title: Neg Control Rep3

city: Clayton

first: David

middle: Richard

last: Powell

state: VIC

address: Wellington Road

department: Bioinformatics Platform

country: Australia

institute: Monash University

data_processing:
Reads were mapped to the mouse genome (GRCm38) using STAR
reads were assigned to gene models (exonic only) from the Gencode M4 annotation using featureCounts
Genome_build: GRCm38
Supplementary_files_format_and_content: read counts tsv format

source_name: Differentiated cells (Lgr5neg-CD24neg)

extract_protocol:
The small intestinal tube was dissected out and flushed with PBS to remove faeces. Small intestinal tissues were opened longitudinally, scraped with a glass coverslip to remove villi, cut into 5-mm pieces and washed with PBS five times to remove unattached epithelial fragments, mucus and faeces. Following incubation for 30 min at 4°C in 4mM EDTA-PBS solution, intestinal crypts were released from small intestinal tissue fragments by mechanically pipetting them with a 10 mL pipette in PBS and repeating this step three times. Isolated intestinal crypts were strained (70 μm cell strainer, BD Biosciences) and centrifugated three times at 1500 rpm for 2 min at 4°C. The collected crypts were maintained for 30 min at 4°C in DMEM/F12 – 10% serum (Gibco) and were then dissociated in TrypLE Express (Invitrogen) supplemented with 10 μM Rock inhibitor (Y-27632, Abcam) and DNAse 1 (Sigma-Aldrich) for 5 min at 37°C. Cell clumps and mucus were removed using a 70 μm cell strainer (BD Biosciences) and the remaining dissociated cells were washed twice with PBS collected by centrifugation at 4°C at 1500 rpm for 3 min. Antibody labelling step as well as the final resuspension of the sample were performed with PBS supplemented with 2mM EDTA, 2% FBS and 10 μM Rock inhibitor (Y-27632). Cellularized crypts were incubated with anti-CD31-BV510 (1:200, clone: MEC 13.3, BD biosciences, #563089), anti-CD45-BV510 (1:200, clone: 30-F11, BD biosciences, #563891) and anti-CD24-PeCy7 (1:100, clone: M1/69, eBioscience, #25-0242-82) antibodies in a 500µl volume for 15 min on ice. After washing twice with PBS, the cells from one animal were resuspended in a final volume of 1 mL, passed through a 70 μm strainer and transferred into appropriate FACS tubes and propidium iodide (PI) added to a concentration of 2 μg/mL. Cell sorting was carried out with a 100 μm nozzle on an Influx instrument (BD Biosciences). Aggregates, debris, dead cells (PI+) and CD45+/CD31+ hematopoietic/endothelial contaminates were depleted. For the Lgr5-GFPhigh cell population, around 2% of the CD24low Lgr5-GFP brightest cells were selected. The subsequent 2% of the CD24low Lgr5-GFP+ cells were considered as Lgr5-GFPmed and Lgr5-GFPlow cell populations. Purity of collected fractions was confirmed by reanalysis of a small fraction of the sorted cells. For single cell applications, cells were double sorted.
Libraries of each biological replicate were prepared with 15ng of RNA using the Nugen Ovation RNA-Seq system V2 kit followed by Nugen Ovation Ultralow System V2 kit. High throughput sequencing was performed with HiSeq3000 with ~30 M reads targeted reads (single end 76nt length) per sample.

treatment_protocol: Lgr5-EGFP C57BL/6 male mice (11-15 week-old, littermates) were injected with two intra-peritoneal doses of NRG1 daily (7.5 µg every 12 hours) or vehicle control (PBS) for 5 days (n=3). On day 6, small intestinal tissues were collected and isolated cell populations analysed.

value: Small intestine

value: 11 week-old

value: PBS treatment

value: Differentiated cells (Lgr5neg-CD24neg)


title: Jleaf_R1

status: Public on Jul 13 2020

type: SRA

city: New Delhi

first: Mukesh

last: Jain

state: New Delhi

address: New Mehrauli Road

country: India

institute: Jawaharlal Nehru University

library_source: transcriptomic

data_processing:
Data obtained in FASTQ files were processed to remove adapter sequences using cutadapt (v1.12) and low-quality reads using qrqc package in R.
High-quality filtered identical reads were collapsed into a unique reads to estimate abundance of small RNAs at different stages of seed development and leaf tissue.
Supplementary_files_format_and_content: FASTA files containing non-redundant reads with their read counts.

molecule: total RNA

organism: Cicer arietinum

source_name: Leaf

growth_protocol: Plants were grown in natural field conditions and seeds undergoing different stages of development were harvested from field-grown plants.

extract_protocol:
Total RNA was isolated followed by preparation of small RNA sequencing libraries using TruSeq Small RNA Sample Prep Kit (Illumina Technologies).
Small RNA libraries were prepared for sequencing using Illumina's standard protocols.

tag: genotype

value: JGK 3

tag: tissue

value: Leaf

tag: development stage


title: Low Ngr1 Rep3

organism: Mus musculus

tag: strain

tag: age

tag: treatment

value: NRG1 treatment

tag: cell type


title: Mo13

city: London

first: Val

last: Yianni

address: Guy's Hospital, Great Maze Pond

department: Centre for Craniofacial & Regenerative Biology

country: United Kingdom

institute: King's College London

description: Molar sc-RNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads trimmed for adaptor sequences using TrimGalore. Then mapped to mm10 using Hisat2(v2) with default parameters.
Clustering analysis performed using Seurat v3
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

molecule: polyA RNA

source_name: Molar

extract_protocol:
XLacZ4 mice were sacrificed. Molars and incisors were isolated and dissociated into single cells. Cell stained with FDG reagent. Cells possitive were isolated using FACS
Smart-Seq2. Libraries constructed using standard Illumina protocols.
Single cell RNAseq.

value: Molar

value: pericytes


title: High Control Rep3

source_name: CBC stem cells (Lgr5high-CD24low)

value: CBC stem cells (Lgr5high-CD24low)


title: Med Ngr1 Rep3

source_name: Immediate progenitors (Lgr5med-CD24low)

value: Immediate progenitors (Lgr5med-CD24low)


title: Neg Ngr1 Rep3


title: Med Control Rep3


title: Mo12

description: Molar sc-RNAseq


title: High Ngr1 Rep3


title: Neg Ngr1 Rep2

value: 15 week-old


title: Low Control Rep3


title: High Ngr1 Rep2


title: KPouC_7465_immune_Stromal

city: La Jolla

first: Zhibo

last: Ma

state: California

address: 10010 N Torrey Pines Rd

country: USA

institute: Salk Institute for Biological Studies

description:
sorted live immune cells (EpCAM-neg;Cd45+) and non-immune stromal cells (EpCAM-neg;Cd45-neg) from caerulein-treated KPouC pancreata
CD45_Stroma_KPouC_7465

data_processing:
Smartseq2: Reads were aligned to the mm10 mouse genome using STAR version 2.5.3a (73). Mapping was carried out using default parameters, filtering non-canonical introns and allowing up to 10 mismatches per read and only keeping uniquely mapped reads. Raw transcript Samrtseq2: counts were obtained using HTSeq version 0.9.1 (74). The union of all detected genes was compiled into a single expression table (156 cells and 27,998 genes)
Smartseq2: Cells with less than 500 unique genes and genes expressed in fewer than 3 cells were filtered using the Seurat R package.  Genes were log-normalized in Seurat.
10x Genomics: fastq files were processed using cellranger 3.1.0 and mm10 reference.The raw sequencing data from each mice was first processed separately in Cell Ranger v3.1.0 using refdata-mm10-3.0.0 and default parameters (10x Genomics). Each dataset captured similar number of cells (~4500 cells/mice) with similar sequencing depth (median ~20k reads/cell). The cellranger filtered gene-by-cell count matrices were loaded to the R package Seurat (v3.1.4) and combined into a single merged matrix. Low-quality cells were further filtered based on the percent of mitochondria gene reads, number of UMI, and number of genes detected (subset = percent.mt <7 & nCount_RNA < 25000 & nFeature_RNA >350)). After removing the low-quality cells, we applied a global-scaling normalization method “LogNormalize” that normalizes the gene expression measurement for each cell by the total expression, mulplies this by a scaling factor of 23,000. The normalized data is further linear transformed by ScaleData() function prior to dimension reduction. Principal components analysis (PCA) was performed on the scaled data by only using the most variable 2000 genes (identified using the default “vst” method). Batch effect between mice were examine in PCA space and no obvious batch effect was observed.
Genome_build: mm10
Supplementary_files_format_and_content: raw read counts per gene per cell

extract_protocol:
Pancreatic tuft cells were isolated from 3, 8-10 month old KC PanIN-bearing.  The pancreas was quickly dissected, minced in 5 ml of DMEM with FBS and allowed to incubate for 2 min.  Supernatant and fat were removed and pancreatic tissue was then incubated in 10 ml DMEM supplemented with 1 mg/ml collagenase I (Sigma), 1 mg/ml soybean trypsin inhibitor (Gibco), 1-1.5 mg/ml hyaluronidase (depending on tumor burden, Sigma), and 250 ml of DNAse I, shaking gently at 37°C for a maximum of 30 min.  Digestion was monitored and tissue was further digested mechanically by pipetting.  Digested tissue was passed through a 100 mm filter, washed with FACS buffer (PBS, 1 mM EDTA, 0.5% BSA), and incubated with ACK lysing buffer (Gibco) to remove red blood cells before staining for FACS. Single cell suspensions were incubated on ice with mouse Fc receptor block (BD Biosciences, 1:200) followed by antigen-specific antibodies in FACS buffer.  DAPI (molecular probes, 1:1000) and Annexin V (Biolegend, Pacific Blue conjugate at 1:200) were used to exclude dead and dying cells.  Cells were labeled with Cd45 (Alexa Fluor 488), EpCAM (Alexa Fluor 647), and Siglec F (PE) (Biolegend, 1:200).  Fluorescence Minus One (FMO) staining controls were included for gating populations of interest. Siglecf+;EpCAM+;Cd45- Cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy; these were deposited directly into lysis buffer composed of DNase/RNase-free water, Triton X-100, and Ribolock (Thermo Fischer) in a 96 well plate.
10x Genomics scRNA-seq was conducted on immune cells and fibroblasts collected by FACS from caerulein-treated KC and KPouC pancreata.  Pancreata were digested and prepared as previously described for tuft cell isolation.  Each sample was prepared by flow sorting live immune cells (EpCAM-neg;Cd45+) and non-immune stromal cells (EpCAM-neg;Cd45-neg); PI was used to exclude dead cells. Immune and non-immune stroma from each independent sample were mixed at a 7:3 ratio, respectively, prior to loading on the microfluidic chip with barcoded beads according to 10X Chromium Next GEM Single Cell 3’ (v3.1, Catalog # 1000128, 10x Genomics Inc).
SmartSeq2 libraries were constructed as previously described (Picelli et al., 2014)
10x Genomics: Cell lysis, first strand cDNA synthesis and amplification were carried out according to 10X v3.1 protocol, with cDNA amplification set for 11 cycles. Following sample indexing and bead-based library purification, cDNA fragments distribution and concentration were measured using TapeStation (Agilent Biosystems) and Qubit (ThermoFisher).The libraries were pooled in equal mole ratio and sequenced in two illumine NextSeq 550 PE-75 high-output runs.

value: Mixed

value: Pancreas

value: immune cells and fibroblasts

value: 8-9 weeks


title: Med Ngr1 Rep2


title: Mo14

description: Molar sc-RNAseq


title: KC_7524_immune_Stromal

description:
sorted live immune cells (EpCAM-neg;Cd45+) and non-immune stromal cells (EpCAM-neg;Cd45-neg) from caerulein-treated KC pancreata
CD45_Stroma_KC_7524

source_name: KrasG12D;Ptf1aCre/+ (KC) mouse


title: KC_pan_tuft_sample3

data_processing:
Sequencing reads were quality checked with FastQC and mapped to the mouse genome (mm9) using Hisat2. Transcript assembly and quantification were performed by Stringtie and Ballgown. Gene expression distribution between samples was checked to ensure similar transcriptome quality. Genes that have RPKM variance across samples < 1 were first removed to exclude non-expressed genes. The RPKM values were then log2 transformed and quantile normalized with the R package preprocessCore. Differential expression analysis between tuft and non-tuft epithelial cells was performed with empirical Bayes shrinkage and moderated t-test using the Limma package and p values were converted into false discovery rates (FDR) using the Benjamini-Hochberg procedure.
Genome_build: mm9
Supplementary_files_format_and_content: Quantile normalized log2(RPKM+1) value for each sample

growth_protocol: The pancreas was quickly dissected, minced in 5 ml of DMEM with FBS and allowed to incubate for 2 min.  Supernatant and fat were removed and pancreatic tissue was then incubated in 10 ml DMEM supplemented with 1 mg/ml collagenase I (Sigma), 1 mg/ml soybean trypsin inhibitor (Gibco), 1-1.5 mg/ml hyaluronidase (depending on tumor burden, Sigma), and 250 ul of DNAse I, shaking gently at 37C for a maximum of 30 min.  Digestion was monitored and tissue was further digested mechanically by pipetting.  Digested tissue was passed through a 100 um filter, washed with FACS buffer (PBS, 1 mM EDTA, 0.5% BSA), and incubated with ACK lysing buffer (Gibco) to remove red blood cells before staining for FACS.

