title: Mock NT 2

data_processing: The ProcessedSignal data column of the Feature Extraction *.txt output file was used, containing the median signals corrected by spatial and multiplicative detrend. Data quality filtering was performed using Agilent GeneSpring GX 11.0, discarding features with the Feature Extraction flag gIsWellAboveBG=0 in any sample, wich is a statistical method approximately equivalent to discarding features with a Signal/Noise ratio smaller than 2.0-3.0, where Signal = (median of the spot - median spot background level) and Noise is the Standard Deviation of the median spot background. Differential gene lists were obtained from filtered data using Microsoft Excel. A threshold of 350.0 in the absolute expression level was chosen to obtain a higher stringency and a smaller relative error of the signal. Differentially expressed genes were identified as those showing an average fold change ratio >1.5 or <1/1.5 in the linear scale.


title: omentum; ASC; M38

status: Public on Mar 22 2024

type: RNA

city: Stanford

first: Heather

last: Clemons

state: CA

address: Beckman Center

department: Dept of Biochemistry

country: USA

institute: Stanford School of Medicine

hyb_protocol: HEEBO oligonucleotide microarrays, containing ~45,000 70-mer oligonucleotide probes, representing ~30,000 unique genes, were printed on epoxysilane-coated glass (Schott Nexterion E) by the Stanford Functional Genomics Facility. Prior to hybridization, slides were first incubated in a humidity chamber (Sigma Cat# H6644) containing 0.5× SSC (1× SSC = 150 mM NaCl, 15 mM sodium citrate [pH 7.0]) for 30 min at room temperature. Slides were snap-dried at 70–80°C on an inverted heat block. The free epoxysilane groups were blocked by incubation with 1M Tris-HCl (pH 9.0), 100 mM ethanolamine, and 0.1% SDS for 20 min at 50 °C. Slides were washed for 1 min in each of 2 wash chambers containing 400 ml of water, and then dried by centrifugation. Slides were used the same day. The sample was incubated at 90 °C for 5 min, spun at 14,000 rpm for 10 min in a microcentrifuge, then hybridized at 65 °C using the MAUI hybridization system (BioMicro) for 12–16 hours.

scan_protocol: Following hybridization, microarrays were washed in a series of four solutions containing 400 ml of 2× SSC with 0.05% SDS, 2x SSC, 1× SSC, and 0.2× SSC, respectively. The first wash was performed for 5 min at 65 °C. The subsequent washes were performed at room temperature for 2 min each. Following the last wash, the microarrays were dried by centrifugation in a low-ozone environment (<5 ppb) to prevent destruction of Cy dyes. Once dry, the microarrays were kept in a low-ozone environment during storage and scanning. Microarrays were scanned using AxonScanner 4000B (Molecular Devices). PMT levels were adjusted manually to achieve minimal saturation. Each element was located and analyzed using SpotReader (Niles Scientific) or GenePix Pro 6.0 (Molecular Devices).

data_processing:
The microarrays were submitted to the Stanford Microarray Database for further analysis. Data were filtered to exclude elements that did not have: a regression correlation of ≥ 0.6 between Cy5 and Cy3 signal over the pixels comprising the array element, and an intensity/background ratio of ≥ 2.5 in at least one channel.
Cy5/Cy3 log2 ratio

molecule: total RNA

organism: Homo sapiens

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

label_protocol: 1 μg of each total RNA sample was amplified using Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821) according to the manufacturer's protocol.  Poly-adenylated RNAs were amplified in the presence of aminoallyl-UTP with Ambion Amino Allyl MessageAmp II-96 Kit (Cat# 1821). For mRNA expression experiments, Universal Reference RNA was used as an internal standard to enable reliable comparison of relative mRNA levels in multiple samples (Stratagene Cat# 740000). 10 μg each of amplified sample and reference RNA was fluorescently labeled with NHS-monoester Cy5 or Cy3 respectively (GE HealthSciences Cat# RPN5661). Differentially dye-labeled sample and reference RNA samples were combined, fragmented (Ambion Cat# 8740), then diluted into in a 50-μl solution containing 3× SSC, 25 mM Hepes-NaOH (pH 7.0), 20 μg of human Cot-1 DNA (Invitrogen Cat# 15279011), 20 μg of poly(A) RNA (Sigma Cat# P9403), 25 μg of yeast tRNA (Invitrogen Cat# 15401029), and 0.3% SDS.

growth_protocol: One-half of each stromal-vascular pellet fraction from the “Tissue Fractionation” procedure was reserved to culture adipose stem cells. The cell suspension was centrifuged at 400g for 7 minutes and the buffer was carefully aspirated with a pipette to avoid losing pelleted cells. Cells originating from the pericolonic or omental depots were additionally treated for 10 min with RBC lysis buffer*, again centrifuged, and the lysis buffer aspirated. Cells were resuspended in 10 ml DMEM + 10% FBS + 2.5 μg/ml Fungizone (Invitrogen Cat# 15290-018) + Pen/Strep/Glutamine (Invitrogen 10378-016). Cells were transferred to the appropriate size culture flask (10-20 g starting tissue in 1 x T25, 20-50g in 1x T75). Additional DMEM (~1ml/5cm2) was added to cells and mixed by pipetting. Cells were incubated overnight or up to 24 hours to allow time for adipose stem cells to adhere. Cells were rinsed with warm PBS and given fresh medium. Presence of adherent stromal cells was assessed visually at 10x magnification. Successful cultures were continually grown in DMEM + 10%FBS + Pen/Strep/Glutamine. Fungizone was no longer added after 2 passages. Cells were split 1 to 3 at 70-90% confluence. When enough cells were obtained (at least 1 confluent T225 flask), cells were rinsed with PBS and trypsinized, pelleted by centrifugation and resuspended in fresh medium. Each of 2, 10 cm dishes were plated, one for pre- and one for post-differentiation RNA collection. For the latter see “Adipocyte Differentiation”. Cells for pre-differentiation RNA collection were plated at 100% confluence in fresh DMEM and incubated overnight. Cells were photographed at 10x magnification to document confluence and morphology of cells.

extract_protocol: Cells were rinsed with warm PBS. PBS was replaced with 6 ml Trizol. Plates were gently scraped and Trizol/cell lysate was transferred to a 15 ml conical tube and stored at -80°C until RNA isolation. Samples in Trizol were removed from the -80°C storage freezer and thawed at room temperature. Chloroform was added to each sample (10 ml to adipocyte, 5 ml to stromal-vascular pellet, 1 ml to cell culture), and tubes were recapped and vigorously shaken. Samples were then centrifuged at 12,000g for 15 minutes at 4°C. Following centrifugation, the aqueous phase was removed and transferred to a fresh conical tube and an equivalent volume of 70% ethanol was added. Tubes were recapped and shaken. Samples were loaded onto RNeasy Maxi Kit (Qiagen Cat# 75152) columns and the RNeasy protocol for RNA washes and elution was followed (RNeasy Midi/Maxi Handbook, “Animal Tissues” Protocol beginning at step 7). RNA was eluted with 1.6 ml water. RNA was precipitated as follows: one-tenth volume 3M sodium acetate and 2.5x volume 100% ethanol were added to the 1.6 ml RNA sample. Tubes were capped, shaken to mix and stored overnight at -80°C. Tubes were removed from -80°C, thawed at room temperature and centrifuged at 16,000g for 20 minutes, 4°C. Tubes were gently removed from the centrifuge, uncapped and quickly inverted to pour off liquid. These were left upside-down on paper towels to dry. Remaining ethanol droplets were aspirated and the RNA pellet was resuspended in 200 μl RNase-free water. RNA concentration was measured (Nanodrop ND-1000 spectrophotometer) and samples were stored at -80°C.

treatment_protocol: Adipose stem cells were grown to confluence as described in “Cell Culture”. Cells were rinsed with warm PBS and trypsinized. Trypsinized cells were transferred to a 15 ml conical tube, pelleted by centrifugation and resuspended in 5 ml DMEM + 10% FBS + Pen/Strep/Glutamine (Invitrogen Cat# 10378-016). Cells were plated to achieve the greatest density possible depending on the number of cells available, as higher confluence yielded a greater percentage of differentiating cells. In general, cells were plated at 100-300% confluence. Cells were incubated overnight and photographed the following day at 10x magnification to document confluence and record the morphology of cells. Cells were rinsed with warm PBS. PBS was replaced with Zen-Bio differentiation medium (Cat# DM-2) and the differentiation procedure was followed as described in Zen-Bio instruction manual ZBM-1. At 16 days following induction of differentiation, cells were photographed at 10x magnification to document the number and morphology of differentiating cells.

