, C1

description:
RNASeq_DTAG-DMSO_log2CPM.txt
SJNORM077216_C1_F_DMSO

source_name: cord-blood CD34+ Cells expressing FKPB12-F36V::UBTF-TD

value: cbCD34+ cells treated with DMSO


title: mds 3 N6

description:
mds 3
10x Genomics

value: BM cells

value: MDS Bone marrow

value: post

value: SD (NR)


title: CB-012 Lot 1 Rep 1 cells post-infusion

description: 10x Genomics


title: HepG2, coumarin 1 μM, rep3

value: 1 μM coumarin for 24 h


title: mds 6 N11

description:
mds 6
10x Genomics

value: pre


title: CB-012 Lot 1 Rep 3 and pNK post-infusion

description: 10x Genomics


title: CB-012 Lot 2 Rep 1 and pNK post-infusion

description: 10x Genomics


title: CB-012 Lot 1 Rep 2 cells post-infusion

description: 10x Genomics


title: CB-012 Lot 1 Rep 2 and pNK post-infusion

description: 10x Genomics


title: HepG2, coumarin 100 μM, rep3


title: CAR KI B2M KO Lot 1 Rep 3and pNK post-infusion

description: 10x Genomics


title: HepG2, coumarin 1 μM, rep2


title: CB-012 Lot 1 Rep 1 and pNK post-infusion

description: 10x Genomics


title: CB-012 Lot 2 Rep 2 cells post-infusion

description: 10x Genomics


title: CAR KI B2M KO Lot 1 Rep 2 and pNK post-infusion

description: 10x Genomics


title: HepG2, coumarin 0.1 μM, rep2

value: 0.1 μM coumarin for 24 h


title: CAR KI B2M KO Lot 1 Rep 1 post-infusion

description: 10x Genomics

value: spleen


title: HepG2, coumarin 0.1 μM, rep3


title: CAR KI B2M KO Lot 1 Rep 1 and pNK post-infusion

description: 10x Genomics

value: Mixed


title: HepG2, coumarin 10 μM, rep1


title: CAR KI B2M KO Lot 1 Rep 2 post-infusion

description: 10x Genomics

value: post-infusion


title: CB-012 Lot 2 cells pre-infusion

description: 10x Genomics

value: pre-infusion


title: CB-012 Lot 1 cells pre-infusion

description: 10x Genomics


title: HepG2, coumarin 0.01 μM, rep2

value: 0.01 μM coumarin for 24 h


title: HepG2, coumarin 0.001 μM, rep3

value: 0.001 μM coumarin for 24 h


title: HepG2, coumarin 0.01 μM, rep3


title: HepG2, coumarin 0.01 μM, rep1


title: siNCoR_3

city: Frankfurt

first: Simonida

last: Zehr

state: Hesse

address: Theodor-Stern-Kai 7

department: Institute for Cardiovascular Physiology

country: Germany

institute: Goethe University, Frankfurt am Main, Germany,

description:
HUVEC_ATAC_NCoR1_KO_peaks_up.bed
HUVEC_ATAC_NCoR1_KO_peaks_down.bed
HUVEC_ATAC_NCoR1_KO_peaks_unchanged.bed

data_processing:
Read Trimming: Trimmomatic (version 0.39)
Read alignment: Bowtie2 (v2.4.5), parameter --very-sensitive
Deduplication: samtools (v1.10)
Read indexing: samtools (v1.10)
Normalised coverage computation: deepTools bamCoverage (v.3.5.1)
Peak calling: MACS2 (v3.0.0), parameters --scale-to-smale --format BAMPE
Differential peak calling: MACS3 bgdiff
Preprocessing for visualisation with IGV: bedtools genomecov
Assembly: GRCh38 (patch release 13)
Supplementary files format and content: HUVEC_ATAC_NCoR1_KO_peaks_up.bed, log-likelihood ratios for regions with downregulated accessibility
Supplementary files format and content: HUVEC_ATAC_NCoR1_KO_peaks_down.bed, log-likelihood ratios for regions with downregulated accessibility
Supplementary files format and content: HUVEC_ATAC_NCoR1_KO_peaks_unchanged.bed, log-likelihood ratios for unchanged regions
Supplementary files format and content: HUVEC_ATAC_NTC_H13.bw, normalised peaks per sample
Supplementary files format and content: HUVEC_ATAC_NTC_H14.bw, normalised peaks per sample
Supplementary files format and content: HUVEC_ATAC_NTC_H42.bw, normalised peaks per sample
Supplementary files format and content: HUVEC_ATAC_NCoR1_KO_H13.bw, normalised peaks per sample
Supplementary files format and content: HUVEC_ATAC_NCoR1_KO_H14.bw, normalised peaks per sample
Supplementary files format and content: HUVEC_ATAC_NCoR1_KO_H42.bw, normalised peaks per sample

source_name: human umbilical vein endothelial cells

growth_protocol: human umbilical vein endothelial cells (HUVECs), obtained from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042), were cultured on fibronectin (1mg/ml) coated dishes to passage 3 and used for experiments at passage 4. Endothelial growth medium (EGM, PeloBiotech) containing 8% FCS , 50 U/ml penicillin and 50 µg/ml streptomycin (Gibco), EndoCGS-Heparin (PeloBiotech) and growth factors (EGF, bFGF, IGF, VEGF, Heparin, L-Glutamin) was used as cell culture medium. In case of starvation, cells were cultured in endothelial basal medium (PeloBiotech) containing 1% FCS, 50 U/ml penicillin and 50 µg/ml streptomycin (Gibco), EndoCGS-Heparin (PeloBiotech) at least 4h prior to an experiment.

extract_protocol: 25.000 FACS sorted cells were collected by centrifugation at 1000g for 5min and used for ATAC Library preparation using Tn5 Transposase from Nextera DNA Sample Preparation Kit (Illumina). Cell pellet was resuspended in 50µl Lysis/Transposition reaction (12.5µl THS-TD-Buffer (Tris-acetate, pH 7.8 132 mM, Potassium acetate (Sigma, 95843-100ML-F) 264 mM, Magnesium acetate (Sigma, 63052-100ML) 40 mM, Dimethylformamide (DMF) (Sigma, Sigma D4551-250ML) 64%, H2O), 2.5µl Tn5, 5µl 0.1% Digitonin and 30µl water) and incubated at 37°C for 30min with occasional snap mixing. Following purification of the DNA fragments was done by MinElute PCR Purification Kit (Qiagen). Amplification of Library together with Indexing Primers was performed as described elsewhere [29].

treatment_protocol: HUVECs were seeded at a concentration of 20.000 cells/cm2 and transfected on the following day in Endothelial basal medium containing 1% FCS using GeneTransII transfection reagent (MoBiTec) according to the manufacturer´s instructions. Briefly, a final concentration of 60 nM siRNA together with GeneTrans II transfection reagent and DNA Diluent B was added to the cells for 4h. Subsequently, the cell culture medium was replaced with EGM and changed again after 24h. 48 h after transfection, cells were used as indicated.

value: human umbilical vein endothelial cells

value: HUVEC

value: siRNA HSS114352


title: HepG2, coumarin 0.001 μM, rep1


title: siNCoR_2


title: HepG2, coumarin 1 μM, rep1


title: siNCoR_1


title: HepG2, coumarin 0 μM, rep3

value: untreated


title: HepG2, coumarin 0 μM, rep2


title: CTL_3

value: negative control siRNA


title: A030  after acupuncture

city: Chengdu

first: Lu

last: Liu

state: Sichuan Province

address: No.37 Shier Qiao Road

institute: Chengdu University of Traditional Chinese Medicine

data_processing:
Illumina Casava1.7 software used for basecalling
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg38 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Differential expression analysis of two conditions/groups was performed with the DESeq package in R (version 1.10.1; R Foundation for Statistical Computing, Vienna, Austria).
Assembly: hg38
Supplementary files format and content: Matrix table with raw miRNAs counts for every miRNA and every sample

source_name: serum

extract_protocol:
Exosome isolation was performed with an exoEasy Maxi kit (product no. 76064; Qiagen, Hilden, Germany) according to the manufacturer’s protocol with minor modifications. Briefly, the platelet-free plasma was filtered with a 0.8-μm pore filter (product no. SLAA033SB; Millipore, Burlington, Massachusetts, United States) to exclude large particles. An equivalent volume of XBP buffer was added to 500 μL of platelet-free plasma, and the sample was mixed well by gently inverting the tube five times. The mixture was added to the exoEasy spin column and centrifuged at 500 g for 1 min at room temperature, and the flow-through was discarded. Next, 10 mL of buffer XWP was added, and the column was centrifuged at 5,000 g for 5 min to remove residual buffer from the column. The column was transferred to a fresh collection tube, and 400 μL of XE buffer was added to the column membrane, which was then incubated for 1 min. The column was centrifuged at 500 g for 5 min to collect the eluate. The methods for identifying the exosomes mainly included transmission electron microscopy (TEM; FEI Tecnai Spirit T12; FEI, Hillsboro, Oregon, United States), exosome size analysis (NanoFCM; Xiamen, China), and western blotting. Total RNA was extracted from exosomes with a miRNeasy Serum/Plasma kit (product no. 217184; Qiagen). RNA purity was checked using a NanoPhotometer spectrophotometer (Implen, München, Germany). RNA concentrations were measured with a Qubit RNA Assay Kit in a Qubit 2.0 fluorometer (Life Technologies, Carlsbad, California, United States), and RNA integrity was assessed with the RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, Santa Clara, California, United States) to ensure that the samples were suitable for sequencing.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Acupuncture was performed by experienced physicians with more than 5 years of clinical experience in acupuncture treatment. All physicians received special training regarding the trial purpose, standard procedure, treatment strategies, and quality control. The acupoint prescriptions, acupoint localisation, acupoint selection, and insertion depth were described in detail in our previous study. Each needle was retained for 30 min. MWoA patients underwent three sessions per week over a 4-week period.

value: collected after acupuncture treatment

value: serum

tag: age


title: A048  after acupuncture


title: CTL_2


title: A028  after acupuncture


title: CTL_1


title: Primary NK cells pre-infusion

description: 10x Genomics

value: NK cells


title: A013  after acupuncture


title: A007  after acupuncture


title: A031  after acupuncture


title: HepG2, coumarin 0.001 μM, rep2


title: A027  after acupuncture


title: A002  after acupuncture


title: HepG2, coumarin 0.1 μM, rep1


title: A048 before acupuncture

value: collected before acupuncture treatment


title: HepG2, coumarin 0 μM, rep1


title: A025 after acupuncture


title: A003  after acupuncture


title: HUVEC+20nM PMA 16h

type: RNA

city: Cleveland

first: Edward

middle: M Medof

last: MD

state: OH

address: 17 1/2 Peppercreek Dr

institute: Case western Reserve University

description: Gene expression data from HUVEC that was treated by 20nM ATO for 16hrs.