extract_protocol:
Single cell suspensions were incubated on ice with mouse Fc receptor block (BD Biosciences, 1:200) followed by antigen-specific antibodies in FACS buffer.  DAPI (molecular probes, 1:1000) and Annexin V (Biolegend, Pacific Blue conjugate at 1:200) were used to exclude dead and dying cells.  Cells were labeled with Cd45 (Alexa Fluor 488), EpCAM (Alexa Fluor 647), and Siglec F (PE) (Biolegend, 1:200).  Fluorescence Minus One (FMO) staining controls were included for gating populations of interest. Cells were FACS purified at the Salk Institute’s Flow Cytometry core facility on a BD Biosciences Influx cell sorter (100-µm size nozzle, 1 x PBS sheath buffer with sheath pressure set to 20 PSI). Cells were sorted in 1-drop Single Cell sort mode for counting accuracy; these were deposited directly into lysis buffer composed of DNase/RNase-free water, Triton X-100, and Ribolock (Thermo Fischer) in a 96 well plate.
Low input bulk RNA sequencing (RNA-seq) on intestinal and pancreatic tuft cells was performed using the Smart-Seq2 protocol as previously described. In brief, three biological replicates, each with 100 tuft cells from an individual mouse, were sorted directly into 2 μl of Smart-Seq2 lysis buffer. Full-length cDNA was generated, and size distribution was checked with Agilent TapeStation 4200 to ensure RNA quality. cDNA were then amplified with 18-24 PCR cycles, tagmentated, and amplified again with 10 PCR cycles using a Nextera XT kit (Illumina FC-131-1096). The sequencing library was purified with AMPure XP beads.
For sequencing of mPSCs and BMMs, RNA quality was assessed using the Agilent TapeStation 4200 and RNA-Seq libraries were prepared using the TruSeq stranded mRNA Sample Preparation Kit v2 according to Illumina protocols. Multiplexed libraries were validated using the Agilent TapeStation 4200, normalized and pooled for sequencing
SmartSeq2 (Picelli et al., 2014) or TruSeq stranded mRNA Sample Preparation Kit v2.

value: 8-10 month


title: Mo15

description: Molar sc-RNAseq


title: Neg Control Rep1

value: Small intestine


title: Low Control Rep1


title: Neg Ngr1 Rep1


title: High Control Rep2


title: Mo16

description: Molar sc-RNAseq


title: KC_7522_immune_Stromal

description:
sorted live immune cells (EpCAM-neg;Cd45+) and non-immune stromal cells (EpCAM-neg;Cd45-neg) from caerulein-treated KC pancreata
CD45_Stroma_KC_7522


title: KC_7464_immune_Stromal

description:
sorted live immune cells (EpCAM-neg;Cd45+) and non-immune stromal cells (EpCAM-neg;Cd45-neg) from caerulein-treated KC pancreata
CD45_Stroma_KC_7464


title: Low Ngr1 Rep2


title: KPouC_7527_immune_Stromal

description:
sorted live immune cells (EpCAM-neg;Cd45+) and non-immune stromal cells (EpCAM-neg;Cd45-neg) from caerulein-treated KPouC pancreata
CD45_Stroma_KPouC_7527


title: Mo17

description: Molar sc-RNAseq


title: High Ngr1 Rep1


title: Med Ngr1 Rep1


title: Low Control Rep2


title: Mo18

description: Molar sc-RNAseq


title: Neg Control Rep2


title: Mo19

description: Molar sc-RNAseq


title: High Control Rep1


title: Incisor 1

description: DPFresh

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads trimmed for adaptor sequences using TrimGalore. Then mapped to mm10 using Hisat2(v2) with default parameters.
Differential expression testing performed using EdgeR
Genome_build: mm10
Supplementary_files_format_and_content: Differential expression testing information for every gene

source_name: Incisor pulp

extract_protocol:
XLacZ4 mice were sacrificed. Molars  were isolated and dissociated into single cells. Cell stained with FDG reagent. Cells possitive were isolated using FACS
Standard Illumina protocols

value: incisor


title: Mo20

description: Molar sc-RNAseq


title: Low Ngr1 Rep1


title: Phf6 KO Retinoic acid-rep.2

city: Seoul

first: Sungryong

last: Oh

address: 599 Gwanak-ro, Gwanak-gu

department: biological sciences

country: South Korea

institute: Seoul National University

data_processing:
RNA-seq reads were aligned to the mm10 genome assembly and the transcriptome using STAR (v2.5.3a) with GENCODE M16 annotation.
RSEM (v1.3.0) was used to calculate the expected read counts, FPKM and TMP for each sample from the corresponding bam files.
The read counts were processed using DESeq2 (v1.18.1) to identify differentailly expressed genes.
The TPM values were extracted and used for following downstream analyses such as hierarchical clustering, K-mean clustering, and GSEA.
Genome_build: mm10

growth_protocol: In the first 1~2 passages, a conditional Oct4-depleted (ZHBTc4) ES cell lines were maintained on mouse primary embryonic fibroblast feeders. After stabilization, mESCs were cultured under feeder-free conditions, using 0.1% gelatin-coated culture dishes. ESCs were maintained in Dulbecco's modified Eagle medium (DMEM; Welgene), supplemented with 15 % fetal bovine serum (FBS; Hyclone), 0.055 mM b-mercaptoethanol, 2 mM L-glutamine, 0.1 mM nonessential amino acid, 5,000 units/ml of penicillin/streptomycin (GIBCO), and 1,000 units/ml of leukemia inhibitory factor (LIF) (Chemicon) in a humidified incubator at 37℃ with 5 % CO2.

extract_protocol:
RNA were harvested using Trizol and RNA were extracted using Qiagen RNeasy Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols.

treatment_protocol: Doxycycline(DOX) (SIGMA; molecular weight 480.90, Cat #D3072) was added to media at 0.5mg/ml for 2 days, All-trans-Retinoic acid(RA) (SIGMA; molecular weight 300.4, Cat #R2625) was treated in -LIF media at 10mM for 4 days

value: embryonic stem cell

tag: genotype/variation

value: Phf6 KO

value: Retinoic acid

tag: passages


title: Mo21

description: Molar sc-RNAseq


title: WT Retinoic acid-rep.2

value: wild type


title: Phf6 KO Retinoic acid-rep.1


title: WT Retinoic acid-rep.1


title: ORT3-opt3-2_root_treated_3-2

city: Columbia

first: Samuel

middle: Alonzo

last: McInturf

state: Missouri

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri - Columbia

data_processing:
Read Cleaning: Reads were cleaned in R using ShortRead::TrimEnds, removing bases from each end until the remainging read has bases p-values all over 0.1.  Afterwards reads shorter than 25bp were removed.
Read Alignment: Reads were aligned to the TAIR10 genome using Tophat2 using default parameters except -g 1, specifying to only retain reads with one valid alignment
Read Counting: Reads were counted in R using GenomicAlignments::summarizeOverlaps with the TAIR10 gff as input and the counting mode of 'union'
FPKM calculations: psuedo-counts (generated from edgeR's library size normalization) were divided by the gene length (in kb) found in the TAIR 10 gff.
Differential Expression: Differential expression was carried out using edgeR with the global coefficient of variation.  Genes with less than 50 counts in any biological replicate had their log2 fold changes set to zero, along with genes with absolute log2 fold changes less than 0.5
Genome_build: TAIR10
Supplementary_files_format_and_content: count_table_Cd_samples_McInturf_2019.txt is a tab delimited text file with genes along the rows and libraries across the columns.  Each column is named by the sample which it belongs to followed by a underscore and the lane of the illumina chip which the reads were obtained.  Genes are represented by their AGI numbers.  The value for each gene-sample combination is the non-normalized feature counts obtained from summarizeOverlaps

organism: Arabidopsis thaliana

source_name: opt3-2 root tissue

growth_protocol: Seedlings were plated on 1/4 strength MS media and stratified at 4C in the dark for 48hr.  Seedlings grew on the plates for 11d before being transferred to minimal hydroponic media for 22 days.  Hydroponic media was airated with a bubble stone.  Plants were grown in a growth chamber with 16 hours light and 8 hours dark with 40% RH and XC.

extract_protocol:
RNA was first isolated by pulverizing 3-4 plants with a LN2 cooled mortar and pestle.  A Qiagen RNeasy Plant Kit was used to isolate RNA.  DNA was digested using Ambion Turbo DNase.  All protocols were followed according to manufacturers protocol
cDNA libraries were constructed using Illumina TruSeq kits according to manufacturers protocol

treatment_protocol: Plants were transferred from minimal media to minimal media with 20uM CdCl2 for 72 hours before being harvested.  Treatment and harvest were both performed at 11:00am.

value: Root

value: CdCl2 72hr

tag: biological replicate

tag: technical replicate


title: ORT3-opt3-2_root_treated_3-1


title: ORT3-opt3-2_root_treated_3-3


title: ORT2-opt3-2_root_treated_2-2


title: ORT2-opt3-2_root_treated_2-1


title: Med Control Rep2

value: PBS treatment


title: Mo23

description: Molar sc-RNAseq

value: Molar

value: pericytes


title: ORT1-opt3-2_root_treated_1-3


title: Incisor 2

description: DPFresh


title: Med Control Rep1

value: 15 week-old

value: Immediate progenitors (Lgr5med-CD24low)


title: Mo24

description: Molar sc-RNAseq


title: Mo25

description: Molar sc-RNAseq


title: ORT1-opt3-2_root_treated_1-1


title: Mo26

description: Molar sc-RNAseq


title: BTBR ob/ob wk12 1

city: South San Francisco

first: Jun-Jae

last: Chung

state: CA

address: 1 DNA Way

institute: Genentech

data_processing:
Basecalling was performed using Illumina Casava 1.8
Reads were demultiplexed based on perfect matches to expected cell barcodes
Transcript reads were aligned to the mouse reference genome (mm10) using GSNAP
Per-gene transcript counts were determined based on the number of unique UMIs (unique molecular identifiers) for mapped reads overlapping exons in sense orientation, allowing for one mismatch when collapsing UMI sequences.
To be considered for downstream analysis, cells were required to exceed a minimum number of detected transcripts, where a sample-specific cutoff was set to 0.1 times the total transcript count for cells at rank 30 (the 99th percentile for 3,000 cells)
Per-gene transcript counts were normalized by dividing by the total transcript count for a given cell and multiplying by a scale factor of 10,000.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include normalized and scaled counts for each sample

source_name: kidney glomerulus

extract_protocol:
10X Genomics Chromium Single Cell 3’ Library and Gel bead kit v2: ~6,000 singlet live cells loaded/lane, cell capture, lysis and mRNA reverse transcription occurred in-droplets.
Libraries were prepared according to 10x Genomics’s instructions. cDNA amplification and preparation of indexed libraries were performed using 12 and 14 cycles of PCR, respectively. Libraries were profiled using the Bioanalyzer High Sensitivity DNA kit (Agilent) and quantified using Kapa Library Quantification Kit (Kapa Biosystems).