tag: tag

value: reference:Stratagene Human Universal Reference

source_name: omentum; ASC; M38, 10 ug labeled aRNA

tag: age

tag: organism part

value: omentum

tag: sample fraction

value: ASC

tag: Sex

value: M


title: breast; ASC; F24

source_name: breast; ASC; F24, 10 ug labeled aRNA

value: breast

value: F


title: Input_Arid1aHet_R2

type: SRA

city: New York City

first: Christopher

middle: Russell

last: Chin

state: NY

address: 413 E 69th Street, Belfer Building, BB-1462

institute: Weill Cornell

library_source: genomic

data_processing:
Processed through nfcore ChIPseq analysis pipeline.
Trimmed by TrimGalore, aligned with BWA, sequences filtered and duplicates marked.
Peak calling by macs2
Assembly: hg38
Supplementary files format and content: bed files for peak calls

molecule: genomic DNA

source_name: cell line

growth_protocol: 20% IMDM with P/S, GlutaMax

extract_protocol:
AMPure XP Beads
NEB Ultra II

tag: tissue

value: cell line

tag: cell line

value: RIVA

tag: cell type

value: B-cell lymphoma ABC-DLBCL

tag: genotype

value: Arid1a HET

tag: antibody

value: Input


title: breast; ASC; F62b

source_name: breast; ASC; F62b, 10 ug labeled aRNA


title: Input_Arid1aHet_R1


title: Pu1_Arid1aWt_R2.ChIP

value: Arid1a WT


title: omentum; ASC; F37a

source_name: omentum; ASC; F37a, 10 ug labeled aRNA


title: breast; ASC; UUi

source_name: breast; ASC; UUi, 10 ug labeled aRNA

value: UUi


title: Smarca4_Arid1aHet_R1.ChIP


title: omentum; ASC; F43b

source_name: omentum; ASC; F43b, 10 ug labeled aRNA


title: Input_Arid1aWt_R1


title: omentum; ASC; F38

source_name: omentum; ASC; F38, 10 ug labeled aRNA


title: omentum; ASC; F24b

source_name: omentum; ASC; F24b, 10 ug labeled aRNA


title: breast; ASC; F23

source_name: breast; ASC; F23, 10 ug labeled aRNA


title: breast; ASC; F50c

source_name: breast; ASC; F50c, 10 ug labeled aRNA


title: Pbrm1_Arid1aHet_R1.ChIP


title: breast; ASC; F34

source_name: breast; ASC; F34, 10 ug labeled aRNA


title: Pu1_Arid1aHet_R2.ChIP


title: Pu1_Arid1aWt_R1.ChIP


title: Pu1_Arid1aHet_R1.ChIP


title: H3K27ac_Arid1aHet_R1.ChIP


title: parse

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

institute: St. Anna Children's Cancer Research Institute (CCRI)

description: all samples were pooled in this scRNA-seq reaction using split Parse Biosciences pool combinatorial barcoding

library_source: transcriptomic single cell

data_processing:
Raw sequencing data were processed with the split-pipe v1.0.6p software (Parse Biosciences) for cell-level demultiplexing and alignment to the human reference transcriptome (refdata-gex-GRCh38-2020-A assembly provided by 10x Genomics; parameters: -m all -c v2).
Assembly: GRCh38
Supplementary files format and content: Matrix and cell metadata files provided by the split-pipe workflow, all_genes.csv is the same file for all samples, samples_parse.csv provides annotations for all samples

source_name: H7, H7-MYCN(dox), H7-17q1q-MYCN(dox), H7-17q-MYCN(dox), H9, H9-17q1q-MYCN(dox)

growth_protocol: hESCs were cultured routinely in feeder-free conditions at 37°C and 5% CO2 in E8 media complemented with GlutaMax (Thermo Fisher Scientific) on Vitronectin (Thermo Fisher Scientific) as an attachment substrate. All cell lines were tested regularly for mycoplasma and expression of pluripotency markers. hESC differentiation toward trunk NC and its derivatives was performed using the protocol described in Frith et al. (2018) and Frith & Tsakiridis (2019).

extract_protocol:
Single-cell suspensions were obtained from cell cultures using Accutase cell dissociation reagent (Stempro)
Cells were harvested with Accutase to create a single-cell suspension, then were counted using Bio-rad Tc10 Automated cell counter in the presence of Trypan Blue Stain (Bio-rad). For cell fixation we used the Evercode Fixation v2 Kit (SKU: ECF 2001, Parse Biosciences, Seattle, USA) as per manufacturer instructions. A maximum of 5,000 cells per sample were multiplexed using the Evercode WT Mega v2 kit (Parse Biosciences). Three rounds of combinatorial barcoding were performed, and cells were then pooled and split into 16 sub-libraries (one small 5,000-cell sub-library and 15 large sub-libraries of 32,000 cells each). After DNA amplification and library prep, the small library was sequenced as part of a larger Illumina NovaSeq 6000 flowcell and the 15 large sub-libraries on one dedicated NovaSeq S4 platform in 2x150 bp paired-end mode.

treatment_protocol: Overexpression of MYCN was induced by supplementing the neural crest media with 100ng/ml of Doxycycline at day 5 (D5) of differentiation in all samples labelled as "..MYCN".

value: human embryonic stem cells and hESC-derived trunk neural crest derivatives

tag: day

tag: treatment

value: one pool of cells was supplemented with DOX at D5 to induce MYCN

tag: sample pool

value: parse

tag: flowcell

tag: lane


title: abdominal; ASC; F50

source_name: abdominal; ASC; F50, 10 ug labeled aRNA

value: abdominal


title: abdominal; ASC; F33

value: reference:Stratagene Human Universal Reference

source_name: abdominal; ASC; F33, 10 ug labeled aRNA


title: breast; ASC; F36a

source_name: breast; ASC; F36a, 10 ug labeled aRNA


title: Smarca4_Arid1aWt_R1.ChIP


title: abdominal; ASC; F66

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: abdominal; ASC; F66, 10 ug labeled aRNA


title: abdominal; ASC; F39a

source_name: abdominal; ASC; F39a, 10 ug labeled aRNA


title: breast; ASC; F34a

source_name: breast; ASC; F34a, 10 ug labeled aRNA


title: GEX24

description: four samples were pooled in this scRNA-seq reaction using CellPlex

data_processing:
Raw sequencing data were processed with the CellRanger multi v7.1.0 software (10x Genomics) for cell-level demultiplexing and alignment to the human reference transcriptome (refdata-gex-GRCh38-2020-A assembly provided by 10x Genomics).
Downstream analysis, quality control and data integration was was performed in an R (Seurat Package, v4.1.0) and with the aid of multiple, additional tools. For details, processing, please refer to the methods of the associated manuscript.
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files, matrix files, binary serialised R file containing a Seurat object

source_name: H7, H7-17q1q-MYCN(dox)

extract_protocol:
Single-cell suspensions were obtained from cell cultures using Accutase cell dissociation reagent (Stempro)
Single-cell suspensions were barcoded using oligo-conjugated lipids following the MULTI-seq workflow and frozen live for G1-G13 (note, G2 was removed due to a technical failure), or frozen live and barcoded after thawing using the CELLPLEX (10x Genomics) workflow for G14-G27. After thawing cells were stained with DAPI. A maximum of 10,000 live cells per sample were sorted with a FACS-Aria v3 and pooled in sets of 3 or 4 samples by differentiation stage (from 3-5 independent replicate differentiation experiments). Each pooled group was processed using the 10X Genomics Single Cell 3’ v3.1 workflow following the manufacturer’s instructions. Enriched barcode libraries were indexed following the MULTI-seq workflow. After quality control, libraries were sequenced on the Illumina NovaSeq S4 (G1-13) or S2 (G14-27) platform in 2x150bp paired-end mode. Supplementary Table 1 includes an overview of sequencing data and performance metrics.