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Human Genome U133 Plus 2.0 chips. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.

scan_protocol: GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.

data_processing: The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.

label: biotin

source_name: Human umbilical vein endothelial cell (Primary cell culture)

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 6 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: K562 cells were suspension cultured in RPMI with 10% FBS medium. HUVEC were adherent cultured with Endothelial Cell Growth Medium from Sigma-Aldrich.

extract_protocol: QIAGEN mini RNeasy kit extraction of total RNA was performed according to the manufacturer's instructions.

treatment_protocol: Log phase growth of human K562 cells or human umbilical vein cells (HUVEC) were incubated with agents known to upregulate CD55 expression [phorbol myristic acid (PMA), atorvastatin, simvastatin, C reactive protein (CRP)] and mRNA upregulation was assessed by gene array.

value: umbilical cord

value: Human umbilical vein endothelial cell

value: Adherent cell culture with 20nM PMA for 16h


title: A028 before acupuncture


title: HUVEC+5µM ATO 16h

description: Gene expression data from HUVEC that was treated by 5µM ATO for 16hrs.

value: Adherent cell culture with 5µM Atovastatin for 16h


title: A013 before acupuncture


title: A031 before acupuncture


title: HUVEC alone 16h control-3

description: Gene expression data from HUVEC alone as a base line for PMA treated HUVEC.

value: Adherent cell culture as control for 16h


title: A007 before acupuncture


title: A027 before acupuncture


title: Hi-C GM19239 rep24

city: Omaha

first: Michael

middle: Jordan

last: Rowley

state: Nebraska

address: 42nd and Emile street

department: Genetics & Cell Biology

institute: University of Nebraska Medical Center

data_processing:
Sequenced reads were preprocessed, mapped to the Human genome build hg38, filtered for quality score ≥30, and processed using juicer tools v1.14.08
Replicates were combined and juicer tools (1.14.08) was used to create .hic files.
Assembly: hg38
Supplementary files format and content: .hic files

source_name: Lymphoblastoid

extract_protocol:
Cells were crosslinked in 1% v/v formaldehyde for ten minutes and quenched by adding 2.5 M glycine to a final concentration of 0.2 M for 5 min. Cells were pelleted by centrifugation at 300 G for 5 min at 4 °C and then washed with cold PBS. Cells were lysed with lysis buffer containing 10 mM Tri-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630 and protease inhibitors for 15 min on ice. Cells were centrifuged at 300 G and washed in that same buffer, and then resuspended in 50 µl 0.5% SDS for 5 min at 62 °C. Afterward, 145 µl of water and 25 µL of Trition X-100 were added and incubated at 37 °C for 15 min.
Chromatin was digested overnight in MboI, MseI, or NlaIII in the corresponding buffer. Fragment overhangs were repaired and biotinylated using equal amounts of biotin-14-dATP, dCTP, dGTP, and dTTP in the presence of 40 units of DNA Polymerase I, Large (Klenow) Fragment at 37 °C for 1 h. Chromatin was ligated in 1x T4 DNA ligase buffer, Triton X-100, 0.12 mg BSA, and 2000 units T4 DNA ligase at room temperature for four hours. Proteins were digested, and chromatin decrosslinked in 0.72 mg/ml proteinase k, 1% SDS, and 0.5 M NaCl for 30 min at 55 °C, followed by 68 °C overnight. Libraries were sequenced and then processed using Illumina HiSeq 4000 software and JuicerTools v1.14.08. As per Harris, Hannah L., et al. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization." Nature Communications 14.1 (2023): 3303.

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

value: No treatment

tag: biomaterial provider


title: HUVEC+100µg/ml CRP 16h

description: Gene expression data from HUVEC that was treated by 100µg/mL CRP for 16hrs.

value: Adherent cell culture with 100µg/mL CRP (C Reactive Protein) for 16h


title: Hi-C GM19239 rep23


title: A003 before acupuncture


title: cord-blood CD34+ cells, MPC-FKBP12-nHA-UBTF-TD, DMSO, KMT2A, rep2

description: Figure 3D-E, Supplemental Figure 3O-P

value: DMSO

value: Human cord-blood CD34+ cells

value: KMT2A (Bethyl Laboratories, A300-086A)


title: A030 before acupuncture


title: HUVEC+5µM SIM 16h

description: Gene expression data from HUVEC that was treated by 5µM SIM for 16hrs.

value: Adherent cell culture with 5µM Simvastatin for 16h


title: Hi-C GM19239 rep22


title: A025 before acupuncture

value: serum


title: HCS22

value: untreated


title: HUVEC alone 16h control-1

description: Gene expression data from HUVEC alone as a base line for SIM treated HUVEC.


title: K562+10mM PMA 16h

description: Gene expression data from K562 cell that was treated by 10 mM PMA for 16 hrs.

source_name: K562 cell line

value: human blood or bone marrow

value: Lymphoblast

value: chronic myelogenous leukemia

value: Suspension culture with 10mM PMA for 16h


title: HUVEC alone 16h control-2

description: Gene expression data from HUVEC alone as a base line for CRP and ATO treated HUVEC.

value: umbilical cord

value: Human umbilical vein endothelial cell


title: Hi-C GM19239 rep21

value: Lymphoblastoid


title: Day 14 differ RNA-rep2

city: RTP

first: NIEHS

last: Microarray Core

state: NC

address: 111 T.W. Alexander Drive

department: DIR

institute: NIEHS

description: Gene expression for Day 14

hyb_protocol: For each sample, 1.65ug of Cy3 labeled cRNAs were fragmented and hybridized for 17 hours in a rotating hybridization oven.

scan_protocol: Slides were washed and then scanned with an Agilent Scanner.

data_processing: Data was obtained using the Agilent Feature Extraction software (v12), using the 1-color defaults for all parameters.

organism: Mus musculus

source_name: Day 14 differ RNA-rep2

label_protocol: Starting with 500ng of total RNA, Cy3 labeled cRNA was produced following the manufacturer’s protocol.

growth_protocol: Cells were cultured in LIF-free ES culture medium for 2 days and then replaced with Glasgow minimum essential medium (GMEM; Gibco USA) containing 2.5% knock serum replacement (KSR, Gibco, USA), 1% NEAA and 10 μM β-ME for next 12 days.

extract_protocol: total RNA was isolated from cultured cells using PureLink RNA mini Kit (Invitrogen, Life Technologies, USA)

treatment_protocol: 5x104 cells were seeded into plates (Nunc 4-well culture dish, Thermo Fisher Scientific, USA) coated with crosslinked ELP

value: embryonic stem cells


title: HCS29


title: Day 9 differ RNA-rep4

description: Gene expression for Day 09

source_name: Day 9 differ RNA-rep4


title: Day 14 differ RNA-rep4

description: Gene expression for Day 14

source_name: Day 14 differ RNA-rep4


title: Day 14 differ RNA-rep1

description: Gene expression for Day 14

source_name: Day 14 differ RNA-rep1


title: Day 9 differ RNA-rep3

description: Gene expression for Day 09

source_name: Day 9 differ RNA-rep3


title: Day 14 differ RNA-rep3

description: Gene expression for Day 14

source_name: Day 14 differ RNA-rep3


title: Day 9 differ RNA-rep2

description: Gene expression for Day 09

source_name: Day 9 differ RNA-rep2


title: Day 9 differ RNA-rep1

description: Gene expression for Day 9

source_name: Day 9 differ RNA-rep1


title: HCS12


title: Hi-C GM19239 rep20

value: cell line

value: MboI restriction enzyme digested


title: K562 alone 16h

description: Gene expression data from K562 cell alone as a base line for PMA treated K562 cell.

value: Suspension culture as control for 16h


title: HCS26


title: Hi-C GM19239 rep19

value: No treatment


title: A002 before acupuncture

value: collected before acupuncture treatment


title: HCS21


title: HCS31


title: Hi-C GM19239 rep18


title: HCS20


title: mESC RNA-rep3

description: Gene expression for mESC

source_name: mESC RNA-rep3


title: Hi-C GM19239 rep17


title: HCS30


title: HCS01(health controls)


title: sgMYC HCC1954 Control R1

city: Boston

first: Cherubin

last: Manokaran

state: Massachusetts

address: 450 Brookline Ave

department: Cancer Biology

institute: Dana Farber Cancer Institute

data_processing:
Basecalls were performed using Illumina CASAVA 1.8
Raw reads containing adapters, base quality scores less than 5 and more than ten percent N’s were removed using Cutadapt v1.16.
Processed reads were then mapped to hg19 with STAR v2.7.3a 2-pass alignment, first using a genome index with 100 bp overhangs and then using an index built with 75 bp overhangs and a combination of the junctions determined from the initial alignments.
Unstranded gene hits were then counted for both alignments using HTSeq v0.9.1 with a minimum alignment quality of 10, and differential expression was determined in DESeq2 using a beta prior. As independent validation, gene-level differential expression was determined from transcript abundances quantified in Kallisto v0.46 using the hg19 transcriptome.
The pre-processed reads were aligned to hg19 also using ENCODE parameters. The bamCoverage function in deepTools v3.5.0 was then run to generate bigwig files of the alignments by dividing the genome into bins of 20 bps and normalizing coverage to 1x.
Genome_build: hg19
Supplementary_files_format_and_content: tab-delimited text files include raw gene counts for every gene and each sample
Supplementary_files_format_and_content: bigwig files were generated using deepTools; scores represent coverage over genome

source_name: Breast cancer cells

extract_protocol:
Total RNA was purified using the Monarch Total RNA Miniprep Kit (New England Biolabs, #T2010). On-column DNase digestion was performed to remove any residual DNA. The integrity of total RNA was assessed by an Agilent Bioanalyzer 2100 at Novogene.
The cDNA library was constructed using NEBNext® Ultra™ II RNA Library Prep with Sample Purification Beads (New England Biolabs, #E7775). Briefly, a total of 400 ng RNA per sample was subjected to poly(A)-selection, followed by reverse transcription to generate cDNA. The resulting cDNA was subjected to adapter ligation and PCR amplification. Library quality control was performed using Labchip and qPCR.Sequencing was then performed on an Illumina Novaseq 6000 to generate 150 bp paired-end reads (Novogene).

treatment_protocol: Cells were treated for 4 hours with the indicated chemicals.

value: 0.4percent DMSO 4 hrs v/v

value: HER2+ breast cancer cells

value: MYC CRISPR


title: mESC RNA-rep4

description: Gene expression for mESC

source_name: mESC RNA-rep4


title: sgMYC HCC1954 K12i R2

value: THZ531 4 hrs 200 nM


title: Hi-C GM19239 rep15


title: sgMYC HCC1954 K12i R1


title: HCS28

value: untreated

value: serum


title: Hi-C GM19239 rep14


title: mESC RNA-rep2

description: Gene expression for mESC

source_name: mESC RNA-rep2


title: mESC RNA-rep1

description: Gene expression for mESC

source_name: mESC RNA-rep1


title: SKBR3 Control R2

value: wild type


title: SKBR3 Control R1


title: Hi-C GM19239 rep13


title: dsG_VG biol rep 2

city: Madrid

first: Francisco

last: Tenllado

address: Ramiro de Maeztu, 9

country: Spain

institute: CSIC

data_processing:
Illumina NovaSeq 6000 System
Clean sequence reads were obtained from raw data by removing reads containing adapter, reads containing ploy-N and low quality reads using in-house perl scripts.
Trimmed sequence reads were mapped to N. benthamiana V0.4.4 using Hisat2 v2.0.5  (parameters- dta --phred33)
Read count extraction and normalization were performed using featureCounts v1.5.0-p3
Assembly: N. benthamiana V0.4.4
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Nicotiana benthamiana

source_name: Leaf

growth_protocol: Nicotiana benthamiana plants were kept in environment-controlled growth chambers with 16/8 h day/night photoperiod, ~2500 lux of daylight intensity and 60% relative humidity.