value: 12 weeks

tag: Sex

value: male

tag: disease model

value: BTBR ob/ob


title: OST3-opt3-2_shoot_treated_3-1

source_name: opt3-2 leaf tissue

value: Shoot


title: BTBR ob/ob wk12 2


title: OST2-opt3-2_shoot_treated_2-2


title: OST2-opt3-2_shoot_treated_2-3


title: BTBR ob/ob wk21 1

value: 21 weeks


title: OST2-opt3-2_shoot_treated_2-1


title: Mo28

description: Molar sc-RNAseq


title: Mo27

description: Molar sc-RNAseq


title: BTBR ob/+ 1

value: BTBR ob/+


title: Mo29

description: Molar sc-RNAseq


title: BTBR ob/+ 2


title: BTBR ob/ob wk21 2


title: OST1-opt3-2_shoot_treated_1-3


title: OST3-opt3-2_shoot_treated_3-2


title: OST1-opt3-2_shoot_treated_1-2


title: ORT2-opt3-2_root_treated_2-3


title: CRT3-Col_root_treated_3-3

source_name: Columbia-0 root tissue

value: Wild type (Col-0)


title: CD2AP KO

value: 3 weeks

value: CD2AP KO


title: ORT1-opt3-2_root_treated_1-2


title: CRT3-Col_root_treated_3-2


title: Mo30

description: Molar sc-RNAseq


title: CD2AP WT

value: CD2AP WT


title: CRT3-Col_root_treated_3-1

value: Root


title: OST3-opt3-2_shoot_treated_3-3

value: CdCl2 72hr


title: Mo31

description: Molar sc-RNAseq


title: CRT2-Col_root_treated_2-3


title: CRT2-Col_root_treated_2-2


title: Mo32

description: Molar sc-RNAseq


title: Molar 2

description: MoFresh

source_name: Molar pulp

value: molar


title: doxorubicin 1

value: doxorubicin


title: CRT1-Col_root_treated_1-2


title: CRT2-Col_root_treated_2-1


title: CRT1-Col_root_treated_1-3


title: CRT1-Col_root_treated_1-1


title: OST1-opt3-2_shoot_treated_1-1


title: nephritis d5 2

value: nephritis d5


title: CST3-Col_shoot_treated_3-3

source_name: Columbia-0 leaf tissue


title: Molar 1

description: MoFresh


title: sciatic nerve input ChIP-Seq, Rnf40_cko P14, biological replicate 3

city: Erlangen

first: Michael

last: Wegner

state: Bavaria

address: Fahrstr. 17

department: Institut of Biochemistry

country: Germany

description:
input ChIPseq data from P14 sciatic nerve (RNF40 cko)
RNF40_cko_input.bigwig

library_source: genomic

data_processing:
Reads were mapped to the mouse reference genome (mm9) using Bowtie2 (version 2.3.4.2).
After removing PCR duplicates with RmDup (version 2.0.1) mapped reads ware converted to BAM format via SAMtools (version 1.1.2).
BAM files were further processed using the BamCoverage tool within the deeptools software (version 3.0.2.0) and normalized to „to 1x“.
For peak calling Model-based Analysis of ChIP-Seq (MACS2) (version 2.1.1.20160309.0) was used with input samples set as background and default parameters (q-value < 0.05).
Genome_build: mm9
Supplementary_files_format_and_content: bigwig files were generated using BamCoverage tool after merging bam files which belong together.

molecule: genomic DNA

source_name: sciatic nerve P14 (Rnf40 cko)

extract_protocol:
Sciatic nerve lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions. Libraries were sequenced following the manufacturer's protocols.

value: mixed 129SvJ/C57Bl/6J background

value: postnatal day 14

value: sciatic nerve

value: Dhh::Cre, Rnf40fl/fl

tag: chip antibody


title: CST3-Col_shoot_treated_3-2


title: CST2-Col_shoot_treated_2-2


title: CST2-Col_shoot_treated_2-3


title: sciatic nerve H2Bub1 ChIP-Seq, Rnf40_cko P14, biological replicate 3

description:
H2Bub1 ChIPseq data from P14 sciatic nerve (RNF40 cko)
RNF40_cko_H2Bub1.bigwig

value: H2Bub1 (Cell Signaling, 5546)


title: CST2-Col_shoot_treated_2-1

value: Shoot


title: nephritis d5 1

value: 12 weeks

value: male


title: nephritis d1 2

value: nephritis d1


title: nephritis d1 1


title: sciatic nerve input ChIP-Seq, Rnf40_cko P14, biological replicate 2


title: doxorubicin 2


title: CST1-Col_shoot_treated_1-3

value: Wild type (Col-0)


title: sciatic nerve H2Bub1 ChIP-Seq, Rnf40_cko P14, biological replicate 2


title: control 3

value: control


title: CST1-Col_shoot_treated_1-2


title: CST1-Col_shoot_treated_1-1


title: sciatic nerve input ChIP-Seq, Rnf40_cko P14, biological replicate 1


title: control 2


title: control 1


title: sciatic nerve H2Bub1 ChIP-Seq, Rnf40_cko P14, biological replicate 1


title: CST3-Col_shoot_treated_3-1


title: sciatic nerve input ChIP-Seq, Rnf40_ctrl P14, biological replicate 3

description:
input ChIPseq data from P14 sciatic nerve (ctrl)
RNF40_ctrl_input.bigwig

source_name: sciatic nerve P14 (Rnf40 ctrl)

value: Rnf40 fl/fl


title: Phf6 KO Doxycycline-rep.1

extract_protocol:
RNA were harvested using Trizol and reverse transcription was performed from 1~2mg total RNAs using the M-MLV cDNA Synthesis kit (Enzynomics).
RNA libraries were prepared for sequencing using standard Illumina protocols.

value: embryonic stem cell

value: Phf6 KO

value: 0.5ug/ml of doxycycline


title: sciatic nerve H2Bub1 ChIP-Seq, Rnf40_ctrl P14, biological replicate 3

description:
H2Bub1 ChIPseq data from P14 sciatic nerve (ctrl)
RNF40_ctrl_H2Bub1.bigwig


title: Phf6 KO Doxycycline-rep.2


title: WT Doxycycline-rep.2

value: wild type


title: sciatic nerve H2Bub1 ChIP-Seq, Rnf40_ctrl P14, biological replicate 2


title: sciatic nerve input ChIP-Seq, Rnf40_ctrl P14, biological replicate 1


title: Phf6 KO control-rep.2


title: WT Doxycycline-rep.1


title: sciatic nerve H2Bub1 ChIP-Seq, Rnf40_ctrl P14, biological replicate 1


title: WT control-rep.2


title: Phf6 KO control-rep.1


title: Skin biopsy Hidradenitis suppurativa 9

type: RNA

city: Washington

first: Victoria

middle: Kate

last: Shanmugam

state: DC

address: 2300 M Street, NW

department: Division of Rheumatology

institute: The George Washington University School of Medicine and Health Sciences

hyb_protocol: RNA (1µg) was amplified, biotin-labeled, purified and hybridized to Illumina HumanHT-12 v4 Expression BeadChips (Illumina Inc., San Diego, CA)

scan_protocol: BeadChips were scanned using a HiScanSQ system (Illumina Inc., San Diego, CA) and fluorescence emission by Cy3 was quantitatively detected for analysis.

data_processing: Raw BeadChip data were analyzed using the limma (http://bioinf.wehi.edu.au/limma) and beadarray  packages. Raw signal intensity data were background corrected using negative control probes followed by quantile normalization. Batch effect correction was performed by COMBAT.

label: biotin

organism: Homo sapiens

source_name: Human Skin

extract_protocol: Punch biopsy samples were immersed in RNA-later solution (Qiagen, Germany) at room temperature for 4 hours, transferred to 4°C for 24-48 hours and subsequently cryopreserved at -80°C. Total RNA was extracted using the RNeasy Fibrous Tissue Kit (Qiagen, Germany). After extraction, RNA integrity was assessed using a Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA) and samples with an RNA Integrity Number (RIN) ≥7 were used for analysis.

tag: disease state

value: Hidradenitis suppurativa

value: skin


title: sciatic nerve input ChIP-Seq, Rnf40_ctrl P14, biological replicate 2

value: mixed 129SvJ/C57Bl/6J background

value: postnatal day 14


title: Skin biopsy Hidradenitis suppurativa 8

label_protocol: RNA (1µg) was amplified, biotin-labeled, purified and hybridized to Illumina HumanHT-12 v4 Expression BeadChips (Illumina Inc., San Diego, CA)


title: Skin biopsy Hidradenitis suppurativa 6


title: Skin biopsy Hidradenitis suppurativa 10


title: sciatic nerve Rnf40_cko P14, biological replicate 3

description: RNAseq data from P14 sciatic nerve (RNF40 cko)

data_processing:
Sequencing data was pooled using the Illumina HiSeq 2500 platform and converted into fastq files.
Reads from rRNA, tRNA, mt-rRNA and mt-tRNA were purged from demultiplexed reads.
Reads were aligned to mm10 reference genome using Bowtie2 (version 2.1.0).
Unique maps were generated using HTSeq count relating to Ensembl genes version 85.
Statistical analysis of raw data was done with DESeq2 by R version 1.10.1.
Genome_build: mm9
Supplementary_files_format_and_content: Tab-delimited text file

extract_protocol:
Total RNA was extracted from P14 sciatic nerves using the RNeasy Mini Kit according to QIAGEN protocol.
RNA libraries were prepared for sequencing using NEB Next Ultra RNA Library Prep Kit for Illumina (NEB).

value: sciatic nerve

value: Dhh::Cre, Rnf40 fl/fl


title: Skin biopsy Hidradenitis suppurativa 7


title: Skin biopsy Hidradenitis suppurativa 3


title: Skin biopsy Normal 8

value: Normal


title: Skin biopsy Normal 11


title: Skin biopsy Hidradenitis suppurativa 5


title: Skin biopsy Hidradenitis suppurativa 2


title: WT control-rep.1


title: sciatic nerve Rnf40_cko P14, biological replicate 2


title: Skin biopsy Normal 9


title: sciatic nerve Rnf40_cko P14, biological replicate 1


title: Skin biopsy Normal 10


title: background (Negative  control)

city: Stanford

first: Fiorella

last: Grandi

address: 300 Pasteur Drive

department: Orthopedic Surgery

institute: Stanford University

data_processing:
Library strategy: RRHP
Illumina Casava1.7 software used for basecalling.
Demultiplex using bcl2fastq version 2.20.0 using bcl2fastq -R --output-dir  --sample-sheet  --barcode-mismatches 1 --use-bases-mask 7:y101,I8,I8,y101 --ignore-missing-bcls --ignore-missing-positions --ignore-missing-filter
Trimming quality and unpaired reads using TrimGalore version 0.5.0_dev with default paramters, looking for adapter sequence GATCGGAAGAGC
Reads were mapped to mm10 using HISAT2  2.1.0 with default parameters
sam files were sorted using samtools sort to create bam files
bedtools bamtobed was used to make bed files
differential CCGG sites were called using diffReps (Shen 2013 PlosOne) using diffReps.pl --treatment --control  --chrlen --window 200 --nrpass 1 and annotated for genes and distance to those genes using beops closet features (closest-features --closest --dist)
Genome_build: mm10
Supplementary_files_format_and_content: bed files contain the peaks called by DiffReps for WT DMM vs Sham, Mut DMM vs WT DMM and Mut DMM vs WT sham and annotated to nearest gene using closetfeature

source_name: knee cartilage

extract_protocol:
cartilage was dissected from the knee joint and frozen in liquid nitrogen, then pulverized. DNA was extracted using trizol, followed by Qiagen DNA micro columns and eluted into water.
dna was processed according to the RRHP kit (Zymo). Briefly, samples were digested with MspI, adapters were ligated and samples (except the control) were subjected to a BGT reaction. Samples were then cleaned up an subjected to a second round of MspI digestion. After the second digest, samples were cleaned up using Amgen XP beads, ligated to barcodes and subjected to 15 cycles of PCR amplification, before QC and pooling.

treatment_protocol: male mice 4-6 months of age were subjected to dmm surgery. For dmm samples, the medial meniscus was removed. For sham mice, the knee joint was opened, but no surgery was performed. Each control is on the contralateral leg.

value: without treatment with the B-Galc enzyme

tag: time

value: 6 weeks post surgery

value: knee cartilage


title: MUT_dmm_rep3

description:
MUT3_dmm
dhCCGGs_MUTdmm_v_WTdmm.bed
dhCCGGs_MUTdmm_v_WTdmm.bed

value: dmm

value: TET-/-


title: Skin biopsy Normal 7


title: Skin biopsy Hidradenitis suppurativa 4


title: MUT_dmm_rep2

description:
MUT2_dmm
dhCCGGs_MUTdmm_v_WTdmm.bed
dhCCGGs_MUTdmm_v_WTdmm.bed


title: Skin biopsy Normal 5


title: Skin biopsy Normal 4


title: Skin biopsy Hidradenitis suppurativa 1


title: MUT_dmm_rep1

description:
MUT1_dmm
dhCCGGs_MUTdmm_v_WTdmm.bed
dhCCGGs_MUTdmm_v_WTdmm.bed


title: sciatic nerve Rnf40_ctrl P14, biological replicate 1

description: RNAseq data from P14 sciatic nerve (ctrl)

value: Rnf40 fl/fl


title: sciatic nerve Rnf40_ctrl P14, biological replicate 2


title: Skin biopsy Normal 3


title: MUT_sham_rep3

value: control


title: WT_dmm_rep2

description:
WT2_dmm
dhCCGGs_WTdmm_v_WTsham.bed
dhCCGGs_MUTdmm_v_WTdmm.bed


title: MUT_sham_rep2


title: MUT_sham_rep1


title: Skin biopsy Normal 6


title: Skin biopsy Normal 1


title: Skin biopsy Normal 2


title: RFX3_OF1_WT_rep6

city: Geneva

first: Sylvain

last: LEMEILLE

address: 1 rue Michel-Servet

department: Department of Pathology and Immunology

country: Switzerland

institute: University of Geneva Medical School

description: processed data file: Raw_counts.txt

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using STAR 2.4 with --outFilterMultimapNmax 1.
Raw count measurements were obtained with featureCounts 1.4.6 keeping only unambiguous reads.
Genome_build: GRCm38.89
Supplementary_files_format_and_content: Raw_counts.txt: Tab-delimited text file includes raw counts.