value: H7, H7-17q1q-MYCN(dox)

value: hESC-derived trunk neural crest derivatives

tag: sample group


title: abdominal; ASC; F33-2

source_name: abdominal; ASC; F33-2, 10 ug labeled aRNA

value: ASC


title: Pbrm1_Arid1aWt_R1.ChIP

source_name: cell line


title: GEX23


title: H3K27ac_Arid1aWt_R1.ChIP


title: abdominal; ASC; F62a

source_name: abdominal; ASC; F62a, 10 ug labeled aRNA


title: abdominal; ASC; F62

source_name: abdominal; ASC; F62, 10 ug labeled aRNA


title: GEX27

value: hESC-derived mature trunk neural crest derivatives


title: GEX26


title: abdominal; ASC; M38

source_name: abdominal; ASC; M38, 10 ug labeled aRNA

value: M


title: GEX25


title: abdominal; ASC; F43

source_name: abdominal; ASC; F43, 10 ug labeled aRNA

value: F


title: GEX19


title: abdominal; ASC; M60

source_name: abdominal; ASC; M60, 10 ug labeled aRNA


title: GEX21

description: three samples were pooled in this scRNA-seq reaction using CellPlex


title: abdominal; ASC; F52f

source_name: abdominal; ASC; F52f, 10 ug labeled aRNA


title: abdominal; ASC; F42

source_name: abdominal; ASC; F42, 10 ug labeled aRNA


title: GEX22


title: thigh; EVD; F58a

source_name: thigh; EVD; F58a, 10 ug labeled aRNA

value: thigh

value: EVD


title: GEX20


title: thigh; EVD; F52e

source_name: thigh; EVD; F52e, 10 ug labeled aRNA


title: thigh; EVD; F62

source_name: thigh; EVD; F62, 10 ug labeled aRNA


title: abdominal; ASC; F37

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: abdominal; ASC; F37, 10 ug labeled aRNA


title: abdominal; ASC; F31b

source_name: abdominal; ASC; F31b, 10 ug labeled aRNA


title: GEX18


title: thigh; EVD; F83

source_name: thigh; EVD; F83, 10 ug labeled aRNA


title: GEX17

source_name: H7, H7-17q1q-MYCN(dox)


title: Patient_3_20ICH00432TA11_DSP.1012550023361.B.A12

city: Los Angeles

first: Sargis

last: Sedrakyan

address: 4650 Sunset Blvd

institute: Children's Hospital Los Angeles

description: Whole Transcriptome Atlas

library_source: transcriptomic

data_processing:
save-interim-files=false
quality-trim-score=20
2color-trimming=True
adapter1=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
adapter2=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
adapter-trim-match-length=10
adapter-trim-max-mismatch=3
barcode-max-mismatch=1
stitching-max-mismatch=2
dedup-hd=1
threads=4
Data processing was performed in R v4.2.1. The RNA count of the negative probes was used to evaluate the limit of quantification (LOQ); in brief the median and standard deviation of the negative probe counts were calculated and we defined the LOQ to be three standard deviations above the median of the negative probe counts. RNA counts below this threshold were converted in missing values. Then the count data was normalized using the trimmed mean of M values (TMM) method with the package EdgeR (v3.40.2). Statistical analysis and figures were generated using the package RomicsProcessor v1.1.0, which is available on GitHub. The large dataset was subsided to perform statistics and comparisons between different groups. PCA and hierarchical clustering were performed to verify the grouping of the sample within each subset. Two-tailed heteroscedastic Student’s t-tests were performed when at least 50% of the samples from each group to be compared were available. To statistically evaluate if the difference between presence and absence of quantitative value between two groups was significant, we used binomial GLM tests. For each test performed, the p-value frequency was plotted to ensure that the p-value threshold was selected appropriately. The p value filter employed were the Benjamini-Hochberg adjusted p value < 0.05 for both T-test and binomial GLM. For multiple comparison 1-way ANOVA was applied. Linear model of the normalized transcript abundances as the dependent variable were fit to the pathological scores (model equation: yi=β0+β1*xi+ϵi). Likelihood ratios tests were conducted to identify the proteins with evidence of significant linear trends with pathological score. Venn diagrams were realized using the package “ggvenn” v0.1.9. Pearson’s correlations were used to identify RNA with abundances positively or negatively correlated to the abundance of transcripts of genes known to participate in glomerular diseases. Trajectory analyses were performed using the package SLICER v0.2.0 [https://genomebiology.biomedcentral .com/articles/10.1186/s13059-016-0975-3].  Enrichment analyses were performed using the homemade package Protein_Minion v0.2.0 (https://github.com/GeremyClair/Protein_MiniOn) the EASE score (DAVID’s modified Fisher’s Exact tests) on GO terms, KEGG and Reactome pathways harvested from Uniprot (01-30-2022). The code to perform the analysis was also uploaded on GitHub to make the data analysis reproducible (https://github.com/GeremyClair/The_spatially_resolved_transcriptome_signatures_of_glomeruli_in_chronic_kidney_disease).
Assembly: N/A, sequencing of synthetic tags and alignment to whitelist of RTS_IDs (probe barcodes) found in the config.ini output from the GeoMx DSP platform, see attached PKC file (Hs_R_NGS_WTA_COVID19_v1.0.pkc)
Supplementary files format and content: Digital Count Conversion (DCC) file format outputted from GeoMx NGS Pipeline, contains software versions, scan attributes, GeoMx NGS pipeline parameters and output metrics, Q30 scores, and list of deduplicated counts per RTS_ID (probe barcode)
Supplementary files format and content: TMM normlized counts
Library strategy: GeoMx Seq

source_name: kidney

extract_protocol:
Serially prepared sections (previously hybridized with Whole Transcriptome Assay (WTA) probes) were also immunostained with CD3, Ki-67, ɑ-Smooth Muscle Actin and SYTO83 to help with region of interest (ROI) selection. Briefly, Morphology Marker Solution was prepared in the following proportions per slide: 22ul SYTO (Thermo Fisher Scientific, Cat#S11364), 5.5 ul ɑ-Smooth Muscle Actin (NanoString Technologies), 5.5 ul CD3 (NanoString Technologies), 5.5 ul Ki-67 (NanoString Technologies), and 181.5 ul Buffer W for a total volume of 220 ul/slide. Slides were incubated in this solution at room temperature for 1 hour followed by successive 2x SSC washes, after which, the slides were loaded into the NanoString GeoMx Digital Spatial Profiler (DSP) where overview scans were captured at 20x to guide the selection of ROIs.  Slides were prepared for hybridization following a modified RNA FFPE BOND RX Slide Preparation Protocol in the GeoMx NGS Slide Preparation User Manual (NanoString Technologies, MAN-10115).  Briefly, deparaffinization, antigen retrieval, and Proteinase K digestion was performed on a Leica BOND-RX instrument with Bond Dewax Solution, Bond Epitope Retrieval Solution 2, and a 37°C Proteinase K digest at 1mg/ml. Human Whole Transcriptome Assay (WTA) probes (NanoString Technologies, Cat#121401102) hybridized at 4nM each in Buffer R, and incubated in a hybridization chamber for 16 hrs at 37°C. Two washes in 50% Formamide/2x SSC (ThermoFisher, Cat#AM9342 / Sigma-Aldrich, Cat#S6639) at 37°C washed non-specifically-bound probes from the slides, which were then blocked prior to antibody staining with 200 ul Buffer W (Nanostring). Regions of interest within the tissue were illuminated with UV light and oligo barcodes were physically aspirated from the tissue and collected into microtiter plates by the GeoMx® Digital Spatial Profiler (DSP) platform. For more information about DSP protocols please see Merritt et al. Nature Biotech 2020 (doi: 10.1038/s41598-020-63539-x)
Each collection of oligo tags from one well (representing an ROI from the tissue section) was indexed with i7xi5 unique dual indexes using GeoMx SeqCode primers with 18 cycles of PCR.  After PCR, indexed AOIs were pooled and purified in two rounds of AMPure XP PCR purification using 1.2x bead:sample ratio.