extract_protocol:
Total RNA was extracted from N. benthamiana inoculated leaves at 4 and 7 days after inoculation and from upper leaves 7 dpi as described (García-Marcos et al., 2013).
RNA libraries for RNA-seq were performed at Novogene in United Kingdom. The integrity and quality of the total RNA were checked using NanoDrop 2000 Spectrophotometer. mRNA was purified from total RNA using poly-T oligo-attached magnetic beads.

treatment_protocol: Nicotiana benthamiana leaves were inoculated with four different treatments, i.e., dsGFP alone (dsG), PVX-GFP combined with dsGFP (dsG_VG), wild-type (Wt) PVX combined with dsGFP (dsG_V) and bacterial nucleic acid extracts not expressing dsRNA as a control (Ctr).

value: Leaf

value: 4 days after treatment

value: infected

value: WT

value: PVX-GFP-infected, dsRNA treated


title: dsG_VG biol rep 3


title: Hi-C GM19239 rep12

value: Lymphoblastoid

value: cell line


title: dsG_VG biol rep 1


title: Hi-C GM19239 rep16

value: MboI restriction enzyme digested


title: SKBR3 K12i R2


title: dsG_V biol rep 3

value: PVX-infected, dsRNA treated


title: sgMYC HCC1954 Control R2


title: SKBR3 K12i R1


title: dsG_V biol rep 2


title: Hi-C GM19239 rep10

value: No treatment


title: Hi-C GM19239 rep11


title: dsG_V biol rep 1


title: HCC1954 Control R2

value: 0.4percent DMSO 4 hrs v/v


title: HCC1954 Control R1

value: HER2+ breast cancer cells


title: Hi-C GM19239 rep9


title: dsG biol rep 3

value: healthy

value: Non-infected, dsRNA treated


title: HCC1954 K7i R2

value: THZ1 4 hrs 200 nM


title: Hi-C GM19239 rep8


title: Hi-C GM19239 rep7


title: HCC1954 K7i R1


title: dsG biol rep 2


title: Non-tumor fetal CD140a+ CTX, sample 4

city: Rochester

first: Steven

last: Goldman

state: NY

address: 601 Elmwood Ave

department: Center for Translational Neuromedicine

institute: University of Rochester Medical Center

description:
CD140a_FETAL_CTX_NONTUMOR_4
Small RNA
miRNA expression from Dissociated cells from normal fetal CTX, sorted on CD140a.

hyb_protocol: Hybridization was performed according to the manufacturer's instructions.

scan_protocol: GeneChip scanning and image processing were performed according to the manufacturer's instructions.

data_processing: Raw intensity values were normalized using Variance Stabilizing Normalization (VSN) with RMA-style probeset summarization, as implemented by the vsnrma function of the VSN package in Bioconductor, in the R statistical software environment. As the Affymetrix miRNA 3.0 array platform includes miRNA for multiple species, prior to differential expression analysis data was filtered to include probes corresponding to mature human miRNAs.

label_protocol: Biotin labeling was performed according to the manufacturer's instructions.

extract_protocol: miRNA was extracted and purified with the Qiagen miRNeasy kit, according to the manufacturer's instructions.

treatment_protocol: Tissue samples were dissociated with papain, cultured in suspension plates in serum-free media, and sorted MACS and FACS on A2B5 (tumor, adult normal samples) or CD140a (fetal normal samples).

tag: tumor type

value: non-tumor (normal)

tag: tumor grade

tag: cell sort marker

value: CD140a+ (PDGFRa)

tag: developmental stage

value: fetal, 21wk

tag: tissue source

value: cortex


title: Non-tumor adult A2B5+ WM, sample 3

description:
A2B5_ADULT_WM_NONTUMOR_3
Small RNA
miRNA expression from Dissociated cells from normal adult WM, sorted on A2B5.

value: adult

value: white matter


title: Non-tumor fetal CD140a+ CTX, sample 3

description:
CD140a_FETAL_CTX_NONTUMOR_3
Small RNA
miRNA expression from Dissociated cells from normal fetal CTX, sorted on CD140a.

value: fetal, 21.1wk


title: Non-tumor fetal CD140a+ CTX, sample 2

description:
CD140a_FETAL_CTX_NONTUMOR_2
Small RNA
miRNA expression from Dissociated cells from normal fetal CTX, sorted on CD140a.

value: fetal, 20.5wk


title: dsG biol rep 1

value: Leaf

value: 4 days after treatment

value: WT


title: HCC1954 K9i R2

value: NVP2 4 hrs 200 nM

value: wild type


title: Hi-C GM19239 rep6

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: Hi-C GM19239 rep5


title: Non-tumor adult A2B5+ WM, sample 4

description:
A2B5_ADULT_WM_NONTUMOR_4
Small RNA
miRNA expression from Dissociated cells from normal adult WM, sorted on A2B5.

value: non-tumor (normal)


title: HCC1954 K9i R1

value: HER2+ breast cancer cells


title: Ctr biol rep 3

value: healthy

value: Non-infected, non-dsRNA treated


title: Ctr biol rep 2


title: Hi-C GM19239 rep4


title: Melanoma III

city: Vienna

first: Beate

middle: Maria

last: Lichtenberger

address: Waehringer Guertel 18-20

department: Dermatology

country: Austria

institute: Medical University of Vienna

data_processing:
Demultiplexed reads were aligned to the human genome (hg19 assembly) and the ERCC spike-in reference using STAR v2.4.2a in two-pass alignment mode (Dobin and Gingeras, 2015). Uniquely aligned reads were transformed into reads per million kilobase (RPKM).
Assembly: hg19
Supplementary files format and content: tab separated value files containing RPKM (cells in columns, genes in rows)

source_name: Acral lentiginous melanoma

extract_protocol:
Fresh 4 mm punch biopsies from central tumor and unaffected skin adjacent to tumors as well as 10x10 cm healthy skin samples from abdominal plastic surgeries were subjected to cell isolation procedure directly after surgery.
Healthy skin samples III-IV were cut into thin strips after removal of the fat layer. Epidermis was separated from dermis by Dispase 2 (1:100, Roche #04942078001, 20mg/mL), digested in PBS at 37°C for one hour before being peeled off. The epidermal sheet was minced and then subjected to enzymatic digestion in Trypsin-EDTA (GIBCO #25300-054) for 20 min at 37°C in a shaking water bath (Epidermal sheet protocol for enrichment of keratinocytes). Healthy skin dermis and tumor samples were cut into tiny pieces and digested with Collagenase 1 (1:100, GIBCO #17100-017, 50mg/mL), Collagenase 2 (1:100, GIBCO #17101-015, 50mg/mL), Collagenase 4 (1:100, Sigma-Aldrich #C5138, 50mg/mL), Hyaluronidase (1:100, Sigma-Aldrich #H3884, 10mg/mL) and DNAseI (1:250, Sigma-Aldrich #DN25, 5 mg/mL) in DMEM/10%FCS for one hour in a 37°C water bath (Protocol for enrichment of fibroblasts, keratinocytes and immune cells). After enzymatic digestion, the cell suspension was filtered and washed in PBS/10% FCS twice before subjecting it to FACS staining.
After Fc blocking (1:500, CD16/CD32 BD #553142, RRID:AB_394656), cell suspensions were stained for 30 min at 4°C in the dark with CD45-BV605 (1:50, BioLegend #304042, RRID:AB_2562106), ITGA6-PeCy7 (1:100, BioLegend #313622, RRID:AB_2561705), CDH1-PeCy7 (1:200, BioLegend #147310, RRID:AB_2564188), FAP-APC (1:20, R&D Systems #FAB3715A, RRID:AB_2884010), CD90-AF700 (1:30, BioLegend #328120, RRID:AB_2203302) and CD31-FITC (1:30, BD Biosciences #563807), CD106-Pacific Blue (1:100, BD Biosciences #744309, RRID:AB_2742138), CD235ab-Pacific Blue (1:1000, BioLegend #306611, RRID:AB_2248153) and DAPI. ITGA6+/CDH1+ keratinocytes, FAP+/CD90+ fibroblasts, CD45+ immune cells and FAP-CD90- double negative cells were single cell sorted directly into Smart-seq2 lysis buffer in 384-well plates. After sorting, plates were stored at -80°C until they were subjected for sequencing
scRNAseq was conducted according to the Smart-seq2 protocol (Picelli et al., 2013).

value: Acral lentiginous melanoma

tag: Sex

value: female


title: Non-tumor adult A2B5+ WM, sample 2

description:
A2B5_ADULT_WM_NONTUMOR_2
Small RNA
miRNA expression from Dissociated cells from normal adult WM, sorted on A2B5.

value: adult

value: white matter


title: Non-tumor fetal CD140a+ CTX, sample 1

description:
CD140a_FETAL_CTX_NONTUMOR_1
Small RNA
miRNA expression from Dissociated cells from normal fetal CTX, sorted on CD140a.

value: CD140a+ (PDGFRa)

value: fetal, 20.3wk

value: cortex


title: Melanoma I

value: male


title: P8NS2

city: Toronto

first: Adelaida

last: Kolaj

state: Ontario

address: 27 King's College Circle

country: Canada

institute: University of Toronto

description: Gene expression data from cultured neurospheres

hyb_protocol: standard Affymetrix protocol

scan_protocol: standard Affymetrix protocol

data_processing: Data was analyzed using R and normalized by RMA

source_name: Precursors cultured as neurospheres

label_protocol: standard Affymetrix protocol

growth_protocol: Neurospheres were generated by dissecting the V-SVZ of the lateral ventricles of P7/P8 CD1 mice, which were mechanically dissociated, and triturated into a single-cell suspension. Cell concentration and viability were determined by trypan blue exclusion and cells were then plated under clonal conditions at a density of 10 cells/ul in 6-well low-attachment dishes (Corning), with pups cultured independently. Cells were maintained in DMEM and F12 medium supplemented with glucose, 2% B27(Gibco), 10ng/ml FGF (Corning), 20 ng/ml EGF (Corning), 2ug/mL heparin (Stem Cell Technologies), 1% penicillin/streptomycin,  and 0.5mM L-glutamine for 7 days

extract_protocol: Neurospheres were triturated mechanially, quantified, lysed, and RNA was extracted 7 days post culturing

tag: tissue, genotype, age

value: V-SVZ neurospheres

value: WT

tag: strain background


title: HCC1954 K12i R2

value: THZ531 4 hrs 200 nM

tag: cell type

value: wild type


title: P8NS3

tag: genotype


title: Non-tumor adult A2B5+ WM, sample 1

description:
A2B5_ADULT_WM_NONTUMOR_1
Small RNA
miRNA expression from Dissociated cells from normal adult WM, sorted on A2B5.