source_name: Ex vivo differentiated ependymal cells

growth_protocol: Lateral ventricular walls from E18.5 embryonic brains were dissected. Cells were dissociated and cultivated ex vivo until confluency. Cell differentiation was next induced by serum deprivation.

extract_protocol:
Total RNA was extracted using Qiagen RNeasy Midi Kit columns and reagents; Cat 75142.
Libraries were prepared according to Illumina's instructions using the TruSeq RNA-seq protocol.

treatment_protocol: Serum was deprived for 4 days and RNA was extracted from cells.

tag: strain/background

value: Wild type

value: Brain lateral ventricles


title: RFX3_OF1_WT_rep3

description: processed data file: Raw_counts.txt


title: WT_dmm_rep1

description:
WT1_dmm
dhCCGGs_WTdmm_v_WTsham.bed
dhCCGGs_MUTdmm_v_WTdmm.bed

tag: genotype


title: RFX3_OF1_WT_rep2

description: processed data file: Raw_counts.txt

tag: tissue


title: RFX3_OF1_WT_rep1

description: processed data file: Raw_counts.txt


title: RFX3_OF1_WT_rep5

description: processed data file: Raw_counts.txt


title: RFX3_OF1_WT_rep4

description: processed data file: Raw_counts.txt


title: RFX3_OF1_KO_rep6

description: processed data file: Raw_counts.txt


title: WT_sham_rep2

description:
WT2_sham
dhCCGGs_WTdmm_v_WTsham.bed
dhCCGGs_MUTdmm_v_WTsham.bed


title: sciatic nerve Rnf40_ctrl P14, biological replicate 3


title: WT_sham_rep3

description:
WT3_sham
dhCCGGs_WTdmm_v_WTsham.bed
dhCCGGs_MUTdmm_v_WTsham.bed


title: WT_dmm_rep3

description:
WT3_dmm
dhCCGGs_WTdmm_v_WTsham.bed
dhCCGGs_MUTdmm_v_WTdmm.bed


title: RFX3_OF1_KO_rep4

description: processed data file: Raw_counts.txt


title: WT_sham_rep1

description:
WT1_sham
dhCCGGs_WTdmm_v_WTsham.bed
dhCCGGs_MUTdmm_v_WTsham.bed


title: RFX3_OF1_KO_rep5

description: processed data file: Raw_counts.txt


title: mips1big_rep2

city: Gif-sur-Yvette

first: Déborah

last: MANZA MIANZA

address: 630 Rue Noetzlin

country: France

institute: Institut des Sciences des Plantes - Paris Saclay

data_processing:
Trimming files where generated with Trimmomatic
RNA-seq reads were aligned to the TAIR10 genome assembly using STAR version 2.7.0d
Read Count were obtained with FeatureCounts v1.6.3 from Subread package
Differential analysis was done with Deseq2. A first filter was done on the raw Count matrix by keeping only genes where at least 2 samples have more than 50 reads. Then the analysis differential analysis was done on the normalized count matrix. The differential analysis result reported contained only genes where the adjusted p.value is less than 0.05.
Genome_build: TAIR10
Supplementary_files_format_and_content: normalized count and differential analysis result

growth_protocol: Arabidopsis thaliana ecotype Colombia (Col-0) and big and mips1 and double mutant big mips1 were used in this study. Seeds were surface-sterilized by treatment with bayrochlore for 20 min, washed, and imbibed in sterile-water for 2–4 days at 4 °C to obtain homogeneous germination. Plants were grown in chambers at 20°C on sterile half-strength MS medium and 0.8% agar under long-days (16h of light at 20°C, 8h of darkness at 18°C) for 1 week and then transferred to soil under SD conditions (8-h day/16-h night, 200 mmol photons s21 m22, 21°C) for 2 weeks. Plants were then subsequently transferred to LD conditions (16-h day/8-h night, 200 mmol photons s21 m22, 21°C) for 5 days.

extract_protocol: Libraries were prepared according to NEB instructions using the « NEBNext Ultra II DNA library kit for Illumina »

tag: ecotype background

value: mips1 big

value: leaves


title: mips1_rep2


title: RFX3_OF1_KO_rep3

description: processed data file: Raw_counts.txt


title: Mut2_12weeks_dmm (RNA-seq)

description:
Counts_6_12_weeks.csv
12weeks_MUTvWTDMM_foldchange.csv
12weeksWTdmm_v6weeksksWTsham_foldchange.csv

data_processing:
Basecalls performed using CASAVA version 1.4
trimmed using Trimmomatic
aligned using HISAT2
transcripts were called using ballgown
Genome_build: mm10
Supplementary_files_format_and_content: fold change from Deseq2; counts from Deseq2

source_name: micro-dissected knee cartilage

extract_protocol:
total rna was extracted from microdissected knee cartilage
libraries were constructed using the SMART-seq2 from Clone Tec, all 12 samples for each time period were indexed and pooled together and sequenced using two lanes per timepoint, data files were processed using the HISAT2 pipeline and DeSeq2 pipeline

treatment_protocol: animals were subjected to dmm surgery or contralateral sham surgery

tag: strain

value: 12 weeks post surgery

value: male


title: mips1big_rep1


title: Mut1_12weeks_dmm (RNA-seq)


title: Mut3_12weeks_dmm (RNA-seq)


title: big_rep1

value: big


title: mips1_rep1


title: big_rep2


title: RFX3_OF1_KO_rep2

description: processed data file: Raw_counts.txt

tag: age


title: RFX3_OF1_KO_rep1

description: processed data file: Raw_counts.txt


title: Col0_rep2

value: wild type


title: Mut3_12weeks_sham (RNA-seq)

tag: treatment

value: sham


title: Col0_rep1


title: RFX2_OF1_WT_rep8

description: processed data file: Raw_counts.txt


title: Mut1_12weeks_sham (RNA-seq)


title: Mut2_12weeks_sham (RNA-seq)


title: Mut3_6weeks_dmm (RNA-seq)

description:
Counts_6_12_weeks.csv
6weeks_MUTvWTDMM_foldchange.csv


city: Pozzuoli

first: Rossella

last: De Cegli

address: Via Campi Flegrei 34

country: Italy

institute: Tigem

description: Transcriptome profile of Chondrocytess from RCS cells ko for the FGF receptors FGFR3 and FGFR4, untreated, biological rep2

data_processing:
Sequence reads were trimmed using Trim Galore software (https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) to remove adapter sequences and low-quality end bases and then aligned on rn6 reference sequence using STAR
Genome_build: rn6
Supplementary_files_format_and_content: tab-delimited text files include raw counts for each Sample

organism: Rattus norvegicus

growth_protocol: RCS chondrocyte wt cell line and RCS chondrocyte obtained from a clone ko for the FGF receptors FGFR3 and FGFR4 were incubated Over night with FGF18 (50ug/ml) and their transcriptional responses were analyzed using QuantSeq 3’ mRNA sequencing. Untreated cells were used as control

extract_protocol:
Extraction of total RNA was performed according to the manufacturer's instructions (RNeasy Mini Kit Cat No./ID: 74106 (250), Quiagen). RNA extract was precisely quantified and mixed at 50ng/5 µL
Total RNA (100 ng) from each sample was prepared using QuantSeq 3'mRNA-Seq Library prep kit  (Lexogen, Vienna, Austria) according to manufacturer's instructions
The amplified fragmented cDNA of 300 bp in size were sequenced in single-end mode using the NextSeq500 (Illumina) with a read length of 75 bp

treatment_protocol: The cells were grown in DMEM plus 5% adult bovin serum supplemented with Pen/Strep. total RNA was extracted from WT and KO RCS cells, treated and untreated with FGF18 (O.N.)

tag: cell type

value: Rat chondrosarcoma chondrocytes (RCS)

value: KO for the FGF receptors FGFR3 and FGFR4

value: untreated


description: Transcriptome profile of Chondrocytess from RCS cells ko for the FGF receptors FGFR3 and FGFR4, treated with FGF18, biological rep1

value: treated with FGF18


description: Transcriptome profile of Chondrocytess from RCS cells ko for the FGF receptors FGFR3 and FGFR4, untreated, biological rep3


description: Transcriptome profile of Chondrocytess from RCS cells ko for the FGF receptors FGFR3 and FGFR4, treated with FGF18, biological rep3


description: Transcriptome profile of Chondrocytess from RCS cells ko for the FGF receptors FGFR3 and FGFR4, untreated, biological rep1


title: Mut2_6weeks_dmm (RNA-seq)

value: dmm

value: 6 weeks post surgery

value: knee cartilage


title: RFX2_OF1_WT_rep7

description: processed data file: Raw_counts.txt

tag: genotype/variation


description: Transcriptome profile of Chondrocytes from RCS wt cells treated with FGF18, biological rep2

value: WT


title: Mut1_6weeks_dmm (RNA-seq)

value: TET-/-


title: RFX2_OF1_WT_rep4

description: processed data file: Raw_counts.txt

value: Wild type

value: Brain lateral ventricles


title: RFX2_OF1_WT_rep6

description: processed data file: Raw_counts.txt


title: RFX2_OF1_WT_rep3

description: processed data file: Raw_counts.txt


description: Transcriptome profile of Chondrocytes from RCS wt cells treated with FGF18, biological rep1


description: Transcriptome profile of Chondrocytes from RCS wt cells untreated, biological rep3


description: Transcriptome profile of Chondrocytes from RCS wt cells untreated, biological rep1


title: RFX2_OF1_WT_rep5

description: processed data file: Raw_counts.txt


title: RFX2_OF1_WT_rep2

description: processed data file: Raw_counts.txt


title: Mut3_6weeks_sham (RNA-seq)

description:
Counts_6_12_weeks.csv
6weeks_WTDMMvsham_foldchange.csv


title: Mut2_6weeks_sham (RNA-seq)


title: RFX2_OF1_WT_rep1

description: processed data file: Raw_counts.txt


title: Mut1_6weeks_sham (RNA-seq)


description: Transcriptome profile of Chondrocytess from RCS cells ko for the FGF receptors FGFR3 and FGFR4, treated with FGF18, biological rep2


title: Fig5-v15-IAA-4

first: Rea

last: Lardelli

address: 9500 Gilman Dr

department: Biology

institute: UCSD

description: total RNA

data_processing:
Demultiplexing: reads were demultiplexed based on the presence of a gene-specific primer at the beginning of R2, and a random-mer was extracted off of the beginning of R1.
Read trimming: reads were trimmed at the 3' end
tail counting: non-pcr duplicate reads were counted by summing reads with the same sequence that did not have the same randommer sequence as any other read.
Genome_build: analysis was done on raw reads without genome mapping
Supplementary_files_format_and_content: Processed files contain trimmed sequence, total read count and unique read count

extract_protocol:
For crosslinking IPs, cells were crosslinked with 0.2% formaldehyde and cells were lysed in RIPA lysis buffer (50 mM Tris-HCl pH 7.5, 1% Nonidet P-40, 0.5% sodium deoxycholate, 0.05% SDS, 1 mM EDTA, 150 mM NaCl, 2 µg/ml aprotinin and leupeptin, 1 mM PMSF) and sonicated 3x for 20 seconds. Lysates were precleared for 1 hr at 4˚C with protein A sepharose and then IPs were carried out with antibodies listed in metasheet at room temperature for 90 minutes before 6x washes in denaturating RIPA buffer and then 3 washes with NET2 before on-bead ligation of AG10/11. Ligated RNA was reverse crosslinked with 70˚C incubation for 45 minutes and then extracted with TRIzol per manufacturer's recommendation. For nascent RNA and total RNA librariers, 2.5 µg of RNA was ligated and then extracted with phenol/chlorofom/isoamyl alcohol. For nascent RNA, Click-iT nascent RNA capture kit (Invitrogen) was used on 1.25 µg of RNA according to manufacturer's protocol with the exception of using Superscript III reverse transcriptase (Invitrogen) for cDNA synthesis.
RNA adapters containing bar-codes and 10-11 nucleotide randomers were ligated to the 3’ ends of total and eluted RNA with T4 RNA ligase (NEB) at 16°C for 16 hours. cDNA was generated from AR-17 primer with Superscript III (Life Technologies). 3’ ends were amplified by Q5 High-Fidelity DNA Polymerase (NEB) first, using snRNA gene-specific primers and AR-17 and then with primers D50x and D70x (Illumina). Libraries were purified on AMPure XP magnetic beads (Beckman), and validated by 2200 Tape Station Instrument (Agilent). Libraries were pooled at 4 nM, denatured with NaOH and diluted in HT1 buffer (Illumina) to 7 pM before sequencing with MiSeq Reagent Kit V2 Nano configuration (Illumina).