value: 25 years

value: Female

tag: roi

tag: segment

value: Glomeruli

value: kidney


title: Patient_3_20ICH00432TA9_DSP.1012550023361.B.A10

description: Whole Transcriptome Atlas

tag: age


title: GEX15


title: shin; EVD; UUh

tag: tag

source_name: shin; EVD; UUh, 10 ug labeled aRNA

tag: organism part

value: shin

value: UUh


title: GEX14


title: thigh; EVD; F29

source_name: thigh; EVD; F29, 10 ug labeled aRNA

tag: sample fraction

tag: Sex


title: Patient_3_20ICH00432TA12_DSP.1012550023361.B.B01

description: Whole Transcriptome Atlas

value: Tubules

tag: tissue


title: thigh; EVD; F73a

source_name: thigh; EVD; F73a, 10 ug labeled aRNA


title: Patient_3_20ICH00432TA8_DSP.1012550023361.B.A09

description: Whole Transcriptome Atlas


title: Patient_3_20ICH00432TA7_DSP.1012550023361.B.A08

description: Whole Transcriptome Atlas


title: shin; EVD; F81a

source_name: shin; EVD; F81a, 10 ug labeled aRNA


title: shin; EVD; M44

source_name: shin; EVD; M44, 10 ug labeled aRNA


title: shin; EVD; M51

source_name: shin; EVD; M51, 10 ug labeled aRNA


title: Patient_3_20ICH00432TA6_DSP.1012550023361.B.A07

description: Whole Transcriptome Atlas


title: shin; EVD; M17a

source_name: shin; EVD; M17a, 10 ug labeled aRNA


title: Patient_3_20ICH00432TA4_DSP.1012550023361.B.A05

description: Whole Transcriptome Atlas


title: shin; EVD; F81

source_name: shin; EVD; F81, 10 ug labeled aRNA


title: Patient_3_20ICH00432TA10_DSP.1012550023361.B.A11

description: Whole Transcriptome Atlas


title: Patient_3_20ICH00432TA5_DSP.1012550023361.B.A06

description: Whole Transcriptome Atlas


title: Patient_3_20ICH00432TA2_DSP.1012550023361.B.A03

description: Whole Transcriptome Atlas


title: Patient_3_20ICH00432TA3_DSP.1012550023361.B.A04

description: Whole Transcriptome Atlas


title: GEX16

tag: cell line

tag: cell type

value: one pool of cells was supplemented with DOX at D5 to induce MYCN


title: shin; ASC; M41

value: reference:Stratagene Human Universal Reference

source_name: shin; ASC; M41, 10 ug labeled aRNA


title: shin; EVD; F83

source_name: shin; EVD; F83, 10 ug labeled aRNA


title: Patient_3_20ICH00432TA1_DSP.1012550023361.B.A02

description: Whole Transcriptome Atlas


title: shin; EVD; M41

source_name: shin; EVD; M41, 10 ug labeled aRNA


title: omentum; EVD; M49a

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

source_name: omentum; EVD; M49a, 10 ug labeled aRNA

value: omentum


title: Patient_10_MS20-16767A6_DSP.1012550003362.C06

description: Whole Transcriptome Atlas

value: 40's years

value: Male


title: omentum; EVD; F24b

source_name: omentum; EVD; F24b, 10 ug labeled aRNA


title: Patient_10_MS20-16767A6_DSP.1012550003362.C07

description: Whole Transcriptome Atlas


title: omentum; EVD; F58c

source_name: omentum; EVD; F58c, 10 ug labeled aRNA


title: omentum; EVD; M62

source_name: omentum; EVD; M62, 10 ug labeled aRNA


title: Patient_10_MS20-16767A6_DSP.1012550003362.C05

description: Whole Transcriptome Atlas

source_name: kidney


title: Patient_10_MS20-16767A6_DSP.1012550003362.C03

description: Whole Transcriptome Atlas


title: omentum; EVD; F37a

source_name: omentum; EVD; F37a, 10 ug labeled aRNA


title: Patient_10_MS20-16767A6_DSP.1012550003362.C04

description: Whole Transcriptome Atlas


title: Patient_9_MS20-16418A13_DSP.1012550003362.C01

description: Whole Transcriptome Atlas

value: 56 years


title: omentum; EVD; F38

source_name: omentum; EVD; F38, 10 ug labeled aRNA


title: Patient_9_MS20-16418A13_DSP.1012550003362.C02

description: Whole Transcriptome Atlas


title: breast; EVD; F23

source_name: breast; EVD; F23, 10 ug labeled aRNA

value: breast


title: breast; EVD; F62b

source_name: breast; EVD; F62b, 10 ug labeled aRNA

value: F


title: Patient_9_MS20-16418A13_DSP.1012550003362.B12

description: Whole Transcriptome Atlas


title: Patient_10_MS20-16767A6_DSP.1012550003362.B11

description: Whole Transcriptome Atlas


title: breast; EVD; F58

source_name: breast; EVD; F58, 10 ug labeled aRNA


title: Patient_9_MS20-16418A13_DSP.1012550003362.B10

description: Whole Transcriptome Atlas


title: breast; EVD; F50c

source_name: breast; EVD; F50c, 10 ug labeled aRNA


title: omentum; EVD; F43b

source_name: omentum; EVD; F43b, 10 ug labeled aRNA


title: breast; EVD; F34

source_name: breast; EVD; F34, 10 ug labeled aRNA


title: Patient_9_MS20-16418A13_DSP.1012550003362.B09

description: Whole Transcriptome Atlas


title: Patient_9_MS20-16418A13_DSP.1012550003362.B08

description: Whole Transcriptome Atlas


title: breast; EVD; F36a

source_name: breast; EVD; F36a, 10 ug labeled aRNA


title: breast; EVD; UUi

source_name: breast; EVD; UUi, 10 ug labeled aRNA

value: UUi


title: Patient_9_MS20-16418A13_DSP.1012550003362.B07

description: Whole Transcriptome Atlas


title: abdominal; EVD; F39a

source_name: abdominal; EVD; F39a, 10 ug labeled aRNA

value: abdominal

value: EVD


title: Patient_9_MS20-16418A13_DSP.1012550003362.B06

description: Whole Transcriptome Atlas


title: IgG_WT_3 (CnR Run B)

description: CnR Run B

data_processing:
*library strategy: CUT&RUN
Reads were trimmed by Trimmomatic and aligned by Bowtie2
After filtering and marking duplicates peaks were called by Seacr in stringent mode
Assembly: hg38
Supplementary files format and content: Peak calls

source_name: cell line

value: cell line

value: RIVA

value: B-cell lymphoma ABC-DLBCL

tag: genotype

value: Arid1a WT

tag: antibody

value: IgG


title: Patient_7_MS19-293000A1_DSP.1012550003362.B04

description: Whole Transcriptome Atlas

value: 62 years

value: Glomeruli

value: kidney


title: abdominal; EVD; F62a

source_name: Stratagene Human Universal Reference, 10 ug labeled aRNA

value: reference:Stratagene Human Universal Reference

source_name: abdominal; EVD; F62a, 10 ug labeled aRNA


title: IgG_WT_2 (CnR Run B)

description: CnR Run B


title: Patient_7_MS19-293000A1_DSP.1012550003362.A06

description: Whole Transcriptome Atlas


title: Patient_7_MS19-293000A1_DSP.1012550003362.A07

description: Whole Transcriptome Atlas


title: Patient_7_MS19-293000A1_DSP.1012550003362.A05

description: Whole Transcriptome Atlas


title: abdominal; EVD; F62

source_name: abdominal; EVD; F62, 10 ug labeled aRNA


title: IgG_WT_1 (CnR Run B)

description: CnR Run B


title: Patient_7_MS19-293000A1_DSP.1012550003362.A04

description: Whole Transcriptome Atlas


title: Patient_7_MS19-293000A1_DSP.1012550003362.A03

description: Whole Transcriptome Atlas


title: Patient_7_MS19-293000A1_DSP.1012550003362.A02

description: Whole Transcriptome Atlas


title: abdominal; EVD; F33

source_name: abdominal; EVD; F33, 10 ug labeled aRNA


title: IgG_HET_3 (CnR Run B)

description: CnR Run B

value: Arid1a HET


title: Patient_8_20-B-01096_DSP.1012550001423.F12

description: Whole Transcriptome Atlas

source_name: kidney

value: 6 years

value: Male


title: Patient_8_20-B-01096_DSP.1012550001423.G01

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.F11

description: Whole Transcriptome Atlas


title: IgG_HET_1 (CnR Run B)