title: P8NS1


title: Ctr biol rep 1

tag: tissue

value: Leaf

tag: time

value: 4 days after treatment

tag: disease state


title: Hi-C GM19239 rep3

source_name: Lymphoblastoid

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

tag: treatment

value: No treatment


title: HCC1954 K12i R1

value: HER2+ breast cancer cells


title: SCC IV

source_name: Squamous cell carcinoma

value: Squamous cell carcinoma


title: Lung, Aged_CS_M4

city: New York

first: Tyler

last: Lu

state: New York

address: 1300 York Avenue

institute: Weill Cornell Medicine

data_processing:
Sample files were checked for sequence quality (FastQC v 0.11.9) and processed using the Expression Explorer 2 (DEE2) (Ziemann et al., 2019) workflow. Adapter trimming was performed with Skewer (v0.2.2) (Jiang et al., 2014). The resultant filtered reads were mapped to the mouse reference genome GRCm38/mm10 using the Kraken package (Davis et al., 2013). Further quality control was carried out with Minion, part of the STAR aligner (Dobin et al., 2013) and gene-wise expression counts generated using the “-quantMode GeneCounts” parameter.
Assembly: GRCm38/mm10
Supplementary files format and content: ALL processed data files are in .tsv format and contain counts

source_name: Lung

extract_protocol:
Murine lung tissues were dissociated by Collagenase Dispase digestion and stained for Lineage cocktail, EPCAM, and CD31. Lymphatic endothelial cells were sorted as live (Dapi negative), Lineage&EPCAM negative, CD31 positive and Prox-1 positive (eGFP reporter) cells. Sorted lymphatic endothelial cells were processed for RNA isolation using a Qiagen Mini Kit and RNA was sequenced.
RNA-seq libraries of polyadenylated RNA were prepared using SMART-Seq® v4 Ultra® Low Input RNA Kit and the Nextera XT DNA Library Preparation Kit.

value: Lung

value: Aged

value: Lymphatic Endothelial Cell

value: M

value: Cigarette Smoke


title: SCC III

value: male


title: Lung, Aged_CS_M3


title: Melanoma II

value: Acral lentiginous melanoma


title: Hi-C GM19239 rep2

tag: cell line


title: SCC II


title: Hi-C GM19239 rep1


title: trb45-1 clf29 rep3

city: CLERMONT FERRAND

first: simon

last: amiard

address: 28 place henry dunant

country: France

institute: CNRS - UMR 6247 - GRED

data_processing:
Home made RNA-seq pipeline
Trimlmed sequences were mapped to TAIR10 using HISAT2
Read count extraction and normalization were performed using Feature counts and DESeq2
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file including read count values for each samples

molecule: polyA RNA

organism: Arabidopsis thaliana

source_name: mature leaves

growth_protocol: seeds were stratified for 2 days at 4°C in the dark, and plants grown under long day conditions (16h light, 8h dark, 23°C). Seeds were grown on soil and leaves collected at day 21.

extract_protocol:
plants were ground in 2 mL tubes using a Tissue Lyser (Qiagen) twice for 30 sec at 30 Hz before RNA extraction using the RNeasy Plant Mini kit (Qiagen)
DNBSEQ stranded mRNA library

treatment_protocol: No treatment

value: mature leaves

value: trb45 clf29


title: Lung, Aged_RA_F

tag: age

value: F

value: Room Air


title: SCC I


title: Lung, Aged_RA_M2


title: trb45-1 clf29 rep2


title: Hi-C GM18526 rep20

value: Lymphoblastoid

tag: biomaterial provider


title: BCC III

source_name: Basal cell carcinoma

value: Basal cell carcinoma


title: Hi-C GM18526 rep19

value: cell line

value: MboI restriction enzyme digested


title: trb45-1 clf29 rep1


title: Lung, Aged_RA_M1


title: BCC II


title: BCC I


title: Hi-C GM18526 rep17

value: No treatment


title: Hi-C GM18526 rep18


title: Hi-C GM18526 rep16


title: clf29 rep2


title: Lung, Aged_CS_M2


title: Lung, Aged_CS_M1


title: Lung, Aged_CS_F


title: trb45-1 rep3


title: Healthy V

source_name: healthy Skin

value: healthy Skin


title: Hi-C GM18526 rep15


title: Healthy IV

value: female


title: Lung, 8wk_RA_M

value: Lung


title: trb45-1 rep2


title: Hi-C GM18526 rep14


title: trb45-1 rep1


title: clf29 rep3


title: Lung, 8wk_RA_F

value: Lymphatic Endothelial Cell


title: Healthy II


title: Hi-C GM18526 rep12


title: Hi-C GM18526 rep13


title: Lung, 8wk_CS_F


title: clf29 rep1


title: Wild Type Col0 rep3

value: WT


title: Wild Type Col0 rep2


title: Healthy I


title: Lung, 8wk_CS_M

value: M

value: Cigarette Smoke


title: Hi-C GM18526 rep11


title: Hi-C GM18526 rep10


title: Wild Type Col0 rep1


title: trb123 rep3

data_processing:
Home made RNA-seq pipeline
Trimlmed sequences were mapped to TAIR10 using STAR (v 2.7.1)
Read count extraction and normalization were performed using Feature counts and DESeq2
Assembly: TAIR10
Supplementary files format and content: tab-delimited text file including RPKM values for each samples

source_name: 7 days old seedlings

growth_protocol: seeds were stratified for 2 days at 4°C in the dark, and plants grown under long day conditions (16h light, 8h dark, 23°C). Seeds were sterilized in 70% EtOH / 0.01% SDS and seedlings were grown in vitro on 1x MS plates containing 1% sucrose

value: 7 days old seedlings

value: No


title: EC, Nogo-B WT replicate 3

first: Olivier

last: Elemento

address: 1305 York Avenue

institute: WEILL MEDICAL COLLEGE OF CORNELL UNIV

description:
10x Genomics
LS5

data_processing:
Fastq files were processed using CellRanger with default parameters, then further analyzed using Seurat v4
Assembly: mm10
Supplementary files format and content: tsv files contain normalized data

source_name: Heart

extract_protocol:
FACS sorted ECs were isolated from hearts of ApoE-/- and Nogo-A/B(ECKO)ApoE-/- mice after 8 weeks post-TAC and were then processed for single cell RNAseq using standard 10x Chromium.
Libraries were prepared as per the manufacturer's protocol (10X genomics, 3' v2 end protocol)

value: EC

value: Heart

tag: strain

value: C57BL/6 ApoE-/-

value: Cre- Nogo-B WT


title: Hi-C GM18526 rep9

value: Lymphoblastoid


title: siNCoR_3 RNA

data_processing:
Read Trimming (Trimmomatic version 0.39)
Read alignment (STAR 2.7.3a)
Read filtering: removal of multi-mapping, ribosomal & mitchondrial reads and deduplication (Picard 2.21.7)
Quantification (featureCounts 1.6.5)
Differential analysis (DESeq2 version 1.26.0)
Assembly: hg38 (Ensemble release 99)
Supplementary files format and content: 2023_Teichmann_NCoR1_RNAseq_NormCounts.xlsx, normalised counts per gene per sample

source_name: human umbilical vein endothelial cells

growth_protocol: Human umbilical vein endothelial cells (HUVECs), obtained from PromoCell (C-12203, Lot No. 405Z013, 408Z014, 416Z042), were cultured on fibronectin (1mg/ml) coated dishes to passage 3 and used for experiments at passage 4. Endothelial growth medium (EGM, PeloBiotech) containing 8% FCS , 50 U/ml penicillin and 50 µg/ml streptomycin (Gibco), EndoCGS-Heparin (PeloBiotech) and growth factors (EGF, bFGF, IGF, VEGF, Heparin, L-Glutamin) was used as cell culture medium. In case of starvation, cells were cultured in endothelial basal medium (PeloBiotech) containing 1% FCS, 50 U/ml penicillin and 50 µg/ml streptomycin (Gibco), EndoCGS-Heparin (PeloBiotech) at least 4h prior to an experiment.

extract_protocol:
RNA was isolated using the RNA Mini Kit (Bio&SELL). To avoid contamination by genomic DNA, samples were subjected to on-column DNase digestion (DNase-Free DNase Set, Qiagen).
Total RNA and library integrity were verified on LabChip Gx Touch 24 (Perkin Elmer). Approximately 900ng of total RNA was used as input for SMARTer Stranded Total RNA Sample Prep Kit - HI Mammalian (Takara Bio).

value: human umbilical vein endothelial cells

value: HUVEC

value: siRNA against NCOR1


title: MBC2, replicate 1, spatial TCR sequencing

first: SIYU

last: HE

institute: Columbia University

data_processing:
The processed data is achieved by using MiXCR. The details follow the Hudson et al 2022, STAR protocol.
Assembly: /
Supplementary files format and content: /
Library strategy: TCR-seq

source_name: primary breast cancer

extract_protocol: To capture spatial TCR clonotype information, we adapted an established protocol that allows spatial mapping of TCRs from cDNA libraries of our samples. The process involves three qPCR steps:  1. First step begins with pooled 43 TCRB primers and truncated Read 1 primer (2uL of cDNA, 1 uL of each forward and reverse primers, and 12.5 uL of NEBNextMasterMix, 0.5uL Sybr, and 8ul water). The PCR is stopped before the plateau phase and cleaned with 0.8X Amupure beads.  2. Second step uses 43 TCRB primers with R2 sequences and truncated Read 1 primer with 1uL of PCR product from step 1.  3. Third step involves indexed Truseq P5 primers and indexed Nextera P7 primers, with 1uL of PCR product from step 2.  Sequencing was conducted on an Illumina NextSeq 500 with the following cycle settings: R1 28, I1 10, I2 10, R2 110. Clonotype analyses were performed with MiXCR. The PCR cycling conditions are as follows:  -Initial Denaturation: 98°C for 3 minutes -Denaturation: 98°C for 15 seconds -Annealing: 62°C (72°C for qPCR step 3) for 20 seconds -Extension: 72°C for 1 minute -Final Extension: 72°C for 1 minute

value: mixed -whole tissue

value: primary breast cancer

value: 52 year-old


title: trb123 rep2


title: Healthy III

value: healthy Skin

value: female


title: EC, Nogo-B WT replicate 2

description:
10x Genomics
LS4


title: siNCoR_2 RNA


title: Hi-C GM18526 rep8

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: trb123 rep1

value: 7 days old seedlings

value: No


title: siNCoR_1 RNA


title: Hi-C GM18526 rep7


title: EC, Nogo-B KO replicate 2

description:
10x Genomics
LS3

value: EC

value: Heart

value: Cre+ Nogo-B KO


title: CTL_3 RNA

value: negative control siRNA


title: trb45 N°2 rep3


title: EC, Nogo-B KO replicate 1

description:
10x Genomics
LS2

value: C57BL/6 ApoE-/-


title: EC, Nogo-B WT replicate 1

description:
10x Genomics
LS1

value: Cre- Nogo-B WT


title: CTL_2 RNA

value: human umbilical vein endothelial cells

value: HUVEC


title: EC, Nogo-B KO replicate 3

description:
10x Genomics
LS6


title: CTL_1 RNA


title: trb45 N°2 rep2


title: Hi-C GM18526 rep4

value: Lymphoblastoid


title: MKP5-/- BMDM,24hr ox-LDL stimulation (3)