treatment_protocol: cells were treated either with 1 ng/ml doxycycline or 500 µM indol-3-acetic acid for 48 hr prior to harvest and in the case of siRNA depletions, cells were transfected with 20 nM siRNA with SilentFect (BioRad)

tag: treatment (dox or iaa)

value: IAA

tag: target gene

tag: ip antibody

tag: adapter


title: Fig5-v15-IAA-2

description: total RNA


title: Fig5-v15-IAA-3

description: total RNA


title: Fig5-v15-IAA-1

description: total RNA


title: RFX2_OF1_KO_rep6

description: processed data file: Raw_counts.txt


description: Transcriptome profile of Chondrocytes from RCS wt cells treated with FGF18, biological rep3


title: RFX2_OF1_KO_rep5

description: processed data file: Raw_counts.txt


title: Fig5-v15-dox-1

description: total RNA

value: dox


title: Fig5-v15-dox-3

description: total RNA


title: Fig5-v15-dox-4

description: total RNA


description: Transcriptome profile of Chondrocytes from RCS wt cells untreated, biological rep2


title: Wt2_12weeks_dmm (RNA-seq)

description:
Counts_6_12_weeks.csv
12weeks_MUTvWTDMM_foldchange.csv

value: 12 weeks post surgery

tag: Sex

value: male


title: RFX2_OF1_KO_rep2

description: processed data file: Raw_counts.txt


title: Fig5-v8-IAA-2

description: total RNA


title: Fig5-v8-dox-3

description: total RNA


title: Fig5-v8-IAA-1

description: total RNA


title: Fig5-v8-IAA-3

description: total RNA


title: Fig5-v8-dox-4

description: total RNA


title: RFX2_OF1_KO_rep1

description: processed data file: Raw_counts.txt


title: Fig5-v8-IAA-4

description: total RNA


title: RFX2_OF1_KO_rep3

description: processed data file: Raw_counts.txt


title: Wt1_12weeks_sham (RNA-seq)


title: Wt3_12weeks_dmm (RNA-seq)


title: Fig5-v15-dox-2

description: total RNA


title: Wt3_6weeks_dmm (RNA-seq)


title: Fig5-v8-dox-1

description: total RNA


title: Fig5-v6-IAA-4

description: total RNA


title: RFX2_OF1_KO_rep4

description: processed data file: Raw_counts.txt


title: Fig5-v6-IAA-2

description: total RNA


title: Fig5-v6-IAA-3

description: total RNA


title: RFX1_OF1_WT_rep3

description: processed data file: Raw_counts.txt


title: Wt1_12weeks_dmm (RNA-seq)


title: Wt2_6weeks_dmm (RNA-seq)


title: Fig5-v6-IAA-1

description: total RNA


title: RFX1_OF1_WT_rep2

description: processed data file: Raw_counts.txt


title: Wt3_12weeks_sham (RNA-seq)


title: Wt2_12weeks_sham (RNA-seq)


title: Fig5-v6-dox-4

description: total RNA


title: Wt3_6weeks_sham (RNA-seq)

description:
Counts_6_12_weeks.csv
6weeks_WTDMMvsham_foldchange.csv
12weeksWTdmm_v6weeksksWTsham_foldchange.csv


title: Fig5-v8-dox-2

description: total RNA


title: Fig5-v6-dox-1

description: total RNA


title: Wt1_6weeks_sham (RNA-seq)


title: Fig5-v6-dox-2

description: total RNA


title: RFX1_OF1_KO_rep3

description: processed data file: Raw_counts.txt


title: RFX1_OF1_WT_rep1

description: processed data file: Raw_counts.txt


title: Fig5-v3-IAA-3

description: total RNA


title: Fig5-v6-dox-3

description: total RNA


title: Fig5-v3-IAA-2

description: total RNA


title: Fig5-v3-IAA-1

description: total RNA


title: Fig5-v3-dox-4

description: total RNA


title: RFX1_OF1_KO_rep1

description: processed data file: Raw_counts.txt


title: Fig5-v3-dox-2

description: total RNA


title: Wt1_6weeks_dmm (RNA-seq)


title: Fig5-v3-dox-3

description: total RNA


title: Fig5-v3-dox-1

description: total RNA


title: Fig5-U1-IAA-3

description: total RNA


title: Fig5-v3-IAA-4

description: total RNA


title: Fig5-U1-IAA-4

description: total RNA


title: RFX1_OF1_KO_rep4

description: processed data file: Raw_counts.txt


title: Fig5-U1-IAA-2

description: total RNA


title: input_RFX2_OF1_exp1

data_processing:
Basecalls performed using CASAVA version 1.8.2.
Reads were mapped to the reference genome using bowtie 0.12.7 with -m 1.
Fragment length was estimated using phantompeakqualtools 2.0.
Peaks were called using macs2 2.0.10.20130520 with -p 0.01 –to-large –nomodel and shiftsize set to half the estimated fragment length using inputs as control.
Reproducible peaks were obtained by IDR procedure with -p 0.01.
Genome_build: GRCm38.89
Supplementary_files_format_and_content: bigWig and bed files

extract_protocol:
Chromatin was isolated, fragmented by sonication and immunoprecipitated with anti-Rfx1 or -RFX2 or -RFX3 antibody.
Libraries were prepared according to Illumina's instructions using the TruSeq ChIP-seq protocol.

value: Mouse embryonic brain, lateral walls

value: wild type

tag: chip antibody


title: input_RFX3_OF1_exp2


title: input_RFX2_OF1_exp2


title: Fig5-U1-IAA-1

description: total RNA


title: RFX1_OF1_KO_rep2

description: processed data file: Raw_counts.txt


title: Fig5-U1-dox-3

description: total RNA


title: Fig5-U1-dox-4

description: total RNA


title: Fig5-U1-dox-1

description: total RNA


title: input_RFX1_OF1_exp2


title: Fig5-U1-dox-2

description: total RNA


title: MSC006_ALL3

city: Utrecht

first: Judith

middle: M.

last: Boer

address: Heidelberglaan 25

country: Netherlands

institute: Prinses Maxima Centrum

description: Source mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

hyb_protocol: Following fragmentation, 10 ug of labeled cRNA was hybridized for 16 hr at 45C on GeneChip Human Genome U133 Plus 2.0 Array. After sample hybridization, GeneChips were stained using phycoerythrin-conjugated streptavidin in an Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the GeneArray Scanner 3000.

data_processing: The CEL files for these samples were read into R using the affy package and normalized at probe-level with vsnrma (Huber et al., Bioinformatics 2002). To identify differentially expressed probesets, Limma R Package (version 3.26.9) was used in R 3.0.1. Principal component analyses were performed in Partek Genomic Suite 6.6.

label_protocol: 100 ng total RNA was used as input for synthesis of two-stranded cDNA. Biotinylated cRNA was synthesized and amplified by in vitro transcription (IVT) of the second-stranded cDNA template using T7 RNA polymerase, according to the standard Affymetrix protocol (GeneChipTM 3' IVT PLUS Reagent Kit, user guide, Affymetrix).

growth_protocol: Bone marrow (BM) aspirates were collected from children with newly diagnosed BCP-ALL (day0‑leukemic‑MSCs) or from children with healthy bone marrow (control-MSCs). MSCs were isolated from these aspirates as described previously. Briefly, BM aspirates were seeded in MSC expansion medium (DMEM low glucose medium (Life Technologies), 15% FCS (Integro), fungizone (Invitrogen), gentamycin (Invitrogen), freshly supplemented with 0.1 mM ascorbic acid (Sigma-Aldrich) and 1 ng/ml basic fibroblast growth factor (bFGF; Serotec, Kidlington, UK)). Non-adherent cells were removed after 24 hours. After a maximum of 10 days, MSC colonies were harvested using trypsin (Thermo Scientific). Cells were further expanded for one or two additional passages in order to isolate RNA and freeze cells in liquid nitrogen for future experiments. MSCs were negative for the hematopoietic markers (CD14, CD34, CD45; BD Biosciences, San Jose, CA, USA), and positive for the mesenchymal markers (CD13, CD29, CD54, CD73, and CD166; BD Biosciences) as detected by flow cytometry (BD Accuri C6 Plus). Multi-lineage potential was confirmed for adipocyte (Oil Red O staining), osteocyte (Alizarin Red S staining), and chondrocyte (Col2a/Thionine/Alcian Blue staining) differentiation.

extract_protocol: Total RNA was isolated out of mesenchymal stromal cells using the RNeasy mini kit (Qiagen, Hilden, Germany). Quality of RNA was checked using an Agilent 2100 Bio-analyzer.

treatment_protocol: Mesenchymal stromal cells were cultured in the presence of four different B-cell precursor acute lymphoblastic leukemia samples. After 40 hours of co-culture, samples were sorted using fluorescence-activated cell sorter (FACS). Microarray analyses were performed on these sorted MSCs.

value: Mesenchymal stromal cells (MSCs)

tag: culture type

value: co-culture

tag: source msc sample

tag: bcp-all sample

tag: bcp-all subtype of source msc sample

value: B-other

tag: bcp-all subtype of bcp-all sample


title: MSC006_none

value: mono-culture


title: MSC006_ALL4


title: MSC006_ALL2


title: Fig4-U4atac-MTR-IAA-4

description: nascent RNA


title: input_RFX1_OF1_exp1

tag: tissue

tag: genotype


title: Fig4-U4atac-MTR-IAA-3

description: nascent RNA


title: ChIP_RFX3_OF1_exp2

tag: age

value: RFX3 antibody (Reith et al., 1994, PMID:2304471)


title: MSC006_ALL1


title: Fig4-U4atac-MTR-IAA-2

description: nascent RNA


title: ChIP_RFX3_OF1_exp1


title: Fig4-U4-MTR-IAA-2

description: nascent RNA


title: Fig4-U4-MTR-IAA-1

description: nascent RNA


title: Fig4-U4-MTR-IAA-4

description: nascent RNA


title: Fig4-U4atac-MTR-IAA-1

description: nascent RNA


title: Fig4-U4-MTR-IAA-3

description: nascent RNA


title: ChIP_RFX2_OF1_exp1

value: RFX2 antibody (Santa Cruz Biotechnology – Catalog # sc-10657 – Lot # L0413)


title: MSC005_none


title: Fig4-U1-MTR-IAA-4

description: nascent RNA


title: ChIP_RFX2_OF1_exp2

value: RFX2 antibody (Santa Cruz Biotechnology – Catalog # sc-10657 – Lot # L0414)


title: ChIP_RFX1_OF1_exp2

value: RFX1 antibody (Herrero-Sanchez et al., 1992, PMID:1508204)


title: Fig4-U1-MTR-IAA-2

description: nascent RNA


title: Fig4-U1-MTR-IAA-3

description: nascent RNA


title: Fig4-U1-MTR-IAA-1

description: nascent RNA


title: Fig4-U4atac-MTR-dox-4

description: nascent RNA


title: Fig4-U4atac-MTR-dox-3

description: nascent RNA


title: ChIP_RFX1_OF1_exp1


title: Fig4-U4atac-MTR-dox-2

description: nascent RNA


title: MSC005_ALL3


title: MSC005_ALL4


title: Fig4-U4atac-MTR-dox-1

description: nascent RNA


title: MSC005_ALL2


title: Fig4-U4-MTR-dox-4

description: nascent RNA


title: glob-micropylar-WOX9-like-ChIP replicate 1

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

data_processing:
Basecalls performed using RTA version 1.12.4.2 for HiSeq 2000 and RTA3 version 3.4.4 for NovaSeq 6000
Sequenced reads passing Illumina quality filter were aligned to the Phaseolus vulgaris genome (v2.1) using Bowtie v0.12.7 with parameters -v 3 -5 0 -3 0 -m 1 --best --strata
Reads were filtered to remove PCR duplicates using samtools (v.0.1.18).
Peaks were identified using MACS2 with default parameters and a q-value threshold of 0.01.
Genome_build: Phaseolus vulgaris v2.1 (Phytozome)
Supplementary_files_format_and_content: NarrowPeak files generated by MACS2

organism: Phaseolus coccineus

source_name: Scarlet runner bean seeds containing globular stage embryos

growth_protocol: Scarlet runner bean plants (Hammond's Dwarf Red Flower) were grown in the UCLA Plant Growth Center using a 16:8 light-dark cycle at 22C. Flowers were hand-pollinated and tagged (Chen et. al., Plant embryogenesis: Methods and protocols, 2020)

extract_protocol:
Chromatin isolation and immunoprecipitation were performed as described in Gendrel AV, Lippman Z, Martienssen R, Colot V. Nat Methods. 2005;2:213–218, except that the isolated nuclei were resuspended in lysis buffer described in by Johnson et al. (2002) and sonicated to achieve chromatin fragments ranging from 100 to 500 bp. Nuclear extracts were either set aside for whole genome extracts (input control) or incubated overnight with 10 ug of an antibody raised against the peptide PNSPTTSVNQTYFQ corresponding to the amino acids 176-190 of Scarlet Runner Bean WOX9-like protein (GenBank No. ACL11801). Crosslinks were reversed and protein digested as described in Dahl and Collas, Nat Protoc. 2008;3(6):1032-45, extracted with phenol:chloroform and precipitated using standard procedures.
ChIP and Input libraries were generated using Nugen Ovation Ultralow System V2, following the manufaturer's instructions and enriched by PCR using 15 cycles.