description: CnR Run B


title: abdominal; EVD; F43

source_name: abdominal; EVD; F43, 10 ug labeled aRNA


title: Patient_9_MS20-16418A13_DSP.1012550003362.B05

description: Whole Transcriptome Atlas

value: 56 years


title: abdominal; EVD; F66

source_name: abdominal; EVD; F66, 10 ug labeled aRNA

value: F


title: Patient_8_20-B-01096_DSP.1012550001423.F10

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.F08

description: Whole Transcriptome Atlas

value: Tubules


title: BN1053, Rep1, GFP::Dam

city: Seville

first: Peter

last: Askjaer

address: UPO Carretera de Utrera km 1

country: Spain

institute: Centro Andaluz de Biología del Desarrollo

data_processing:
FASTQ files from the NextSeq500 platform were processed in R Studio using the pipelines RDamIDSeq (https://github.com/damidseq/RDamIDSeq) and RGeneDamIDSeq (https://github.com/damidseq/-RGeneDamIDSeq-) (Sharma et al. 2016) for mapping of reads to bins of fixed size (e.g. 2 kb, 10 kb or 100 kb) and to genes, respectively. The pipelines include a quality check where only reads that contain the DamID adapter (“CGCGGCCGAG”) and map to GATC sites in the C. elegans genome are retained for further analysis. The number of reads fulfilling these criteria ranged from 0.5 to 9 million (see Supplementary Table S7). Both pipelines also provide mapped read numbers per individual GATC fragment. For mapping to genes, the script was modified to include 500 bp distal to transcriptional start and termination sites. UCSC genome version ce11 (BSgenome.Celegans.UCSC.ce11) was used for alignment.
The DESeq2 package (Love et al. 2014) was used to identify bins with significantly more reads with either Dam::BAF-1  or Dam::BAF-1(G12T) compared to GFP::Dam across the 3 replicas. A false discovery rate (FDR) of 0.05 was used as threshold. Next, for each sample a pseudocount of 1 was added to each bin and the relative number of reads per bin was calculated followed by averaging across the replicas. The ratio of Dam::BAF-1  or Dam::BAF-1(G12T) to GFP::Dam was calculated for each bin and log2-transformed. Finally, normalization was done by subtracting the genome-wide average log2 ratio from the log2 ratio of each bin (Brueckner et al. 2020).
Assembly: ce11
Supplementary files format and content: Files contain columns for gene names (except in 2 kb bin files), coordinates, log2 values (Dam::BAF-1/GFP::Dam or Dam::BAF-1(G12T)/GFP::Dam)(average and individual replicas), bin (or gene) number and padj value.

organism: Caenorhabditis elegans

source_name: Intestine

growth_protocol: Worms were grown asynchronically at 20C on NGM plates seeded with E. coli GM119 for at least two generations before egg-prepping with hypochlorite. Hatched L1s were counted the day after and 1000 L1s were aliquoted onto 10 cm NGM plates seeded with E. coli GM119 as described above. Worms were grown at 20C for 48 h before collecting 4000 L4 stage nematodes per strain and washed 8 times with 15 ml of M9 with 0.01% Tween-20. Worms were transferred to 1.5 ml tubes with M9 with 0.01% Tween-20 using Pasteur pipettes followed by two additional washes. Supernatants were aspirated and aliquots of 30 µl were snap frozen in liquid nitrogen and maintained at -80C until DNA extraction.

extract_protocol:
To purify genomic DNA, samples were lysed in 5 freeze/thaw cycles (1min in liquid nitrogen; 3min in 37C shaker) and processed with DNeasy Blood and Tissue Kit (QIAGEN #69504).
DamID was performed on 400 ng genomic DNA  extracted from 4000 L4 animals cultured and collected as indicated above. Three replicates were performed as described (de la Cruz Ruiz et al. 2022), using primer AdR (5'-NNNNGTGGTCGCGGCCGAGGATC) and 22 PCR cycles. Successful amplification of Dam-methylated genomic DNA yielded a smear of ~400-~1500 bp fragments when analyzed on Agilent Bioanalyzer. 400 ng of PCR amplified fragments were used for library preparation as described (de la Cruz Ruiz et al. 2022), using E7370 NEBNext® Ultra™ DNA Library Prep Kit for Illumina. Library amplicons’ size distribution was checked to be maintained as for PCR fragments indicated above followed by pooling, repurification and sequencing on a Illumina NextSeq500 platform at EMBL GeneCore.

value: Intestine


title: Patient_8_20-B-01096_DSP.1012550001423.F09

description: Whole Transcriptome Atlas


title: MuSCs, TAM, H3K9Me3, rep1

status: Public on Mar 23 2024

city: Lyon

first: Pauline

last: GARCIA

address: 8 avenue Rockefeller

country: France

institute: INMG

data_processing:
Nf-core/chipseq v2.0.0 was used on a singularity container, in standard and custom parameters to compute a rds archive readable in R and different files in multiple formats (bigwig, bed, bam, broadpeak). BWA aligner v0.7.17-r1188 was used, the read length used to calculate MACS2 genome size for peak calling was 50bp and the broad cutoff was 0.1.
Broadpeak output files were used to identify broad regions specific to one condition or both. Regions were annotated with ChIPseeker (v1.30.3) from TxDB.Mmusculus.UCSC.mm10.knownGene : the region range of TSS was [-2500;2500].
To determine the nearest repeat element to regions, distances were calculated by distanceToNearest function from GenomicRanges, references used from UCSC rmsk database. Visualization of regions with broadpeak in control-condition and absent broadpeak in KO-condition were managed by Gviz package (v1.38.4).
Assembly: Mus Musculus
Supplementary files format and content: H3K9me3_KO_REP2_peaks.broadPeak
Supplementary files format and content: H3K9me3_WT_REP2_peaks.broadPeak

organism: Mus musculus

source_name: Muscle

growth_protocol: Cells were maintained in growth medium before the experiment.

extract_protocol:
Around 1 × 10^7 cells were col- lected, washed with PBS and resuspended in 250ul of ice- cold Douncing buffer (10 mM Tris-HCl (pH 7.5), 4 mM MgCl2 , 1 mM CaCl2 , 0.2% Triton X100), followed by ho- mogenization with syringe with 26 gauge X1/2 needles (BD Microlance; Cat#: BD 303800). To obtain mononu- cleosomes, cells were digested with 1.25 ul of micrococ- cal nuclease (Mnase) (0.5 U/ul; Sigma-Aldrich; Cat#: N3755-500UN) for 5 min at 37C with 600 rpm. The reaction was stopped with 10 mM EDTA, pH 8. Nu- clei were swollen to release chromatin after addition of Hypotonization buffer (0.2 mM EDTA (pH 8), FPIC (Fast Protease Inhibitors cocktail; Sigma-Aldrich; Cat#: S8830-20TAB), DTT). Chromatin corresponding to 8 ug of DNA was incubated with anti-H3K9me3 (Diagenode; Cat#: C15410193), anti-H3K27me3 (Diagenode; Cat#: C15410069), anti-H3K27ac (Diagenode; Cat#: C15410196) or anti-H3K4me3 (Diagenode; Cat#: C15410003) antibod- ies overnight at 4C. The DNA protein antibody com-plexes were captured by DiaMag protein A-coated mag- netic beads (Diagenode; Cat#: C03010020) by incubating at 4C for 2 h. Magnetic beads were then washed with Low- Salt buffer (20 mM Tris?HCl (pH 8), 0.1% SDS, 1% Tri- ton X100, 2 mM EDTA (pH 8), 150 mM NaCI and FPIC) and High-Salt buffer (20 mM Tris?HCl (pH 8), 0.1% SDS, 1% Triton X100, 2 mM EDTA (pH 8), 500 mM NaCI and FPIC). DNA was eluted with TE buffer (100 mM Tris-HCl (pH 8), 1% SDS, 1 mM EDTA (pH 8)) from the beads overnight, inputs corresponding to 1% of IP were treated as well, followed by incubation with 1 _x0002_l of RNase A (10 ug/ml; Sigma-Aldrich; Cat#: R4642) for 1 h. DNA was pu- rified using MinElute PCR Purification Kit (Qiagen; Cat#: 28004).
Libraries were prepared using the MicroPlex V2 library preparation Kit (Diagenode; Cat#: C05010012), following the manufacturer's instructions, 10ul of DNA was used as starting material. After end repair of the double-stranded DNA templates, cleavable stem-loop adaptors were ligated, and then adaptor enriched DNA was amplified with 10 PCR cycles to add Illumina compatible indexes. The li- braries were then purified with the Agencourt AMPure XP bead-based purification system. Final libraries were quan- tified with Qubit dsDNA HS assay (Thermo Fisher; Cat#: Q32851), and size distribution was monitored by capillary electrophoresis on Agilent 2100 Bioanalyzer using DNA High Sensitivity HS Kit. Libraries were then normalized to 10 pM and pooled before sequencing. Libraries were sequenced on an Illumina Nextseq 500 in a paired-end mode in two independent biological replicates at Platform GENOM IC Institute Cochin.