city: Philadelphia

first: Jun

last: Yu

state: PA

address: 1058 MERB, CMDR, 3500 N Broad St

department: CMDR

institute: Temple University

data_processing:
STAR Aligner and SAM Tool installation
Generate genome into Star Aligner using Comprehensive gene annotation (CHR) and Genome Sequence (GRCM39)(ALL) Fasta file with 100 base overhang
Trim and align sample with the genome created using 8 threads creating unsorted BAM files
Sort the alignments of the unsorted BAM files using SAM Tools
Aligned BAM files were imported into Qlucore Omics Explorer 3.9.11 where raw expression counts were counted and then normalized to TMM.
This normalized TMM count is what was taken to the Log2() to generate Log2(Normalized Counts).
Assembly: GRCm39
Supplementary files format and content: Log2(Normalized Counts)

source_name: bone-marrow-derived macrophages

extract_protocol:
RNA was harvested using the RNeasy mini plus kit (Qiagen). 1µg of the total RNA was used for the generation of the data.
Library construction for the RNA-seq was performed by the company Genewiz/Azenta

value: bone-marrow-derived macrophages

value: oxidized-LDL stimulation


title: Hi-C GM18526 rep6


title: trb45 N°1 rep3


title: Treg.OSM.KO.VAT#3

first: CBDM

last: Lab

state: MA

address: 77 Avenue Louis Pasteur

department: Microbiology and Immunobiology

institute: Harvard Medical School

data_processing:
Reads were mapped to the mouse reference genome (mm10) with STAR 2.7.3a
Non-uniquely mapped reads were discarded.
The uniquely mapped reads were assigned to genes using featureCounts with GENCODE annotation (vM25)
Additional quality control after normalization included removal of biological replicates with a poor Pearson’s correlation (<0.9) and/or poor congregation by principal component analysis of the top 1000 variable genes. Genes with fewer than 15 reads across samples or a high coefficient of variation (>0.30) were removed in Multiplot Studio (GenePattern; Broad Institute).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include raw read counts for each Sample

source_name: eVAT

extract_protocol:
For freshly-isolated samples, 1000 cells were double-sorted into 5ul TCL buffer (Qiagen) containing 1% 2-mercaptoethanol (Sigma-Aldrich). For cultured cells in 96-well plate, 20ul TCL buffer containing 1% 2-mercaptoethanol was used to lyse cells and 5ul of that was submitted to RNA-seq. Floating adipocytes were lysed in QIAzol followed by RNA isolation according to the manufacturer's protocol and 2 ng RNA were resuspended in 5 microliters of TCL buffer containing 1% 2-mercaptoethanol.
Library construction was performed according to the standard Immunological Genome Project protocols (https://www.immgen.org/img/Protocols/ImmGenULI_RNAseq_methods.pdf).

value: eVAT

value: Treg

value: OSMf/f


title: trb45 N°2 rep1


title: trb45 N°1 rep2


title: Hi-C GM18526 rep3

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: MKP5-/- BMDM,24hr ox-LDL stimulation (2)


title: MKP5-/- BMDM,24hr ox-LDL stimulation (1)


title: Hi-C GM18526 rep1


title: Treg.OSM.KO.VAT#2


title: Treg.OSM.KO.VAT#1


title: Wild Type plant Col0 rep3

value: 7 days old seedlings

value: WT

value: No


title: WT BMDM,24hr ox-LDL stimulation (3)


title: trb45 N°1 rep1


title: WT BMDM,24hr ox-LDL stimulation (2)


title: Hi-C GM13977 rep15


title: Treg.OSM.WT.VAT#3

value: OSM+/+


title: Wild Type plant Col0 rep2


title: Treg.OSM.WT.VAT#2


title: WT BMDM,24hr ox-LDL stimulation (1)


title: Hi-C GM13977 rep14


title: Hi-C GM18526 rep2


title: Treg.OSM.WT.VAT#1


title: WT BMDM,0hr ox-LDL stimulation (3)


title: Hi-C GM13977 rep13


title: WT BMDM,0hr ox-LDL stimulation (2)


title: Nut_1x_4

city: Lausanne

first: Jean-Yves

last: Roignant

address: Quartier Unil Sorge, Bâtiment Génopode

department: CIG

country: Switzerland

institute: UNIL

data_processing:
After removal of adapter sequences by trimmomatic v0.39, reads < 40nt were selected and mapped to the D. melanogaster rRNA sequences FBtr0346885 (28S), FBtr0346878 (18S) and FBtr0346887 (5.8S) using bowtie2 in End-to-End mode.
Reads’ extremities (5’-ends and 3’-ends) were counted and the different RiboMethSeq scores were calculated.
A combination of ScoreMean >0.92 and ScoreA >0.5.
ScoreC (MethScore) was used for quantification of the methylation level.
Assembly: dm6 (ensembl103)
Supplementary files format and content: csv files include coverage, mean2, scoreA2 and scoreC2 for each high- and low-confidence Nm site
Library strategy: RiboMethSeq  (Marchand,V. 2016)

organism: Drosophila melanogaster

source_name: Head

growth_protocol: D. melanogaster S2R+ cells were grown in Schneider`s medium (Gibco) supplemented with 10% FBS (Sigma) and 1% penicillin–streptomycin (Sigma).

extract_protocol:
Total RNA from S2R+ cells was isolated with Trizol (Invitrogen).
150 ng of total RNA were subjected to alkaline hydrolysis for 16 min at 96°C followed by ethanol precipitation. The extremities of RNA fragments were end-repaired and converted to libraries using NEBNext Small RNA library preparation kit according to the manufacturer’s recommendations. Libraries were quantified and multiplexed and subjected for high-throughput sequencing on a NextSeq2000 instrument with a 50 bp single read mode.

treatment_protocol:
For RNA interference (RNAi) experiments, PCR templates for the dsRNA were prepared using T7 megascript Kit (NEB).
dsRNA against bacterial β-galactosidase gene (lacZ) was used as a control for all RNA interference (RNAi) experiments

value: Head

value: Female

value: 1x home made food for 10d


title: Wild Type plant Col0 rep1


title: nt-shRNA - Biol rep 2

city: Cambridge

first: Eliezer

last: Calo

address: 31 Ames St

institute: Massachusetts Institute of Technology

data_processing:
Quality control performed with fastqc
Trimmed reads aligned to mm10 with STAR aligner
Gene counts generated with featurecounts
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes counts for each sample, as generated by FeatureCounts

growth_protocol: R1-mESCs were maintained in N2B27 media supplemented with 2i + Lif on Poly-L-Ornithine and Laminin-coated plates

extract_protocol:
RNA was extracted with trizol-choloroform extraction, and precipitated in isopropanol.
NEBNext Ultra II with Poly-A selection

treatment_protocol: 2 day infection with shRNA-containing lentivirus; 3 day puromycin selection for shRNA-expressing cells

value: embryonic stem cells


title: Nut_1x_3


title: Hi-C GM13977 rep12

data_processing:
Sequenced reads were preprocessed, mapped to the Human genome build hg38, filtered for quality score ≥30, and processed using juicer tools v1.14.08
Replicates were combined and juicer tools (1.14.08) was used to create .hic files.
Assembly: hg38
Supplementary files format and content: .hic files

value: Lymphoblastoid


title: Hi-C GM13977 rep11


title: Hi-C GM13977 rep10


title: Hi-C GM13977 rep16


title: Eftud2 shRNA2 - Biol rep 3


title: Nut_1x_2


title: Eftud2 shRNA2 - Biol rep 2


title: Nut_Low_s_aa_4

value: 0.25x sugar, no a.a. for 10d


title: Nut_1x_1


title: Hi-C GM13977 rep9


title: AgRP-Gq_POMC-Gi_CNO_1

city: Köln

first: Jens

middle: C

last: Brüning

address: Gleueler Str. 50

department: Neuronal Control of Metabolism

institute: Max Planck Institute for Metabolism Research

description: 10x Genomics

data_processing:
Raw sequencing data were demultiplexed, aligned to the mouse reference genome GRCm38 and counted using Cell Ranger (version 7.0.0; 10x Genomics).
Data was processed using Seurat (version 4.3.0), doublet detection was conducted using scDblFinder. Low dimensional embeddings were obtained using scvi. Clustering was conducted using Seurat.
meta_data.tsv contains clustering, annotation and analysis results per cell for all samples
Assembly: GRCm38 (mm10)
Supplementary files format and content: Tab-separated files for barcodes(cells) and features(genes) and matrix file for raw counts corresponding to the Cellranger output.

molecule: nuclear RNA

source_name: hindbrain

extract_protocol:
A portion of the hindbrain containing the AP and NTS was dissected in HibernateA Medium (A1247501) on ice and snap frozen on liquid nitrogen and  stored at -80°C overnight. Homogenates were produced using a Dounce homogeniser in 1 ml of homogenate buffer (100 µM of DTT, 0.1% Triton X-100, 2X EDTA-free Protease Inhibitor, 0.4 U/µl of RNasin RNase inhibitor, and 0.2 U/µl of Superase.In RNase Inhibitor in nuclei isolation medium [250 mM of sucrose, 25 mM of KCl, 5 mM of MgCl2, and 10 mM of Tris buffer at a pH of 8.0 in nuclease-free water with 1 µl/ml of DRAQ5 on ice. The homogenates were centrifuged at 900xg for 10 min at 4 C, and pellets were then resuspended in homogenate buffer with 25% Opti-Prep diluted in iodixanol dilution medium (250 mM of sucrose, 150 mM of KCl, 30 mM of MgCl2, and 60 mM of Tris buffer with a pH of 8 in nuclease-free water). Each suspension was layered on top of separate 29% OptiPrep solutions and centrifuged for 20 min at 13,500xg at 4 C. For each sample, the pellet was removed and resuspended in 500 µl of wash buffer (1% BSA, 0.4 U/µl of RNasin, and 0.2 of U/µl in PBS). The samples were passed through a 35 µm cell strainer. Fluorescent-activated cell sorting (FACS) was performed using a BD Influx cell sorter (BD Biosciences, Franklin Lakes, NJ, USA). The gating was set according to size and granularity using FSC and SSC to capture singlets and remove debris, and fluorescence at 647/670 nm to detect DraQ5 staining. Each sample was sorted into separate tubes, each with a total of 20,000 particles/40ul.
Sequencing libraries for the single-nuclei suspension samples were generated using 10X Genomics Chromium Single-Cell 3’ Reagent kit according to the standardized protocol. RNA from lysed nuclei was reverse transcribed and cDNA was PCR amplified for 19 cycles.

value: hindbrain

value: CNO


title: Hi-C GM13977 rep8

extract_protocol:
Cells were crosslinked in 1% v/v formaldehyde for ten minutes and quenched by adding 2.5 M glycine to a final concentration of 0.2 M for 5 min. Cells were pelleted by centrifugation at 300 G for 5 min at 4 °C and then washed with cold PBS. Cells were lysed with lysis buffer containing 10 mM Tri-HCl pH 8.0, 10 mM NaCl, 0.2% Igepal CA630 and protease inhibitors for 15 min on ice. Cells were centrifuged at 300 G and washed in that same buffer, and then resuspended in 50 µl 0.5% SDS for 5 min at 62 °C. Afterward, 145 µl of water and 25 µL of Trition X-100 were added and incubated at 37 °C for 15 min.
Chromatin was digested overnight in MboI, MseI, or NlaIII in the corresponding buffer. Fragment overhangs were repaired and biotinylated using equal amounts of biotin-14-dATP, dCTP, dGTP, and dTTP in the presence of 40 units of DNA Polymerase I, Large (Klenow) Fragment at 37 °C for 1 h. Chromatin was ligated in 1x T4 DNA ligase buffer, Triton X-100, 0.12 mg BSA, and 2000 units T4 DNA ligase at room temperature for four hours. Proteins were digested, and chromatin decrosslinked in 0.72 mg/ml proteinase k, 1% SDS, and 0.5 M NaCl for 30 min at 55 °C, followed by 68 °C overnight. Libraries were sequenced and then processed using Illumina HiSeq 4000 software and JuicerTools v1.14.08. As per Harris, Hannah L., et al. "Chromatin alternates between A and B compartments at kilobase scale for subgenic organization." Nature Communications 14.1 (2023): 3303.