treatment_protocol: Six days after hand pollination, seeds with length between 1.6mm and 2.5mm were harvested and only micropylar half seeds containing globular-stage embryos were collected and crosslinked under vaccuum for 10 minutes in Buffer A (0.4M sucrose, 10 mM Tris pH 8.0, 1mM EDTA pH 8.0) containing 1% formaldehyde, at room temperature, then quenched in 100 mM Glycine for 5 minutes. Tissues were rinsed twice with deionized water and stored at -80C until use.

tag: cultivar

value: Hammond's Dwarf Red Flower

tag: developmental stage

value: globular stage

value: micropylar half seeds

tag: antibody

value: anti-peptide PcWOX9-like


title: MSC004_ALL4

tag: cell type


title: Fig4-U4-MTR-dox-3

description: nascent RNA

tag: treatment (dox or iaa)

value: dox

tag: target gene


title: Fig4-U4-MTR-dox-2

description: nascent RNA

tag: ip antibody

tag: adapter


title: MSC004_none


title: MSC004_ALL2


title: MSC005_ALL1


title: Fig4-U1-MTR-dox-4

description: nascent RNA


title: Fig4-U4-MTR-dox-1

description: nascent RNA


title: MSC004_ALL3


title: Fig4-U1-MTR-dox-3

description: nascent RNA


title: glob-micropylar-Input replicate 1


title: Fig4-U4-CtrlIAA-4

description: nascent RNA

value: IAA


title: MSC004_ALL1


title: Fig4-U1-MTR-dox-2

description: nascent RNA


title: Fig4-U4-CtrlIAA-3

description: nascent RNA


title: Fig4-U4-CtrlIAA-2

description: nascent RNA


title: Fig4-U1-MTR-dox-1

description: nascent RNA


title: Fig4-U4-CtrlIAA-1

description: nascent RNA


title: MSC003_ALL4

description: Source mesenchymal stromal cells derived from a healthy pediatric control.


title: Fig4-U1-CtrlIAA-4

description: nascent RNA


title: Fig4-U1-CtrlIAA-3

description: nascent RNA


title: Fig4-U1-CtrlIAA-2

description: nascent RNA


title: Fig4-U1-CtrlIAA-1

description: nascent RNA


title: 23_Mat_WT_4

city: Cambridge

first: John

middle: Robert

last: Ferdinand

address: Department of Medicine

institute: University of Cambridge

data_processing:
Files were demutiplexed using Casava
Reads were checked for quality with FastQC and trimmed using TrimGalore!
Trimed reads were alligned to the mm10 genome with Hisat2 and counted usign Feature Counts from Rseubread
Genome_build: mm10
Supplementary_files_format_and_content: count, normalized counts from DeSeq2

source_name: MB1 Cre +/WT_VHL flox/WT_Mature B Cell

extract_protocol:
Cells were sorted into lysis buffer and RNA extracted using Rneasy plus micro kit (Qiagen)
Librarys were prepaired using SMARTer® Universal Low Input RNA Kit (Takara Bio)

value: MB1 Cre +/WT

tag: vhl-flox

value: VHL flox/WT

value: Bone Marrow

tag: celltype

value: Mature B Cell


title: WT

city: Padova

first: Silvio

last: Bicciato

address: via U. Bassi 59/b

department: Molecular Medicine

institute: University of Padova

data_processing:
Demultiplexing, filtering and alignment to the Mouse mm10 genome were done with 10x Cell Ranger v3.0.2.
The resulting combined gene x cell UMI count matrix was used for downstream analysis with Seurat v3 R package.
Genome_build: mm10
Supplementary_files_format_and_content: UMI count expression matrix

source_name: tumor-infiltrating myeloid cells

extract_protocol:
Tumors isolated from PyMT-WT and PyMT-Dab2 KO mice were cut in small pieces with scissors, enzymatically digested at 37°C for 1h with a solution containing collagenase IV (1mg/ml), hyaluronidase (0.1mg/ml) and DNase (4.5mg/ml) (Sigma-Aldrich, Saint Louis, MO, USA). Cells were then collected, filtered and used for the isolation of tumor-infiltrating myeloid cells. Cell suspension was loaded on a GemCode Single Cell Instrument (10x Chromium System) to generate single cell GEMs.
Single cell RNA-Seq libraries were prepared using GemCode Single Cell 3’ Gel Bead and Library Kit v2 (10x Genomics) following  manufacturer instructions.

tag: strain

value: tumor

value: tumor-infiltrating myeloid cells


title: Fig4-U4-Ctrldox-3

description: nascent RNA


title: Fig4-U4-Ctrldox-2

description: nascent RNA


title: MSC003_none

value: Mesenchymal stromal cells (MSCs)

tag: culture type

value: mono-culture

tag: source msc sample

tag: bcp-all sample


title: 24_Pro_WT_4

source_name: MB1 Cre +/WT_VHL flox/WT_proBpreB B cell

tag: tissue

value: proBpreB B cell


title: Fig4-U4-Ctrldox-4

description: nascent RNA


title: KO

tag: genotype


title: MSC003_ALL3

value: co-culture

tag: bcp-all subtype of source msc sample

tag: bcp-all subtype of bcp-all sample


title: Fig4-U4-Ctrldox-1

description: nascent RNA


title: 22_Imm_WT_4

source_name: MB1 Cre +/WT_VHL flox/WT_Immature B cell

value: Immature B cell


title: Fig4-U1-Ctrldox-4

description: nascent RNA


title: Fig4-U1-Ctrldox-3

description: nascent RNA


title: 21_Pro_KO_4

source_name: MB1 Cre +/WT_VHL flox/flox_proBpreB B cell

value: VHL flox/flox


title: Fig4-U1-Ctrldox-2

description: nascent RNA


title: MSC002_none


title: MSC003_ALL1

value: B-other


title: Fig4-U1-Ctrldox-1

description: nascent RNA


title: RFX1_OF1_WT_rep4

description: processed data file: Raw_counts.txt

tag: strain/background

tag: genotype/variation

value: Wild type

value: Brain lateral ventricles

tag: age


title: 20_Mat_KO_4

source_name: MB1 Cre +/WT_VHL flox/flox_Mature B Cell


title: MSC003_ALL2

tag: cell type


title: Fig3-U4atac-BRR2-3

description: crosslink IP RNA

tag: treatment (dox or iaa)

tag: target gene


title: MSC002_ALL3


title: MSC001_none


title: Fig3-U4atac-BRR2-1

description: crosslink IP RNA

tag: ip antibody

tag: adapter


title: MSC001_ALL4


title: Fig3-U4-BRR2-3

description: crosslink IP RNA


title: Fig3-U4atac-BRR2-2

description: crosslink IP RNA


title: 17_Mat_WT_3

tag: vhl-flox

tag: celltype


title: Fig3-U4-BRR2-1

description: crosslink IP RNA


title: Fig3-U1-BRR2-2

description: crosslink IP RNA


title: Fig3-U1-BRR2-1

description: crosslink IP RNA


title: Fig3-U4atac-SNUPN-3

description: crosslink IP RNA


title: MSC002_ALL4

tag: culture type


title: 15_Pro_KO_3


title: MSC002_ALL2

tag: source msc sample


title: 19_Imm_KO_4

source_name: MB1 Cre +/WT_VHL flox/flox_Immature B cell


title: MSC001_ALL3

tag: bcp-all sample


title: MSC001_ALL1


title: 18_Pro_WT_3

tag: tissue


title: Fig3-U4-BRR2-2

description: crosslink IP RNA


title: Fig3-U4atac-SNUPN-2

description: crosslink IP RNA


title: Fig3-U4atac-SNUPN-1

description: crosslink IP RNA


title: Fig3-U4-SNUPN-3

description: crosslink IP RNA


title: 14_Mat_KO_3


title: MSC001_ALL2


title: Fig3-U1-BRR2-3

description: crosslink IP RNA


title: Fig3-U1-SNUPN-3

description: crosslink IP RNA


title: Fig3-U4-SNUPN-2

description: crosslink IP RNA


title: Fig3-U4-SNUPN-1

description: crosslink IP RNA


title: Fig3-U1-SNUPN-2

description: crosslink IP RNA


title: MSC085_Day79_remission

description:
MSC085
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

growth_protocol: Bone marrow (BM) aspirates were collected from children with newly diagnosed BCP-ALL (day0‑leukemic‑MSCs), after 79 days of induction and consolidation treatment (day79-remission-MSCs), Relapsed BCP-ALL (Relapse-MSCs) or from children with healthy bone marrow (control-MSCs). MSCs were isolated from these aspirates as described previously. Briefly, BM aspirates were seeded in MSC expansion medium (DMEM low glucose medium (Life Technologies), 15% FCS (Integro), fungizone (Invitrogen), gentamycin (Invitrogen), freshly supplemented with 0.1 mM ascorbic acid (Sigma-Aldrich) and 1 ng/ml basic fibroblast growth factor (bFGF; Serotec, Kidlington, UK)). Non-adherent cells were removed after 24 hours. After a maximum of 10 days, MSC colonies were harvested using trypsin (Thermo Scientific). Cells were further expanded for one or two additional passages in order to isolate RNA and freeze cells in liquid nitrogen for future experiments. MSCs were negative for the hematopoietic markers (CD14, CD34, CD45; BD Biosciences, San Jose, CA, USA), and positive for the mesenchymal markers (CD13, CD29, CD54, CD73, and CD166; BD Biosciences) as detected by flow cytometry (BD Accuri C6 Plus). Multi-lineage potential was confirmed for adipocyte (Oil Red O staining), osteocyte (Alizarin Red S staining), and chondrocyte (Col2a/Thionine/Alcian Blue staining) differentiation.

extract_protocol: Total RNA was isolated out of mesenchymal stromal cells using Trizol reagent (Invitrogen, Bleiswijk, Netherlands). Quality of RNA was checked using an Agilent 2100 Bio-analyzer.

treatment_protocol: No treatment protocol was applied.