treatment_protocol: Cells were treated with either Ethanol or 4-Hydroxytamoxifen in order to induce Setdb1 deletion.

value: Muscle

value: primary cell line

value: Muscle stem cells

tag: treatment

tag: chip antibody


title: abdominal; EVD; F24a

source_name: abdominal; EVD; F24a, 10 ug labeled aRNA

value: abdominal

value: EVD


title: IgG_WT_3 (CnR Run A)

description: CnR Run A

value: cell line

value: RIVA

value: B-cell lymphoma ABC-DLBCL

value: Arid1a WT

value: IgG


title: abdominal; EVD; M38

value: reference:Stratagene Human Universal Reference

source_name: abdominal; EVD; M38, 10 ug labeled aRNA

value: M


title: Patient_8_20-B-01096_DSP.1012550001423.F07

description: Whole Transcriptome Atlas

value: 6 years

value: Male

value: kidney


title: IgG_WT_2 (CnR Run A)

description: CnR Run A


title: IgG_WT_1 (CnR Run A)

description: CnR Run A


title: abdominal; EVD; F38

source_name: abdominal; EVD; F38, 10 ug labeled aRNA

value: F


title: Patient_8_20-B-01096_DSP.1012550001423.F02

description: Whole Transcriptome Atlas

value: Tubules


title: IgG_HET_4 (CnR Run A)

description: CnR Run A

value: Arid1a HET


title: Patient_8_20-B-01096_DSP.1012550001423.E12

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.F01

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.F03

description: Whole Transcriptome Atlas


title: IgG_HET_2 (CnR Run B)

description: CnR Run B


title: Patient_8_20-B-01096_DSP.1012550001423.F05

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.E09

description: Whole Transcriptome Atlas


title: abdominal; EVD; F37

source_name: abdominal; EVD; F37, 10 ug labeled aRNA


title: IgG_WT_4 (CnR Run A)

description: CnR Run A


title: Patient_8_20-B-01096_DSP.1012550001423.E11

description: Whole Transcriptome Atlas


title: IgG_HET_3 (CnR Run A)

description: CnR Run A


title: Patient_8_20-B-01096_DSP.1012550001423.E07

description: Whole Transcriptome Atlas

value: Glomeruli


title: IgG_HET_1 (CnR Run A)

description: CnR Run A


title: abdominal; EVD; M60

source_name: abdominal; EVD; M60, 10 ug labeled aRNA


title: Patient_8_20-B-01096_DSP.1012550001423.E03

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.F06

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.E10

description: Whole Transcriptome Atlas


title: H3K27me3_WT_1

description: CnR Run A


title: abdominal; EVD; F52f

source_name: abdominal; EVD; F52f, 10 ug labeled aRNA


title: H3K27me3_HET_2

description: CnR Run A


title: IgG_HET_2 (CnR Run A)

description: CnR Run A


title: abdominal; EVD; F31b

source_name: abdominal; EVD; F31b, 10 ug labeled aRNA


title: Patient_8_20-B-01096_DSP.1012550001423.E08

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.F04

description: Whole Transcriptome Atlas


title: Patient_2_19-B-01500_DSP.1012550001423._D09

description: Whole Transcriptome Atlas

value: 9 years

value: Female


title: Patient_8_20-B-01096_DSP.1012550001423.E06

description: Whole Transcriptome Atlas


title: H3K27ac_FL_Shox2trac_E135_INACTIVE_rep1

city: Geneva

first: Guillaume

last: Andrey

address: Rue Michel-Servet 1

department: Department of Genetic Medicine and Development

country: Switzerland

institute: University of Geneva

description: sorted cells ChIP-seq

data_processing:
TruSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -q30 -m15). Reads were then mapped to mm39_dsmCherry_P2A_CRE_EYFP custome genome using Bowtie2 v2.3.5.1 with default parameters. Reads were then filtered for a MAPQ≥30 using Samtools view v1.10 and the coverage was obtained after extension of the reads by 200 bp using MACS2 v2.2.7.1 (callpeak --nomodel --call-summits --extsize 200). Coverage was normalized by the number of million tags used by MACS2. broad peak calling was performed by MACS2 using the following parameters --broad --nolambda --broad-cutoff 0.05 --nomodel --gsize mm --extsize 200 -B 2.
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: BigWig + MACS2 broadPeaks

source_name: Embryonic Forelimb

growth_protocol: Forelimbs and Hindlimbs from E10.5, E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal.

extract_protocol:
After sorting, cells were centrifuged for 5’ at 400g at 4°C and supernatant was discarded. Cells for ChIP-seq were resuspended in 10% FCS/PBS and fixed in 1% PFA at room temperature. The fixation was blocked by the addition of 1M glycine, cells were isolated by centrifugation (1000g, at 4°C for 8’), resuspended in cold lysis buffer (10 mM Tris, pH 7.5, 10 mM NaCl, 5 mM MgCl2, 1mM EGTA, Protease Inhibitor (Roche, 04693159001)) and incubated on ice for 10’ to isolate the cell nuclei. The nuclei were isolated by centrifugation (1000g, at 4°C for 3’), washed in cold 1X PBS, centrifuged again (1000g, at 4°C for 1’) and stored frozen at -80°C after removal of the PBS supernatant.
500000 fixed nuclei were sonicated to a 200-500bp length with the Bioruptor Pico sonicator (Diagenode). H3K27Ac ChIP was (Diagenode C15410174) was performed as previously described (Lee et al. 2006; Rouco et al. 2021) with the addition of 5mM of Na-Butyrate to all buffers. Libraries were then prepared following the Illumina ChIP TruSeq protocol and sequenced as 50bp single-end reads on an Illumina NovaSeq 6000. Libraries were prepared starting with below <10ng quantities of ChIP-enriched DNA as starting material and processed with the Illumina TruSeq ChIP kit according to manufacturer specifications. Libraries were validated on a Tapestation 2200 (Agilent) and a Qubit fluorimeter (Invitrogen – Thermofisher Scientific). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000 sequencer.