title: WT_CNO_2

description: 10x Genomics


title: AgRP-Gq_POMC-Gi_CNO_2

description: 10x Genomics


title: Eftud2 shRNA1 - Biol rep 3


title: Eftud2 shRNA2 - Biol rep 1


title: Nut_Low_s_aa_3


title: WT_CNO_1

description: 10x Genomics


title: Hi-C GM13977 rep7


title: WT BMDM,0hr ox-LDL stimulation (1)

value: bone-marrow-derived macrophages


title: nt-shRNA - Biol rep 1


title: Nut_Low_s_aa_2


title: Hi-C GM13977 rep6


title: FDDwfemale

city: newark

first: Luciano

last: D'Adamio

state: New Jersey

address: 205 s orange ave CC-H-13

department: PPN

institute: rutgers

description: 10x Genomics

data_processing: Sequencing was performed by Azenta life science following standard 10x Genomics v3 procedure. Raw data were pre-filtered through Cell Ranger Software.

source_name: Brain

extract_protocol: 10X single-cell from 10X genomics 3' HT scRNAseq v3.1

value: Brain

tag: gender

value: female

value: 9-12 month

value: Microglia

value: CD11b magnetic beads filted


title: Eftud2 shRNA1 - Biol rep 2

value: WT


title: Hi-C GM13977 rep5

first: Michael

last: Rowley

institute: University of Nebraska Medical Center

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: Nut_Low_s_aa_1

value: Head

value: Female


title: Eftud2 shRNA1 - Biol rep 1

value: embryonic stem cells


title: FDDwmale

description: 10x Genomics

value: male


title: Hi-C GM13977 rep4

value: Lymphoblastoid


title: Heat_29_3

value: 29C darkness for 8d


title: ovWT2

data_processing:
Adapters and low quality reads were trimmed from fastq files with cutadapt (version 3.4).
rRNA sequences were filtered out with bowtie2 (-p 20 -L 15 -k 20 --fr --end-to-end) losing up to 4% of reads.
The remaining reads were mapped with STAR as described in (Boivin, RNA, 2018) (version 2.7.8a).
Reads were counted with CoCo (cc -c both -p -s 1) (Deschamps-Francoeur, Bioinformatics, 2019).
Assembly: dm6 (ensembl103)
Supplementary files format and content: CSV files include counts from the CoCo output
Library strategy: TGIRT-seq (Boivin,V. 2018)

source_name: Mated Canton-S females, 3-4 days-old

extract_protocol:
Total RNA from S2R+ cells was isolated with Trizol (Invitrogen).
3 µg of total RNA were DNAsed with DNase I treatment (New England Biolabs). RNA was directly ribodepleted with the riboPOOL kit (siTOOLs) that was completed with oligos hybridising to 5S and 2S rRNAs following the manufacturer’s instructions.

value: ovaries


title: FBDwmale

description: 10x Genomics


title: Hi-C GM13977 rep3


title: Heat_29_2


title: Hi-C GM13977 rep2


title: ovWT1


title: Heat_29_1


title: bri2trem2dkomale1

description: 10x Genomics


title: Heads_rep3

source_name: Mated Canton-S female, 8 days-old

value: heads


title: Hi-C GM13977 rep1

source_name: Lymphoblastoid


title: Heat_25_4

value: 25C darkness for 8d


title: Heads_rep2

value: female


title: trem2kofemale1

description: 10x Genomics

value: Brain

value: 9-12 month


title: Heat_29_4


title: FBDwfemale

description: 10x Genomics

value: Microglia

value: CD11b magnetic beads filted


title: Heads_rep1


title: Heat_25_3


title: Heat_25_2


title: trem2komale1

description: 10x Genomics


title: Hi-C GM13976 rep15

value: cell line


title: ovWT3


title: bri2kofemale2

description: 10x Genomics


title: Hi-C GM13976 rep16

value: MboI restriction enzyme digested


title: Heat_25_1


title: bri2trem2dkofemale1

description: 10x Genomics


title: Hi-C GM13976 rep13

value: No treatment


title: Hi-C GM13976 rep14


title: bri2kofemale1

description: 10x Genomics


title: Heat_18_4

value: Head

value: 18C darkness  for 8d


title: bri2komale2

description: 10x Genomics


title: Hi-C GM13976 rep12


title: S2R+ cells LacZ KD rep 3

data_processing:
Adapters and low quality reads were trimmed from fastq files with cutadapt (version 3.4).
rRNA sequences were filtered out with bowtie2 (-p 20 -L 15 -k 20 --fr --end-to-end) losing up to 4% of reads.
The remaining reads were mapped with STAR as described in (Boivin, RNA, 2018) (version 2.7.8a).
Reads were counted with CoCo (cc -c both -p -s 1) (Deschamps-Francoeur, Bioinformatics, 2019).
Assembly: dm6 (ensembl103)
Supplementary files format and content: tab-delimited text files include counts, CPM and TPM from the CoCo output

extract_protocol:
Total RNA from S2R+ cells was isolated with Trizol (Invitrogen).
3 µg of total RNA were DNAsed with DNase I treatment (New England Biolabs). RNA was directly ribodepleted with the riboPOOL kit (siTOOLs) that was completed with oligos hybridising to 5S and 2S rRNAs following the manufacturer’s instructions.
TGIRT-seq (Boivin,V. 2018)

value: late embryonic stage

value: LacZ knockdown


title: Hi-C GM13976 rep11

value: Lymphoblastoid


title: S2R+ cells LacZ KD rep 2


title: Hi-C GM13976 rep10


title: controlfemale2

description: 10x Genomics

value: wildtype


title: S2R+ cells Fib KD rep 3

value: Fib knockdown


title: controlfemale1

description: 10x Genomics


title: controlmale1

description: 10x Genomics

value: male


title: S2R+ cells LacZ KD rep 1


title: d17_PQ_3

value: Female

value: 5% Sucrose + 2.5nM Paraquat for 8d


title: S2R+ cells Fib KD rep 1


title: Heat_18_1


title: HCT116_dKO_WGBS

city: Paris

first: Pierre-Antoine

last: Defossez

address: 35 rue Hélène Brion

institute: Epigenetics and Cell Fate Unit

data_processing:
As described in Miura et al 2019 NAR, the sequenced reads were mapped with BMap and summarized with an in-house pipeline, with custom scripts archived using GitHub (https://github.com/FumihitoMiura/Project-2).
Assembly: hg38
Supplementary files format and content: Processed data files were obtained with above data processing steps. The methylexport data includes chromosome number, cytosine position in CpG, strand, methylated C reads, total C reads in each columns.

source_name: Colon

growth_protocol: HCT116 cells were maintained in McCoy’s 5A medium with L-glutamine supplemented with 10% FBS and 1% Penicillin/Streptomycin.

extract_protocol:
Genomic DNA was isolated using the DNeasy Tissue & Blood kit (Qiagen) according to the manufacturer's protocol.
The library preparation for WGBS was performed with the tPBAT protocol described previously (Miura F, Nucleic Acids Res, 2012; Miura F, Nucleic Acids Res, 2019). One hundred nanograms of genomic DNA spiked with 1% (w/w) of unmethylated lambda DNA (Promega) was used for the library preparation.

treatment_protocol: To facilitate the auxin treatment, HCT116 cells were cultured in a medium supplemented with 2 μg/mL doxycycline and 20 μM auxinole for a duration of one day. Subsequently, the cells were maintained in a medium containing 2 μg/mL doxycycline and 500 μM auxin. During the course of the auxin treatment, the medium was refreshed every two days to ensure a consistent concentration of doxycycline and auxin throughout the experimental period.

value: Colon

value: Colorectal cancer cell

value: HCT116 DKO (DNMT1 hypomorphic and DNMT3B KO) from the Vogelstein lab


title: d17_PQ_2


title: HCT116_WT_WGBS

value: HCT116 WT from the Vogelstein lab


title: Dko3

first: Pierre

last: de la Grange

address: 29, rue du Faubourg Saint-Jacques

department: Paris Biotech Santé

institute: GenoSplice technology

data_processing:
Sequencing, data quality, reads repartition (e.g., for potential ribosomal contamination), and insert size estimation were performed using FastQC, Picard-Tools, Samtools and rseqc
Reads were mapped using STAR_2.7.5a
Assembly: mm10
Supplementary files format and content: Gene expression values normalized by DESeq2 using FAST DB v2018_1 annotations

source_name: cortex

extract_protocol:
RNA was extracted and DNAse treated using RNeasy Mini Kit (Qiagen). 0.2 ug of total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the TruSeq Stranded mRNA kit protocol (Illumina technology)  according to the manufacturer's instructions.

value: cortex

value: Sam68:Slm2 ko

value: embryonal day 18.5


title: bri2komale1

description: 10x Genomics

value: Brain

value: 9-12 month

value: Microglia

value: CD11b magnetic beads filted


title: UHRF1-AID/DNMT1-AID_WGBS_Day12_Rep3

value: Auxin treatment

tag: time point

value: 12 days


title: Hi-C GM13976 rep9

address: 42nd and Emile street

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: Heat_18_3

value: Head

value: Female

value: 18C darkness  for 8d


title: Dko2


title: d17_PQ_1

value: 5% Sucrose + 2.5nM Paraquat for 8d


title: Heat_18_2


title: d17_CTR_3

value: 5% Sucrose for 8d


title: Hi-C GM13976 rep7


title: S2R+ cells Fib KD rep 2

value: late embryonic stage

value: Fib knockdown


title: Hi-C GM13976 rep8


title: Hi-C GM13976 rep5


title: UHRF1-AID/DNMT1-AID_WGBS_Day12_Rep2

value: Colon

value: Colorectal cancer cell


title: d17_CTR_2


title: Wt3

value: cortex

value: wt

value: embryonal day 18.5


title: Hi-C GM13976 rep4


title: UHRF1-AID/DNMT1-AID_WGBS_Day12_Rep1

value: Auxin treatment

value: 12 days


title: d17_CTR_1


title: UHRF1-AID/DNMT1-AID_WGBS_Day8_Rep3

value: 8 days


title: Wt2


title: Hi-C GM13976 rep3

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested


title: Hi-C GM13976 rep6

value: No treatment


title: LacZ_KD_4

value: mesenchymal stem cells

value: LacZ knockdown


title: UHRF1-AID/DNMT1-AID_WGBS_Day8_Rep2


title: LacZ_KD_3


title: Hi-C GM13976 rep2


title: UHRF1-AID/DNMT1-AID_WGBS_Day6_Rep2

value: 6 days


title: UHRF1-AID/DNMT1-AID_WGBS_Day8_Rep1


title: Hi-C GM12892 rep3


title: UHRF1-AID/DNMT1-AID_WGBS_Day6_Rep3


title: Dko1

value: Sam68:Slm2 ko


title: Hi-C GM13976 rep1


title: Mice primary cultured cortical neurons, Ltn1 KO, Control RNAi, 3 min

city: Wako

first: Nayan

last: Suryawanshi

state: Saitama

address: Hirosawa 2-1

department: Center for Brain Science

country: Japan

institute: RIKEN

description:
LTNTTC
Ltn1 KO + Scrambled RNAi + 3 min harringtonine
Ribosome footprints