value: Child

tag: disease stage

value: Remission BCP-ALL

tag: bcp-all subtype


title: 13_Imm_KO_3

value: MB1 Cre +/WT


title: Fig3-U1-SNUPN-1

description: crosslink IP RNA

value: IAA


title: MSC084_Day79_remission

description:
MSC084
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: 11_Mat_KO_2

value: Bone Marrow


title: MSC083_Day0_leukemic

description:
MSC083
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Newly diagnosed BCP-ALL


title: Fig3-U4atac-SMN-3

description: crosslink IP RNA


title: MSC082_Day79_remission

description:
MSC082
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: MSC081_Day0_leukemic

description:
MSC081
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig3-U4atac-SMN-1

description: crosslink IP RNA


title: MSC080_Day0_leukemic

description:
MSC080
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig3-U4-SMN-3

description: crosslink IP RNA


title: 9_Pro_WT_2

value: VHL flox/WT


title: Fig3-U4atac-SMN-2

description: crosslink IP RNA


title: Fig3-U4-SMN-2

description: crosslink IP RNA


title: Fig3-U4-SMN-1

description: crosslink IP RNA


title: 8_Mat_WT_2

value: Mature B Cell


title: Fig3-U1-SMN-3

description: crosslink IP RNA


title: 10_Imm_KO_2


title: 12_Pro_KO_2


title: Fig3-U1-SMN-2

description: crosslink IP RNA


title: 7_Imm_WT_2


title: Fig3-U1-SMN-1

description: crosslink IP RNA


title: FIg3-U4atac-PHAX-3

description: crosslink IP RNA


title: 6_Pro_WT_1


title: FIg3-U4atac-PHAX-2

description: crosslink IP RNA


title: FIg3-U4atac-PHAX-1

description: crosslink IP RNA


title: MSC079_Day79_remission

description:
MSC079
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: Mesenchymal stromal cells (MSCs)


title: 5_Mat_WT_1


title: FIg3-U4-PHAX-3

description: crosslink IP RNA


title: 4_Imm_WT_1


title: FIg3-U4-PHAX-1

description: crosslink IP RNA


title: 3_Pro_KO_1


title: Fig3-U1-PHAX-3

description: crosslink IP RNA


title: Fig3-U1-PHAX-2

description: crosslink IP RNA


title: MSC078_Day0_leukemic

description:
MSC078
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: High hyperdiploid


title: Fig2-U4atac-BRR2-3

description: crosslink IP RNA

value: dox

value: rabbit anti-BRR2 (Bethyl)


title: Fig3-U1-PHAX-1

description: crosslink IP RNA


title: Fig2-U4atac-BRR2-2

description: crosslink IP RNA


title: 1_Imm_KO_1

value: Immature B cell


title: MSC076_Day79_remission

description:
MSC076
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig2-U4atac-BRR2-1

description: crosslink IP RNA


title: FIg3-U4-PHAX-2

description: crosslink IP RNA


title: MSC077_Day0_leukemic

description:
MSC077
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig2-U4-BRR2-3

description: crosslink IP RNA


title: Fig2-U4-BRR2-2

description: crosslink IP RNA


title: Fig2-U4-BRR2-1

description: crosslink IP RNA


title: 2_Mat_KO_1

value: VHL flox/flox


title: Fig2-U1-BRR2-3

description: crosslink IP RNA


title: Fig2-U1-BRR2-2

description: crosslink IP RNA


title: Fig2-U1-BRR2-1

description: crosslink IP RNA


title: Fig2-U4atac-SNUPN-3

description: crosslink IP RNA

value: rabbit anti-SNUPN (Sigma)


title: MSC074_Day79_remission

description:
MSC074
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig2-U4atac-SNUPN-2

description: crosslink IP RNA


title: MSC075_Day79_remission

description:
MSC075
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig2-U4atac-SNUPN-1

description: crosslink IP RNA


title: MUV043/R2

city: Boston

first: Li

last: Jiang

state: MA

address: 360 Longwood Ave

department: Pediatric Oncology

institute: Dana Farber Cancer Institute

description:
Frozen nucleus sample
EPN_count_matrix_TPM.txt

data_processing:
Illumina bcl2fastq 1.5 is used for demultiplexing
Sequenced reads were mapped to hg19 whole genome using bowtie (v0.12.7) with parameters -q --phred33-quals -n 1 -e 99999999 -l 25 -I 1 -X 2000 -a -m 15 --best -S -p 6
TPM were calculated using RSEM (v1.2.19) with parameters --estimate-rspd --paired-end -sam -p 6
Genome_build: hg19
Supplementary_files_format_and_content: a single tab-delimited text files include TPM values for all Samples

source_name: Human ependymoma cells

extract_protocol:
Smart-seq2 protocol
Illumina, Nextera XT Library Prep kit,

tag: tissue type

value: Human ependymoma

tag: age at diagnosis

tag: gender

value: male


title: BT1412


title: BT1480

value: female


title: MUV043/R1


title: MUV068

description:
Fresh whole-cell sample
EPN_count_matrix_TPM.txt


title: MSC073_control

description:
MSC073
Mesenchymal stromal cells derived from a healthy pediatric control.

source_name: Control-MSCs

tag: age

value: Child

value: Healthy

value: Control


title: MSC071_Day79_remission

description:
MSC071
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

tag: cell type

value: Remission BCP-ALL


title: BT1678


title: MSC068_Relapse

description:
MSC068
Mesenchymal stromal cells derived from pediatric BCP-ALL patient at Relapse.

source_name: Relapse-MSCs

value: Relapsed BCP-ALL


title: MSC069_Day79_remission

description:
MSC069
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig2-U4-SNUPN-2

description: crosslink IP RNA

tag: treatment (dox or iaa)


title: MSC067_Day79_remission

description:
MSC067
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig2-U4-SNUPN-1

description: crosslink IP RNA

tag: target gene


title: MSC006_Day0_leukemic

description:
MSC006
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Newly diagnosed BCP-ALL

value: B-other


title: MSC005_Day0_leukemic

description:
MSC005
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Mesenchymal stromal cells (MSCs)


title: MSC072_Day0_leukemic

description:
MSC072
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MUV006


title: MSC070_Day0_leukemic

description:
MSC070
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig2-U1-SNUPN-3

description: crosslink IP RNA

tag: ip antibody


title: Fig2-U1-SNUPN-2

description: crosslink IP RNA

tag: adapter


title: Fig2-U1-SNUPN-1

description: crosslink IP RNA


title: Peds4


title: Fig2-U4atac-SMN-3

description: crosslink IP RNA

value: rabbit anti-SMN (MBL)


title: Fig2-U4-SNUPN-3

description: crosslink IP RNA

value: dox


title: MSC066_control

description:
MSC066
Mesenchymal stromal cells derived from a healthy pediatric control.


title: Fig2-U4atac-SMN-1

description: crosslink IP RNA


title: MUV056


title: Fig2-U4atac-SMN-2

description: crosslink IP RNA


title: CPDM0785


title: Fig2-U4-SMN-1

description: crosslink IP RNA


title: Fig2-U4-SMN-2

description: crosslink IP RNA


title: MUV043/R4


title: MSC065_Day0_leukemic

description:
MSC065
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: High hyperdiploid


title: Fig2-U1-SMN-2

description: crosslink IP RNA


title: Fig2-U1-SMN-3

description: crosslink IP RNA


title: Fig2-U1-SMN-1

description: crosslink IP RNA


title: BT1030


title: Fig2-U4atac-PHAX-3

description: crosslink IP RNA

value: rabbit anti-PHAX (Bethyl)


title: MSC063_Day0_leukemic

description:
MSC063
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC062_control

description:
MSC062
Mesenchymal stromal cells derived from a healthy pediatric control.


title: MUV063


title: MSC064_Day0_leukemic

description:
MSC064
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC004_Day0_leukemic

description:
MSC004
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig2-U4atac-PHAX-2

description: crosslink IP RNA


title: Fig2-U4atac-PHAX-1

description: crosslink IP RNA


title: MUV052


title: Fig2-U4-PHAX-3

description: crosslink IP RNA


title: Fig2-U4-SMN-3

description: crosslink IP RNA


title: MSC060_Day79_remission

description:
MSC060
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: MSC061_Day0_leukemic

description:
MSC061
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MUV051

description:
Fresh whole-cell sample
EPN_count_matrix_TPM.txt


title: Fig2-U4-PHAX-2

description: crosslink IP RNA


title: Fig2-U4-PHAX-1

description: crosslink IP RNA


title: MUV013


title: Fig2-U1-PHAX-3

description: crosslink IP RNA


title: Fig2-U1-PHAX-2

description: crosslink IP RNA


title: 16_Imm_WT_3

value: MB1 Cre +/WT

tag: vhl-flox

value: VHL flox/WT

value: Bone Marrow

value: Immature B cell


title: BT1334

value: Human ependymoma

value: female


title: Fig2-U1-PHAX-1

description: crosslink IP RNA


title: Fig2-U4atac-3

description: total RNA from crosslink lysate


title: MUV071


title: Fig2-U4atac-1

description: total RNA from crosslink lysate


title: Fig2-U4tot-4

description: total RNA from crosslink lysate


title: Fig2-U4atac-2

description: total RNA from crosslink lysate


title: MSC058_Day0_leukemic

description:
MSC058
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Child


title: MSC057_Day79_remission

description:
MSC057
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: MUV053


title: Fig2-U4tot-2

description: total RNA from crosslink lysate


title: MSC056_Day79_remission

description:
MSC056
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig2-U4tot-1

description: total RNA from crosslink lysate


title: MUV038

value: male


title: MSC086_Day79_remission

description:
MSC086
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: Remission BCP-ALL


title: MSC059_Day0_leukemic

description:
MSC059
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig2-U1tot-1

description: total RNA from crosslink lysate


title: MUV021


title: Fig2-U4atac-4

description: total RNA from crosslink lysate


title: Fig2-U1tot-2

description: total RNA from crosslink lysate


title: BT1313


title: Fig2-U1tot-3

description: total RNA from crosslink lysate


title: MSC052_Day79_remission

description:
MSC052
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: MUV018


title: MSC054_control

description:
MSC054
Mesenchymal stromal cells derived from a healthy pediatric control.

value: Healthy

value: Control


title: MSC053_control

description:
MSC053
Mesenchymal stromal cells derived from a healthy pediatric control.


title: MUV014


title: Fig2-U4tot-3

description: total RNA from crosslink lysate


title: FigS1-U1dox-degron2

description: total RNA


title: FigS1-U1IAA-degon1

description: total RNA

value: IAA


title: MSC055_Day79_remission

description:
MSC055
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: Mesenchymal stromal cells (MSCs)


title: Fig2-U1tot-4

description: total RNA from crosslink lysate


title: FigS1-U1dox-degron1

description: total RNA


title: FigS1-U1dox-het

description: total RNA


title: FigS1-U1IAA-wt

description: total RNA


title: FigS1-U1dox-wt

description: total RNA


title: Fig1-U12IAA-7

description: nascent RNA


title: input MCF7 vehicle Rep2

city: Ciudad Autónoma de Buenos Aires

first: Alberto

middle: R

last: Kornblihtt

address: Pabellón IFIBYNE, Ciudad Universitaria

country: Argentina

institute: CONICET_Universidad de Buenos Aires

data_processing:
Single-end ChIP-seq reads were mapped to hg19 genome using using Bowtie v1.0.0. Only sequences uniquely aligned with ≤1 mismatch were retained. Only reads that map uniquitely were retained.
Duplicated reads were removed using the samtools rmdup command
Number of reads per kilobase per million mapped reads was counted using the bamCoverage command from deepTools and bigwig files were generated. Reads were extended to 200 pb
Genome_build: hg19
Supplementary_files_format_and_content: bigWig files

source_name: input MCF7 vehicle

growth_protocol: MCF7 cells were grown in grown in Dulbecco's Modified Eagle Medium: Nutrient Mixture F-12 (DMEM/F-12) supplemented with 10% Fetal Bovine Serum (FBS) and 100 µg/ml of Primocin. Prior to experimet cells were starved with phenol red free DMEM suplemented with 2 % charcoal stripped serum for 3 days

extract_protocol:
MCF7 cells were crosslinked, chromatin from nuclear lisates was sonicated and protein-DNA complexes were isolated with antibody. Input samples correspond to 10% of the material before antibody isolation.
Libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina according to the manufacturer’s instructions. NEBNext Multiplex Oligos for Illumina were used during library amplification

treatment_protocol: MCF7 cells were treated with eiher vehicle (ethanol) or estradol 10 nM for 1 hour.

tag: cell line

tag: source tissue

value: mammary gland, breast; derived from metastatic site:pleural effusion

tag: treatment

value: Vehicle (ethanol) 1h

tag: chip antibody


title: input MCF7 estradiol Rep2

source_name: input MCF7 estradiol

value: Estradiol 10 nM 1h


title: Fig1-U12IAA-6

description: nascent RNA


title: input MCF7 vehicle Rep1


title: Fig1-U12IAA-5

description: nascent RNA


title: MSC050_Day79_remission

description:
MSC050
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: High hyperdiploid


title: Fig1-U12IAA-4

description: nascent RNA


title: MSC049_control

description:
MSC049
Mesenchymal stromal cells derived from a healthy pediatric control.