tag: background

value: Embryonic Forelimb

tag: embryonic stage

tag: facs-sorted status

value: dmCherry-/EYFP-

tag: biological replicate


title: Patient_8_20-B-01096_DSP.1012550001423.E04

description: Whole Transcriptome Atlas

tag: roi

tag: segment


title: H3K27ac_FL_Shox2trac_E125_INACTIVE_rep1

description: sorted cells ChIP-seq


title: H3K27me3_WT_2

description: CnR Run A

source_name: cell line

value: cell line

value: RIVA


title: PU1_WT_2

description: CnR Run A

value: B-cell lymphoma ABC-DLBCL

value: Arid1a WT


title: Patient_8_20-B-01096_DSP.1012550001423.E02

description: Whole Transcriptome Atlas

tag: age


title: PU1_WT_1

description: CnR Run A


title: H3K27ac_HL_Shox2trac_E135_DECOM_rep1

description: sorted cells ChIP-seq

source_name: Embryonic Hindlimb

value: Embryonic Hindlimb

value: dmCherry-/EYFP+


title: H3K27me3_HET_1

description: CnR Run A


title: Patient_2_19-B-01500_DSP.1012550001423._D11

description: Whole Transcriptome Atlas


title: PU1_HET_2

description: CnR Run A


title: Patient_2_19-B-01500_DSP.1012550001423._D12

description: Whole Transcriptome Atlas


title: Patient_2_19-B-01500_DSP.1012550001423._D04

description: Whole Transcriptome Atlas


title: Patient_2_19-B-01500_DSP.1012550001423.E01

description: Whole Transcriptome Atlas


title: Patient_2_19-B-01500_DSP.1012550001423._D10

description: Whole Transcriptome Atlas


title: Patient_2_19-B-01500_DSP.1012550001423._D03

description: Whole Transcriptome Atlas


title: Patient_8_20-B-01096_DSP.1012550001423.E05

description: Whole Transcriptome Atlas

value: 6 years


title: PU1_HET_1

description: CnR Run A


title: Patient_2_19-B-01500_DSP.1012550001423._D07

description: Whole Transcriptome Atlas


title: Patient_5_19-B-01576_DSP.1012550001423._D01

description: Whole Transcriptome Atlas

value: 25 years

value: Male


title: Patient_2_19-B-01500_DSP.1012550001423._D06

description: Whole Transcriptome Atlas

value: kidney


title: H3K27ac_FL_Shox2trac_E115_INACTIVE_rep1

description: sorted cells ChIP-seq


title: H3.3-active_WT_3

description: CnR Run B


title: H3K27ac_HL_Shox2trac_E135_MAINTAIN_rep1

description: sorted cells ChIP-seq

value: dmCherry+/EYFP+


title: Patient_5_19-B-01576_DSP.1012550001423.C11

description: Whole Transcriptome Atlas

value: Tubules


title: H3.3-active_WT_2

description: CnR Run B


title: Patient_2_19-B-01500_DSP.1012550001423._D05

description: Whole Transcriptome Atlas

value: Glomeruli


title: Patient_5_19-B-01576_DSP.1012550001423.C10

description: Whole Transcriptome Atlas


title: H3K27ac_HL_Shox2trac_E115_MAINTAIN_rep1

description: sorted cells ChIP-seq


title: H3.3-active_WT_1

description: CnR Run B


title: H3K27ac_FL_Shox2trac_E135_MAINTAIN_rep1

description: sorted cells ChIP-seq


title: Patient_5_19-B-01576_DSP.1012550001423.C06

description: Whole Transcriptome Atlas


title: Patient_5_19-B-01576_DSP.1012550001423.C07

description: Whole Transcriptome Atlas


title: H3.3-active_HET_3

description: CnR Run B

value: Arid1a HET


title: H3.3-active_HET_2

description: CnR Run B


title: Patient_2_19-B-01500_DSP.1012550001423._D02

description: Whole Transcriptome Atlas

value: 9 years

value: Female


title: H3K27ac_FL_Shox2trac_E115_MAINTAIN_rep1

description: sorted cells ChIP-seq

value: Embryonic Forelimb


title: Patient_5_19-B-01576_DSP.1012550001423.C05

description: Whole Transcriptome Atlas


title: H3.3-active_HET_1

description: CnR Run B

value: cell line


title: H3K27ac_FL_Shox2trac_E115_DECOM_rep1

description: sorted cells ChIP-seq


title: Patient_5_19-B-01576_DSP.1012550001423.C12

description: Whole Transcriptome Atlas


title: Patient_4_20-B-00423_DSP.1012550001423.C02

description: Whole Transcriptome Atlas

value: 21 years


title: H3K27ac_FL_Shox2trac_E105_MAINTAIN_rep1

description: sorted cells ChIP-seq


title: Patient_4_20-B-00423_DSP.1012550001423.C01

description: Whole Transcriptome Atlas


title: Patient_2_19-B-01500_DSP.1012550001423._D08

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E125_MAINTAIN_rep2

description: sorted cells RNA-seq

data_processing:
NextSeq adapter sequences and bad quality bases were removed using CutAdapt v1.18 (-a CTGTCTCTTATACACATCTCCGAGCCCACGAGAC -q30 -m15). Unstranded reads were then mapped to the custom genom mm39_dsmCherry_P2A_CRE_EYFP. We used STAR v2.7.2b with a filtered GTF allowing to get a gene quantification simultaneously (--outSAMstrandField intronMotif --sjdbOverhang '99' --sjdbGTFfile $gtfFile --quantMode GeneCounts --outFilterType BySJout --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverReadLmax 0.04 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --alignSJoverhangMin 8 --alignSJDBoverhangMin 1). FPKM values were determined by Cufflinks v2.2.1 (--max-bundle-length 10000000  --max-bundle-frags 100000000 -- multi-read-correct --library-type “fr-firststrand” --no-effective-length-correction -M MTmouse.gtf). Normalized FPKM were then computed by determining coefficients extrapolated from a set of 1000 house-keeping stably expressed genes, in between the series of compared RNA-seq datasets. Coverage was computed with Bedtools v2.28.0 using uniquely mapped reads (NH:i:1 tag). When indicated, coverage profiles represent an average of the replicates, this was done by dividing each replicate by the number of millions of uniquely mapped reads (for normalization) and calculating the average coverage.
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: BigWig

molecule: polyA RNA

growth_protocol: Forelimbs and Hindlimbs from E10.5, E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal. Also entire forelimbs from E10.5, E11.5 and E14.5 Shox2trac embryos, entire forelimbs at E10.5 and E14.5 from Shox2Δearly embryos and entire forelimbs from E11.5 and E14.5 Shox2Δlate embryos were microdissected in PBS and dissociated in a cell suspension.

extract_protocol:
Forelimbs and Hindlimbs sorted cells and entire forelimbs cell suspession were centrifuged for 5’ at 400g at 4°C, supernatant was discarded and cells frozen at -80°C. Total RNA was isolated using the RNeasy Micro Kit (QIAGEN, ID:74004) following manufacturer’s instructions and then stored frozen at -80°C. Total RNA was quantified with a Qubit (fluorimeter from Life Technologies) and RNA integrity assessed with a Bioanalyzer (Agilent Technologies).
The SMART-Seq v4 kit from Clontech, (#634893) was used for the reverse transcription and cDNA amplification according to manufacturer’s specifications, starting with 5 ng of total RNA as input. 200 pg of cDNA were used for library preparation using the Nextera XT kit from Illumina, FC-131-1096. Library molarity and quality was assessed with the Qubit and Tapestation using a DNA High sensitivity chip (Agilent Technologies). Libraries were pooled at 2 nM and loaded for clustering on a Single-read Illumina Flow cell for an average of 35 mio reads / library. Reads of 50 bases were generated using the TruSeq SBS chemistry on an Illumina HiSeq 4000 or Illumina NovaSeq 6000 sequencer.