data_processing:
Sequence reads were trimmed for adaptor sequence/low-quality sequence using fastx_clipper and fastx_trimmer.
Trimmed sequence reads were mapped to GrCM38/mm10 using Bowtie (parameters- seedlen=23).
Read count extraction were performed using samtools and bedtools and normalization were performed using custom R script.
Assembly: mm10
Supplementary files format and content: meta2rpm.txt: Space-delimited text file includes RPM for all samples.
Library strategy: Ribo-Seq

source_name: primary cultured cortical neurons

extract_protocol:
Harringtonine treated mice primary cultured cortical neurons rapidly lysed in polysome buffer (20mM Tris-Cl, pH 7.5, 150mM NaCl, 5 mM MgCl2, 1 mM DTT and 100 μg/ml cycloheximide) supplemented with 1% TritonX-100 and DNase I 10units/mL (Roche).
RNA libraries for RNA-seq (Ribo-seq) were prepared as described in C.W. Chen, M. Tanaka, Genome-wide Translation Profiling by Ribosome-Bound tRNA Capture. Cell Rep. 23, 608-621 (2018).

treatment_protocol: Mice primary cultured cortical neurons were treated with harringtonine (5 µg/ml) for 3 minutes.

value: primary cultured cortical neurons

value: Ltn1 KO

tag: RNAi

value: Scrambled RNAi

value: harringtonine

tag: treatment duration

value: 3 min


title: Mice primary cultured cortical neurons, WT, Control RNAi, 3 min

description:
WTTTC
WT + Scrambled RNAi + 3 min harringtonine
Ribosome footprints

value: WT


title: Fib_KD_4

value: Fib knockdown


title: Fib_KD_3


title: Mice primary cultured cortical neurons, Ltn1 KO, Ttc3 RNAi, 3 min

description:
LTNSC
Ltn1 KO + Ttc3 RNAi + 3 min harringtonine
Ribosome footprints

value: Ttc3 RNAi


title: Mice primary cultured cortical neurons, WT, Ttc3 RNAi, 3 min

description:
WTSC
WT + Ttc3 RNAi + 3 min harringtonine
Ribosome footprints


title: Fib_KD_2


title: Hi-C GM12892 rep2


title: Hi-C GM12892 rep1


title: UHRF1-AID/DNMT1-AID_WGBS_Day4_Rep3

value: Colon

value: Colorectal cancer cell

value: Auxin treatment

value: 4 days


title: Hi-C GM12891 rep4

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: Vehicle Multi 4

city: South San Francisco

first: David

last: Tatarakis

email: tatarakis@dnli.com, genomics@dnli.com

address: 161 Oyster Point Blvd

department: Discovery Genomics

institute: Denali Therapeutics

description: SampleID: PG24

data_processing:
alignment and quantification. cellranger-6.0.1
downstream analysis/filtering/differential expression Seurat v4
Assembly: mm10
Supplementary files format and content: final analysis object counts matrix (.mtx) and meta data table (.csv)

source_name: Brain tissue

extract_protocol:
Single nuclei suspension was prepared by dissociating frozen tissue in Nuclei EZ Prep buffer (Sigma Aldrich, # NUC101) with 15-25 strokes each of pestle A and B using a 2 mL glass dounce homogenizer. A final concentration of 0.2 U/uL RNase inhibitor (Ambion, cat. no. AM2682) were added to the Nuclei EZ Prep buffer for 2 rounds of lysis incubation on ice, pelleting the nuclei in between each lysis. After a couple rounds of washing, the lysate was resuspended in 0.5 - 1 mL of 1% BSA in PBS with DAPI, then passed through a 30-um strainer, and FACS sorted directly into 10x Genomics RT master mix
RT enzyme was added immediately prior to microfluidic loading on Chromium for nuclei capture, and libaries were prepared per 10X Genomics user guide.

treatment_protocol: Intravenous dosing of test articles diluted in sterile saline

value: Human TfR knock-in

tag: Sex

value: Female

value: months

tag: organ

value: Brain

tag: region

value: Posterior

value: Multiple

value: hTfR KI HOM

value: Saline

value: 4X 50mpk

value: mg per kg

value: days


title: LacZ_KD_2

tag: cell type

value: mesenchymal stem cells

value: LacZ knockdown


title: Wt1

value: cortex

tag: genotype

value: wt

value: embryonal day 18.5


title: Hi-C GM12891 rep3

city: Omaha

tag: tissue

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: LacZ_KD_1


title: UHRF1-AID/DNMT1-AID_WGBS_Day6_Rep1

value: Colon

value: Colorectal cancer cell

value: Auxin treatment

value: 6 days


title: UHRF1-AID/DNMT1-AID_WGBS_Day4_Rep2

value: 4 days


title: ASO Multi 4

description: SampleID: PG23

value: Human TfR knock-in

value: Female

value: months

value: Brain

value: Posterior

value: Multiple

value: hTfR KI HOM

value: Malat1 ASO

value: 4x 2mpk


title: UHRF1-AID/DNMT1-AID_WGBS_Day4_Rep1


title: OTV Multi 3

description: SampleID: PG22

value: 4X 50mpk

value: mg per kg

value: days


title: Hi-C GM12891 rep2

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: TfR-Malat1 Multi 6

description: SampleID: PG21


title: UHRF1-AID/DNMT1-AID_WGBS_Day2_Rep3

value: Colon

value: Colorectal cancer cell

value: Auxin treatment

value: 2 days


title: wild-type, quiescence, day 8, steady state RNA, 5782, replicate 2

city: Seattle

first: Alison

last: Greenlaw

state: WA

address: 1100 Fairview Ave N

department: Basic Sciences

institute: Fred Hutch Cancer Center

description: R1 and R3 are, respectively, forward and reverse reads; R2 are UMI indices.

data_processing:
Paired-end reads underwent quality assessment with FastQC and MultiQC. Unique Molecular Identifier (UMI) sequences were appended to the reads using UMI-tools, and adapter and quality trimming were performed with Atria. For nascent transcriptome assembly, reads were additionally subjected to k-mer adjustment using Rcorrector. For more details, see Greenlaw et al.
Using the aligner STAR, processed reads were aligned to a concatenated multi-organism reference genome consisting of the S. cerevisiae, K. lactis, and 20S narnavirus genomes. Non-k-mer-adjusted bams (*.UTPD.bam) were indexed and filtered (with Samtools) to retain only primary alignments, and technical duplicates were removed using UMI-tools. k-mer-adjusted bams (*.UTKPSSc.bam) were indexed and filtered to retain both primary and secondary alignments; alignments associated with the K. lactis and 20S narnavirus genomes were then filtered out. For more details, see Greenlaw et al.
Gene Transfer Format (gtf) and Gene Feature Format (gff3) files were obtained or derived from publicly available sources using custom scripts. Additionally, some files were generated via nascent transcriptome assembly and annotation using Trinity, GffRead, and custom scripts. To perform feature-level quantification, we used htseq-count with the gtf and gff3 files in conjunction with processed non-k-mer-adjusted bams. For more details, see Greenlaw et al.
To generate normalized coverage tracks (*.bw), we used processed non-k-mer-adjusted bams as input to the utility bamCoverage (deepTools) in one of two ways: (a) For the bins per million (BPM) normalization method, mapped reads were normalized by their library size while excluding all rRNA and tRNA regions. The bin size for this method was set to 1 base pair. (b) For the K. lactis scaled coverage (SC) method, library size estimates were first calculated using K. lactis spike-in counts. The bam files were then processed by supplying the reciprocals of the estimates as arguments (--scaleFactor) to bamCoverage. Again, the bin size was set to 1 base pair. For more details, see Greenlaw et al.
Assembly: sacCer3 R64-1-1
Supplementary files format and content: bams for individual replicates (non-k-mer-adjusted and k-mer-adjusted) and merged replicates (k-mer-adjusted)
Supplementary files format and content: bw files for individual and merged replicates, derived from non-k-mer-adjusted bams, and normalized using either the BPM calculation or the K. lactis spike-in-scaled coverage calculation
Supplementary files format and content: gtf and gff3 files obtained or derived from publicly available sources, or generated via custom transcriptome assembly and annotation
Supplementary files format and content: tab-delimited text files containing sample-specific raw counts for features in the various gtf and gff3 files

organism: Saccharomyces cerevisiae

growth_protocol: Quiescent cells were grown for 8 days to saturation in YEP with 2% glucose and then purified using a gradient method.

extract_protocol:
To prepare 4tU-seq libraries, we employed the Universal Plus™ Total RNA-Seq library preparation kit and custom yeast rRNA depletion (AnyDeplete®).
RNA was extracted using yeast RiboPure™ RNA Purification Kit from Invitrogen™
4tU-seq

value: WT


title: Hi-C GM12891 rep1


title: OTV Multi 2

description: SampleID: PG18

value: Human TfR knock-in

value: Female

value: months

value: Brain

value: Posterior


title: wild-type, quiescence, day 8, steady state RNA, 5781, replicate 1


title: UHRF1-AID/DNMT1-AID_WGBS_Day0_Rep3

value: Before auxin treatment


title: UHRF1-AID/DNMT1-AID_WGBS_Day2_Rep2


title: Fib_KD_1

value: mesenchymal stem cells

value: Fib knockdown


title: Hi-C AK1 rep9

value: Lymphoblastoid


title: TfR-Malat1 Multi 4

description: SampleID: PG13

value: Multiple

value: hTfR KI HOM

value: 4X 50mpk

value: mg per kg

value: days


title: UHRF1-AID/DNMT1-AID_WGBS_Day2_Rep1

value: Colon

value: Colorectal cancer cell

value: Auxin treatment


title: TfR-Malat1 Multi 5

description: SampleID: PG17

value: Human TfR knock-in


title: Hi-C AK1 rep7

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: Vehicle Multi 3

description: SampleID: PG12

value: Female

value: months

value: Brain

value: Posterior

value: Saline


title: wild-type, G1, day 1, steady state RNA, 5782, replicate 2

growth_protocol: G1 arrest was induced by adding α factor at a concentration of 5 μg/ml to early log phase yeast. The arrest was evaluated via microscope, and a second dose of α factor was added at 90 minutes if necessary.