title: FigS1-U1IAA-het

description: total RNA


title: MSC051_Day0_leukemic

description:
MSC051
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Newly diagnosed BCP-ALL


title: MSC046_Day0_leukemic

description:
MSC046
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig1-U12IAA-1

description: nascent RNA


title: AGO1 ChIP MCF7 estradiol Rep1

source_name: AGO1 ChIP MCF7 estradiol

value: anti AGO1 (clone 4B8, Sigma-Aldrich)


title: input MCF7 estradiol Rep1


title: AGO1 ChIP MCF7 estradiol Rep2


title: Fig1-U12IAA-3

description: nascent RNA


title: Fig1-U12IAA-2

description: nascent RNA


title: MSC047_Day79_remission

description:
MSC047
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: MSC044_Relapse

description:
MSC044
Mesenchymal stromal cells derived from pediatric BCP-ALL patient at Relapse.

value: Relapsed BCP-ALL


title: Fig1-U12dox-7

description: nascent RNA

value: dox


title: AGO1 ChIP MCF7 vehicle Rep2

source_name: AGO1 ChIP MCF7 vehicle


title: Fig1-U12dox-6

description: nascent RNA


title: MSC048_Day0_leukemic

description:
MSC048
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC043_Day79_remission

description:
MSC043
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: B-other


title: MSC045_control

description:
MSC045
Mesenchymal stromal cells derived from a healthy pediatric control.


title: CRC_scATACseq

city: New York

first: Caleb

last: Lareau

state: New York

address: 417 E 68th St, Zuckerman - ZRC 1132

institute: Memorial Sloan Kettering

data_processing:
R1 and R3 are the biological fastq files, whereas R2 is the technical fastq. All 16 bases in R2 correspond to the barcode. There are no UMIs as part of this dataset.
Fastqs were demultiplexed using CellRanger-ATAC mkfastq (v1.2.0)
Sequencing reads were aligned to a modified hg19 reference using CellRanger-ATAC count (v1.2.0). Single-cells were called using the default parameters from this step.
Genome_build: hg19
Supplementary_files_format_and_content: Processed fragment files from 10x CellRanger-ATAC count

source_name: Colorectal cancer tumor

extract_protocol:
NP40 lysis, see method sections for full details
Custom 10x Genomics scATAC-seq (mtscATAC-seq)

tag: tissue

value: Colorectal cancer tumor


title: AGO1 ChIP MCF7 vehicle Rep1


title: MSC042_Day79_remission

description:
MSC042
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: Child

tag: disease stage


title: Fig1-U12dox-5

city: La Jolla

description: nascent RNA


title: Fig1-U12dox-3

description: nascent RNA


title: Fig1-U12dox-4

description: nascent RNA


title: Fig1-U12dox-2

description: nascent RNA


title: Fig1-U11dox-3

description: nascent RNA


title: Fig1-U12dox-1

description: nascent RNA


title: Fig1-U11IAA-3

description: nascent RNA


title: PBMC_scATACseq_rep1

source_name: Peripheral blood mononuclear cells

tag: individual

value: 47 year old healthy volunteer

value: Peripheral blood mononuclear cells

tag: timepoint

value: month 3


title: CD34_scATACseq_rep1

source_name: CD34+ hematopoietic cells

value: CD34+ hematopoietic cells

value: month 0


title: PBMC_scATACseq_rep2


title: Fig1-U11IAA-2

description: nascent RNA

value: IAA


title: Fig1-U11IAA-1

description: nascent RNA


title: Fig1-U11dox-1

description: nascent RNA


title: Fig1-U11dox-2

description: nascent RNA


title: CD34_scATACseq_rep2


title: MSC041_Day0_leukemic

description:
MSC041
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Mesenchymal stromal cells (MSCs)

tag: bcp-all subtype


title: Fig1-U8IAA-4

description: nascent RNA


title: MSC040_Relapse

description:
MSC040
Mesenchymal stromal cells derived from pediatric BCP-ALL patient at Relapse.


title: MSC039_Day0_leukemic

description:
MSC039
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Mo22

city: London

first: Val

last: Yianni

address: Guy's Hospital, Great Maze Pond

institute: King's College London

description: Molar sc-RNAseq

data_processing:
Illumina Casava1.7 software used for basecalling.
Reads trimmed for adaptor sequences using TrimGalore. Then mapped to mm10 using Hisat2(v2) with default parameters.
Clustering analysis performed using Seurat v3
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: Molar

extract_protocol:
XLacZ4 mice were sacrificed. Molars and incisors were isolated and dissociated into single cells. Cell stained with FDG reagent. Cells possitive were isolated using FACS
Smart-Seq2. Libraries constructed using standard Illumina protocols.
Single cell RNAseq.

value: Molar

tag: strain

value: pericytes


title: Fig1-U8IAA-3

description: nascent RNA


title: Fig1-U8IAA-2

description: nascent RNA


title: MSC038_control

description:
MSC038
Mesenchymal stromal cells derived from a healthy pediatric control.

tag: age

value: Healthy

value: Control


title: Fig1-U8dox-3

description: nascent RNA


title: CLL_PT2_CD19neg_scATACseq

data_processing:
Fastqs were demultiplexed usiing CellRanger-ATAC mkfastq (v1.0.0)
Sequencing reads were aligned to a modified hg19 reference using CellRanger-ATAC count (v1.0.0). Single-cells were called using the default parameters from this step.
Genome_build: hg19
Supplementary_files_format_and_content: Processed fragment files from 10x CellRanger-ATAC count

growth_protocol: Cryopreserved cells were thawed in RPMI with 10% FBS and washed in media. CD19 positive and negative fractions were flow cytometry sorted/ enriched using magnetic beads or used in bulk prior to 10x scATAC-seq.

tag: subject status

value: chronic lymphocytic leukemia patient

tag: subject id

value: Patient 2

tag: cell type

value: Peripherial blood mononuclear cells

tag: enrichment

value: CD19 negative


title: CLL_PT2_CD19pos_scATACseq

value: CD19 positive


title: Fig1-U8IAA-1

description: nascent RNA

tag: treatment (dox or iaa)

tag: target gene

tag: ip antibody

tag: adapter


title: CLL_PT1_CD19pos_scATACseq

value: Patient 1


title: Fig1-U8dox-1

description: nascent RNA

value: dox


title: Fig1-U5IAA-6

description: nascent RNA


title: Fig1-U8dox-2

description: nascent RNA


title: Fig1-U5IAA-5

description: nascent RNA


title: Fig1-U5IAA-4

description: nascent RNA


title: CLL_PT1_CD19neg_scATACseq


title: Fig1-U5IAA-3

description: nascent RNA


title: CLL_PT1_bulk1_scATACseq


title: MSC034_Day0_leukemic

description:
MSC034
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Child

value: Newly diagnosed BCP-ALL

value: B-other


title: MSC033_Day79_remission

description:
MSC033
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).

value: Remission BCP-ALL


title: CLL_PT1_bulk2_scATACseq


title: Fig1-U5IAA-2

description: nascent RNA

value: IAA


title: MSC037_Day0_leukemic

description:
MSC037
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.

value: Mesenchymal stromal cells (MSCs)


title: MSC036_Day0_leukemic

description:
MSC036
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig1-U5IAA-1

description: nascent RNA


title: Fig1-U8dox-4

description: nascent RNA


title: CD34_800_Day20

growth_protocol: StemSpan II supplemented with P/S and 1x CC100 cytokine mix. For differentiation, IMDM-based media containing human serum and plasma was supplemented with erythropoietin, stem cell factor and interleukin-3; see method section for detailed information)

value: CD34+ hematopoietic cells

tag: culture input cell #

value: Day 20


title: Fig1-U5dox-5

description: nascent RNA


title: Fig1-U5dox-6

description: nascent RNA


title: MSC032_control

description:
MSC032
Mesenchymal stromal cells derived from a healthy pediatric control.

value: Healthy


title: CD34_800_Day14

value: Day 14


title: MSC035_Day79_remission

description:
MSC035
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig1-U5dox-4

description: nascent RNA


title: CD34_800_Day08

value: Day 8


title: Fig1-U5dox-2

description: nascent RNA


title: MSC003_control

description:
MSC003
Mesenchymal stromal cells derived from a healthy pediatric control.

value: Control


title: CD34_500_Day14


title: Fig1-U4atacIAA-6

description: nascent RNA


title: MSC030_Relapse

description:
MSC030
Mesenchymal stromal cells derived from pediatric BCP-ALL patient at Relapse.

value: Relapsed BCP-ALL


title: MSC029_Day0_leukemic

description:
MSC029
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig1-U4atacIAA-4

description: nascent RNA


title: Fig1-U4atacIAA-5

description: nascent RNA


title: Fig1-U4atacIAA-3

description: nascent RNA


title: Fig1-U4atacIAA-2

description: nascent RNA


title: MSC027_Day0_leukemic

description:
MSC027
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC028_Relapse

description:
MSC028
Mesenchymal stromal cells derived from pediatric BCP-ALL patient at Relapse.

value: High hyperdiploid


title: Fig1-U4atacdox-5

description: nascent RNA


title: Fig1-U4atacIAA-1

description: nascent RNA


title: Fig1-U4atacdox-6

description: nascent RNA


title: MSC025_Day79_remission

description:
MSC025
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig1-U5dox-3

description: nascent RNA


title: Fig1-U4atacdox-3

description: nascent RNA


title: Fig1-U4atacdox-2

description: nascent RNA


title: Fig1-U4atacdox-1

description: nascent RNA


title: Fig1-U4atacdox-4

description: nascent RNA


title: CD34_500_Day08


title: FigS1-U1IAA-degron2

description: total RNA


title: Fig1-U4IAA-4

description: nascent RNA


title: Fig1-U4IAA-3

description: nascent RNA


title: Fig1-U4IAA-2

description: nascent RNA


title: Fig1-U4IAA-1

description: nascent RNA


title: Fig1-U4dox-4

description: nascent RNA


title: Fig1-U4dox-3

description: nascent RNA


title: Fig1-U4dox-2

description: nascent RNA


title: MSC026_Day79_remission

description:
MSC026
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: MSC031_Relapse

description:
MSC031
Mesenchymal stromal cells derived from pediatric BCP-ALL patient at Relapse.


title: MSC024_Day79_remission

description:
MSC024
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: MSC002_Day0_leukemic

description:
MSC002
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC023_control

description:
MSC023
Mesenchymal stromal cells derived from a healthy pediatric control.


title: Fig1-U3IAA-3

description: nascent RNA


title: MSC020_Day0_leukemic

description:
MSC020
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig1-U3IAA-1

description: nascent RNA


title: FIg1-U3dox-4

description: nascent RNA


title: MSC021_Day79_remission

description:
MSC021
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: FIg1-U3dox-2

description: nascent RNA


title: MSC019_Day0_leukemic

description:
MSC019
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC022_control

description:
MSC022
Mesenchymal stromal cells derived from a healthy pediatric control.


title: MSC018_Day0_leukemic

description:
MSC018
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC017_control

description:
MSC017
Mesenchymal stromal cells derived from a healthy pediatric control.


title: Fig1-U4dox-1

description: nascent RNA


title: MSC016_Day79_remission

description:
MSC016
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: FIg1-U3dox-1

description: nascent RNA


title: Fig1-U3IAA-4

description: nascent RNA


title: Fig1-U2dox-4

description: nascent RNA


title: Fig1-U2IAA-2

description: nascent RNA


title: Fig1-U2IAA-1

description: nascent RNA


title: Fig1-U2IAA-3

description: nascent RNA


title: Fig1-U3IAA-2

description: nascent RNA


title: FIg1-U3dox-3

description: nascent RNA


title: Fig1-U2dox-3

description: nascent RNA


title: Fig1-U2dox-2

description: nascent RNA


title: MSC014_control

description:
MSC014
Mesenchymal stromal cells derived from a healthy pediatric control.


title: MSC013_control

description:
MSC013
Mesenchymal stromal cells derived from a healthy pediatric control.


title: MSC015_Day0_leukemic

description:
MSC015
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: Fig1-U2IAA-4

description: nascent RNA


title: Fig1-U2dox-1

description: nascent RNA


title: MSC011_Day0_leukemic

description:
MSC011
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at initial diagnosis.


title: MSC012_Day79_remission

description:
MSC012
Mesenchymal stromal cells derived from a pediatric BCP-ALL patient at day 79 of treatment (after induction and consolidation therapy).


title: Fig1-U1IAA-3

description: nascent RNA


title: Fig1-U1IAA-2

description: nascent RNA


title: Fig1-U1dox-4

description: nascent RNA


title: Fig1-U1dox-3

description: nascent RNA


title: Fig1-U1IAA-1

description: nascent RNA


title: Fig1-U1dox-2

description: nascent RNA


title: Fig1-U1dox-1

description: nascent RNA