extract_protocol:
To prepare RNA-seq libraries, we employed the Universal Plus™ Total RNA-Seq library preparation kit and custom yeast rRNA depletion (AnyDeplete®).
RNA was extracted using yeast RiboPure™ RNA Purification Kit from Invitrogen™
4tU-seq

value: WT


title: Hi-C AK1 rep6

value: Lymphoblastoid


title: UHRF1-AID/DNMT1-AID_WGBS_Day0_Rep1

value: Before auxin treatment


title: wild-type, G1, day 1, steady state RNA, 5781, replicate 1


title: UHRF1-AID/DNMT1-AID_WGBS_Day0_Rep2


title: Hi-C AK1 rep5


title: DNMT1-AID_WGBS_Day12_Rep3

value: 12 days


title: TfR-Malat1 Multi 3

description: SampleID: PG9

value: Multiple

value: hTfR KI HOM

value: 4X 50mpk

value: mg per kg

value: days


title: rrp6∆, quiescence, day 8, steady state RNA, 7079, replicate 1

growth_protocol: Quiescence cells were grown 8 days to saturation in YEP with 2% glucose and were purified using gradient method


title: Hi-C AK1 rep4

value: cell line


title: Hi-C AK1 rep8

value: MboI restriction enzyme digested


title: wild-type, quiescence, day 8, nascent RNA, 5782, replicate 2


title: wild-type, quiescence, day 8, nascent RNA, 5781, replicate 1


title: rrp6∆, quiescence, day 8, steady state RNA, 7078, replicate 2


title: ASO Multi 3

description: SampleID: PG11

value: Human TfR knock-in

value: Malat1 ASO

value: 4x 2mpk


title: Vehicle Multi 2

description: SampleID: PG8

value: Female

value: months

value: Brain


title: Hi-C AK1 rep3

value: No treatment


title: DNMT1-AID_WGBS_Day12_Rep2

value: Colon

value: Colorectal cancer cell

value: Auxin treatment


title: DNMT1-AID_WGBS_Day12_Rep1

value: 12 days


title: ASO Multi 2

description: SampleID: PG7

value: Posterior

value: Multiple

value: hTfR KI HOM


title: rrp6∆, quiescence, day 8, nascent RNA, 7078, replicate 2


title: Hi-C AK1 rep2

value: Lymphoblastoid


title: OTV Multi 1

description: SampleID: PG6

value: 4X 50mpk

value: mg per kg

value: days


title: DNMT1-AID_WGBS_Day8_Rep3

value: 8 days


title: TfR-Malat1 Multi 2

description: SampleID: PG5

value: Human TfR knock-in


title: DNMT1-AID_WGBS_Day8_Rep2


title: rrp6∆, G1, day 1, steady state RNA, 7079, replicate 1


title: DNMT1-AID_WGBS_Day8_Rep1


title: HepG2_coumarin 100 μM_rep3

city: Beijing

first: Yuan

last: Li

address: 38 Science Park Road, National Center for Protein Sciences (Beijing), Changping District, Beijing

institute: Beijing Proteome Research Center

data_processing:
Cleaned reads were aligned to the genome reference of Ensembl GRCh38 with Hisat2 using strand specific parameters.
For RNAseq data, a stringent pre-filtering criterion of median counts over all samples < 5 was carried out. The normalization and analysis of differentially expressed genes (DEGs) were conducted by using DESeq2
Assembly: genome reference of Ensembl GRCh38
Supplementary files format and content: Matrix table with raw gene counts and fpkm for every gene and every sample

source_name: HepG2 cells

growth_protocol: About 5×107 HepG2 cells were treated in triplicates using 6 concentrations of coumarin and a control for 6 h.

extract_protocol:
After the culture medium with coumarin was removed, the cells were harvested by digestion of trypsin-EDTA solution and washed with ice-cold PBS twice and then centrifuged at 12,000 g for 15 min at 4 °C. RNAs were then purified by Trizol reagent. RNAs were quantified by a NanoPhotometer.
The RNA samples were purified by poly (dT) beads, converted to cDNA using SmartScribe Rtase kit according to manufacturer’s protocol.

treatment_protocol: Coumarin was dissolved in DMEM (100 mM stock solutions). Further dilutions were made with serum-free DMEM. At the time of coumarin exposure, after the FBS-DMEM culture medium was removed, HepG2 cells were washed with PBS once and were finally treated in the fresh serum-free DMEM culture medium containing different concentrations of coumarin (0-100 μM) for 6 h.

value: HepG2 cells

value: treated with 100 uM coumarin for 6 h


title: HepG2_coumarin 100 μM_rep2


title: Vehicle Multi 1

description: SampleID: PG4

value: Female

value: months

value: Brain

value: Saline


title: HepG2_coumarin 100 μM_rep1


title: OsTIR-AID, quiescence, day7, steady state RNA, 6126, replicate 2

growth_protocol: Quiescent cells were grown for 7 days to saturation in YEP with 2% glucose and then purified using a gradient method.

value: OsTIR-AID

value: IAA powder (98% purity, Sigma-Aldrich) was added at a concentration of 1 mg/mL.


title: ASO Multi 1

description: SampleID: PG3

value: Posterior

value: Malat1 ASO

value: 4x 2mpk


title: OsTIR-AID, quiescence, day7, steady state RNA, 6125, replicate 1


title: Hi-C AK1 rep1

value: Lymphoblastoid

value: cell line

value: MboI restriction enzyme digested

value: No treatment


title: DNMT1-AID_WGBS_Day6_Rep3

value: Colon

value: Colorectal cancer cell

value: Auxin treatment

value: 6 days


title: rrp6∆, quiescence, day 8, nascent RNA, 7079, replicate 1


title: TfR-Malat1 Multi 1

description: SampleID: PG1

value: Human TfR knock-in

value: Female

value: Multiple

value: hTfR KI HOM

value: 4X 50mpk

value: mg per kg

value: days


title: DNMT1-AID_WGBS_Day6_Rep2


title: HepG2_coumarin 10 μM_rep3

value: HepG2 cells

value: treated with 10 uM coumarin for 6 h


title: OTV_Multi_5

data_processing:
alignment and quantification. cellranger-5.0.0
downstream analysis/filtering/differential expression Seurat v4
Assembly: mm10
Supplementary files format and content: final analysis object counts matrix (.mtx) and meta data table (.csv)

extract_protocol:
Single nuclei suspension was prepared by dissociating frozen tissue in Nuclei EZ Prep buffer (Sigma Aldrich, # NUC101) with 25 strokes each of pestle A and B using a 2 mL glass dounce homogenizer. A final concentration of 1X protease inhibitor (Complete, EDTA-free (Roche, cat. no. 11873580001) and 0.4 U/uL RNase inhibitor (Ambion, cat. no. AM2682) were added to the Nuclei EZ Prep buffer for 25-30 minutes of lysis incubation on ice. The lysate was centrifuged at 300g for 5 mins, resuspended in 500 uL of 1% BSA in PBS for purification in a 2M sucrose cushion at 13000g for 45 mins. After the final wash, nuclei pellet was resuspended in 2% BSA in PBS, then passed through a 30-um strainer, and counted on a Vi-CELL.
Single nuclei capture (target capture of 10,000 cells/nuclei) and library prep was performed per manufacturer’s protocol (CG000204 Rev B)

value: Male

value: months

value: Brain

value: Posterior

value: 4X 60mpk


title: Nab3-AID, quiescence, day7, steady state RNA, 7718, replicate 2

value: IAA powder (98% purity, Sigma-Aldrich) was added at a concentration of 1 mg/mL.


title: OsTIR-AID, quiescence, day7, nascent RNA, 6126, replicate 2

value: OsTIR-AID


title: HepG2_coumarin 1 μM_rep3

value: treated with 1 uM coumarin for 6 h


title: RSV-ASO_Multi_5

value: Human TfR knock-in


title: DNMT1-AID_WGBS_Day6_Rep1

value: Colon

value: Colorectal cancer cell

value: Auxin treatment

value: 6 days


title: DNMT1-AID_WGBS_Day4_Rep1

value: 4 days


title: ASO_Multi_5

value: Multiple

value: hTfR KI HOM

value: Malat1 ASO

value: 4X 2.5mpk

value: mg per kg

value: days


title: HepG2_coumarin 10 μM_rep2

value: HepG2 cells

value: treated with 10 uM coumarin for 6 h


title: DNMT1-AID_WGBS_Day2_Rep3

value: 2 days


title: DNMT1-AID_WGBS_Day4_Rep3


title: OsTIR-AID, quiescence, day7, nascent RNA, 6125, replicate 1

value: OsTIR-AID

value: IAA powder (98% purity, Sigma-Aldrich) was added at a concentration of 1 mg/mL.


title: HepG2_coumarin 1 μM_rep1

value: treated with 1 uM coumarin for 6 h


title: DNMT1-AID_WGBS_Day4_Rep2

value: Colon


title: rrp6∆, G1, day 1, steady state RNA, 7078, replicate 2


title: HepG2_coumarin 10 μM_rep1


title: Nab3-AID, quiescence, day7, steady state RNA, 7716, replicate 1


title: ATV:BACE1_Multi_5

value: Human TfR knock-in

value: Male

value: months

value: Brain

value: Posterior

value: 4X 57mpk


title: HepG2_coumarin 1 μM_rep2


title: DNMT1-AID_WGBS_Day2_Rep1

value: Colorectal cancer cell

value: Auxin treatment


title: HepG2_coumarin 0.1 μM_rep2

value: treated with 0.1 uM coumarin for 6 h


title: OTV_Multi_4

value: Multiple

value: hTfR KI HOM

value: 4X 60mpk

value: mg per kg

value: days


title: HepG2_coumarin 0.1 μM_rep1

value: HepG2 cells


title: DNMT1-AID_WGBS_Day0_Rep2

value: Before auxin treatment


title: DNMT1-AID_WGBS_Day2_Rep2

value: Colon

value: 2 days


title: Nab3-AID, quiescence, day7, nascent RNA, 7716, replicate 1

extract_protocol:
To prepare 4tU-seq libraries, we employed the Universal Plus™ Total RNA-Seq library preparation kit and custom yeast rRNA depletion (AnyDeplete®); .
RNA was extracted using yeast RiboPure™ RNA Purification Kit from Invitrogen™
4tU-seq

value: IAA powder (98% purity, Sigma-Aldrich) was added at a concentration of 1 mg/mL.


title: Nab3-AID, quiescence, day7, nascent RNA, 7718, replicate 2


title: HepG2_coumarin 0.1 μM_rep3


title: RSV-ASO_Multi_4

value: Human TfR knock-in

value: Male

value: months


title: OTV_Multi_1

value: Female

value: Brain

value: Posterior


title: DNMT1-AID_WGBS_Day0_Rep1

value: Colorectal cancer cell


title: HepG2_coumarin 0.01 μM_rep3

value: treated with 0.01 uM coumarin for 6 h


title: ATV:BACE1_Multi_4

value: Multiple

value: hTfR KI HOM

value: 4X 57mpk


title: RSV-ASO_Multi_1

value: 4X 60mpk

value: mg per kg

value: days


title: DNMT1-AID_WGBS_Day0_Rep3

value: Colon

value: Before auxin treatment


title: ASO_Multi_1

value: Malat1 ASO

value: 4X 2.5mpk


title: ATV:BACE1_Multi_1

value: Human TfR knock-in


title: HepG2_coumarin 0.01 μM_rep1

value: HepG2 cells


title: HepG2_coumarin 0.01 μM_rep2


title: UHRF1-AID_WGBS_Day12_Rep2

value: Auxin treatment

value: 12 days