title: SMARCC1_WT_3

description: CnR Run B

value: RIVA

value: B-cell lymphoma ABC-DLBCL


title: SMARCC1_WT_2

description: CnR Run B

value: Arid1a WT


title: Patient_4_20-B-00423_DSP.1012550001423.B11

description: Whole Transcriptome Atlas


title: H3K27ac_FL_Shox2trac_E125_MAINTAIN_rep1

description: sorted cells ChIP-seq


title: HL_Shox2trac_E125_MAINTAIN_rep1

description: sorted cells RNA-seq

value: Embryonic Hindlimb


title: Patient_5_19-B-01576_DSP.1012550001423.C08

description: Whole Transcriptome Atlas


title: Patient_5_19-B-01576_DSP.1012550001423.C04

description: Whole Transcriptome Atlas


title: Patient_6_18-B-02912_DSP.1012550001423.B08

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E125_INACTIVE_rep2

description: sorted cells RNA-seq

value: dmCherry-/EYFP-


title: Patient_6_18-B-02912_DSP.1012550001423.B10

description: Whole Transcriptome Atlas


title: Patient_6_18-B-02912_DSP.1012550001423.B09

description: Whole Transcriptome Atlas


title: SMARCC1_HET_2

description: CnR Run B


title: Patient_6_18-B-02912_DSP.1012550001423.B07

description: Whole Transcriptome Atlas


title: Patient_4_20-B-00423_DSP.1012550001423.C03

description: Whole Transcriptome Atlas


title: SMARCC1_WT_1

description: CnR Run B


title: SMARCC1_HET_3

description: CnR Run B


title: Patient_6_18-B-02912_DSP.1012550001423.B05

description: Whole Transcriptome Atlas


title: Patient_6_18-B-02912_DSP.1012550001423.B06

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E125_INACTIVE_rep1

description: sorted cells RNA-seq


title: Patient_5_19-B-01576_DSP.1012550001423.C09

description: Whole Transcriptome Atlas

value: 25 years


title: Patient_6_18-B-02912_DSP.1012550001423.B03

description: Whole Transcriptome Atlas


title: Patient_6_18-B-02912_DSP.1012550001423.B04

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E125_DECOM_rep1

description: sorted cells RNA-seq

value: dmCherry-/EYFP+


title: HL_Shox2trac_E125_DECOM_rep2

description: sorted cells RNA-seq


title: SMARCC1_HET_1

description: CnR Run B


title: BRD9_WT_3

description: CnR Run B


title: Patient_4_20-B-00423_DSP.1012550001423.B12

description: Whole Transcriptome Atlas

value: Male

value: kidney


title: Patient_1_18-B-00496_DSP.1012550001423.B01

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E115_MAINTAIN_rep2

description: sorted cells RNA-seq

value: dmCherry+/EYFP+


title: Patient_6_18-B-02912_DSP.1012550001423.B02

description: Whole Transcriptome Atlas

value: Glomeruli


title: Patient_1_18-B-00496_DSP.1012550001423.A12

description: Whole Transcriptome Atlas

value: Tubules


title: mESC_Dnmt3ab_Setd2_tKO_H3K4me3_rep2

city: Beijing

first: Bofeng

last: Liu

address: Haidian District

department: School of Life Science

country: China

institute: Tsinghua University

description: STAR ChIP-seq

data_processing:
Basecalls performed using CASAVA version 1.8.
STAR ChIP-seq reads were aligned to the mm9 genome using bowtie 2.2.2. Replicates of same stage were pooled together and rpkm in wiggle files were counted by the number of reads falling into 100bp bin in the genome.
Assembly: mm9
Supplementary files format and content: bigWig files

source_name: Embryonic stem cell

extract_protocol: STAR ChIP-seq was performed as previously described (Zhang et al., 2016). Briefly, samples were lysed followed by fragmented by micrococcal nuclease (MNase, Sigma, N3755-200UN) at 37 °C for 5 min. After being terminated, the supernatant containing chromatin was incubated with the primary antibody at 4 °C overnight with rotation. The next day, 100 μg of Protein A/G dynabeads (mixed at 1:1, Thermo Fisher Scientific) was added to each sample and incubated at 4 °C for 2–3 h with rotation. The beads were then washed five times with 150 μl RIPA buffer and once with 150 μl LiCl buffer. For each sample, beads were resuspended with 28 μl H2O, 1 μl 10× Ex-Taq buffer (Takara, RR006B) and 1 μl proteinase K (NEB, P8107S) and incubated at 55 °C for 90 min, followed by incubation at 72 °C for 40 min to inactivate the proteinase K. Samples were then subjected to Truseq library preparation using NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). STAR ChIP-seq libraries were sequenced using the HiSeq X Ten system or NovaSeq (Illumina) according to the manufacturer’s protocol.

value: Embryonic stem cell

value: Dnmt3a/b KO

tag: developmental stage

value: H3K27ac (Active Motif 39133)


title: Patient_1_18-B-00496_DSP.1012550001423.A09

description: Whole Transcriptome Atlas

value: 9 years


title: BRD9_WT_1

description: CnR Run B

value: cell line


title: Patient_1_18-B-00496_DSP.1012550001423.A11

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E115_MAINTAIN_rep1

description: sorted cells RNA-seq


title: BRD9_WT_2

description: CnR Run B

value: RIVA


title: Patient_1_18-B-00496_DSP.1012550001423.A07

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E115_LowEYFP_rep1

description: sorted cells RNA-seq


title: HL_Shox2trac_E115_INACTIVE_rep2

description: sorted cells RNA-seq


title: Patient_1_18-B-00496_DSP.1012550001423.A08

description: Whole Transcriptome Atlas


title: BRD9_HET_3

description: CnR Run B

value: B-cell lymphoma ABC-DLBCL

value: Arid1a HET


title: Patient_1_18-B-00496_DSP.1012550001423.A06

description: Whole Transcriptome Atlas


title: Patient_1_18-B-00496_DSP.1012550001423.A05

description: Whole Transcriptome Atlas


title: HL_Shox2trac_E115_Interm_rep1

description: sorted cells RNA-seq

value: Embryonic Hindlimb


title: TR

city: Rome

first: Gerardo

last: Pepe

address: via della ricerca scientifica

country: Italy

institute: Tor Vergara University

data_processing:
Paired-end reads were produced with a 100x coverage, and a median of 40 M reads per sample.
The raw data were analyzed by Next Generation Diagnostics srl Cancer haemo Exome pipeline (v1.0) which involves a cleaning step by UMI removal, quality filtering and trimming, alignment to the reference genome, removal of duplicate reads and variant calling.
Illumina NovaSeq 6000 base call (BCL) files were converted into fastq files through bcl2fastq (2019) (version v2.20.0.422). UMI removal was carried out with UMI-tools 1.1.1. Data quality control was performed with FastQC v.0.11.9 and reads were trimmed and cleaned using Trimmomatic 0.38.
Alignment to human reference (hg38, GCA_000001405.15), deduplication, and variant calling were performed with Sentieon 202011.01.
Gene counts tables were generated from bam files using Rsubread v. 2.8.2.
Assembly: hg38, GCA_000001405.15
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample

source_name: Peripheral blod

extract_protocol:
RNA was extracted from PBMCs using the RNeasy Mini Kit (Qiagen, Germany), retro-transcribed in cDNA and quantified using the Qubit 4.0 fluorimetric Assay (Thermo Fisher Scientific) and sample integrity, based on the DIN (DNA integrity number), was assessed using a Genomic DNA ScreenTape assay on TapeStation 4200 (Agilent Technologies)
Genomic DNA was Libraries were prepared from 100 ng of total DNA using the NEGEDIA Cancer Haemo Exome sequencing service (Next Generation Diagnostic srl)

value: Peripheral blod

tag: subject status

value: treatment naïve patients with de novo FLT3 ITD driven-AML diagnosis

value: PBMCs


title: ARID1A_WT_3

description: CnR Run B

value: Arid1a WT


title: BRD9_HET_2

description: CnR Run B


title: SE


title: ARID1A_WT_2

description: CnR Run B


title: Patient_1_18-B-00496_DSP.1012550001423.A04

description: Whole Transcriptome Atlas

source_name: kidney

tag: Sex

value: Male

value: kidney


title: Patient_1_18-B-00496_DSP.1012550001423.A03

description: Whole Transcriptome Atlas

value: Glomeruli

tag: tissue


title: BRD9_HET_1

description: CnR Run B

tag: cell line


title: RL.2

tag: cell type


title: Patient_1_18-B-00496_DSP.1012550001423.A10

description: Whole Transcriptome Atlas

value: Tubules


title: SF


title: HL_Shox2trac_E115_DECOM_rep2

description: sorted cells RNA-seq

tag: genotype

value: dmCherry-/EYFP+


title: NG


title: RL.1


title: SM


title: ARID1A_HET_3

description: CnR Run B

tag: antibody


title: HL_Shox2trac_E115_dmCherry_rep1

description: sorted cells RNA-seq

value: dmCherry+/EYFP-


title: MD


title: LS


title: HL_Shox2trac_E115_INACTIVE_rep1

description: sorted cells RNA-seq

value: dmCherry-/EYFP-


title: Patient_1_18-B-00496_DSP.1012550001423.A02

description: Whole Transcriptome Atlas

value: 9 years


title: FF


title: HL_Shox2trac_E105_MAINTAIN_rep2

description: sorted cells RNA-seq

value: dmCherry+/EYFP+


title: ARID1A_HET_2

description: CnR Run B

value: cell line

value: RIVA


title: FE


title: HL_Shox2trac_E115_dmCherry_rep2

description: sorted cells RNA-seq


title: DNF


title: ARID1A_HET_1

description: CnR Run B

value: B-cell lymphoma ABC-DLBCL

value: Arid1a HET


title: DN

value: Peripheral blod


title: HL_Shox2trac_E105_MAINTAIN_rep1

description: sorted cells RNA-seq

value: Embryonic Hindlimb


title: pSM33 cells, 10min 5EU feed

city: Pasadena

first: Mitchell

last: Guttman

address: 1200 E. California Blvd

department: Biology and Biological Engineering

institute: California Institute of Technology

data_processing:
Align RNA to mm10 using STAR-2.5.3a
Count spliced and unspliced reads via kallisto-bustools workflow (Melsted, P. et al. Nat Biotechnol 39, 813–818 (2021))
Assembly: mm10
Supplementary files format and content: comma separated file of kallisto counts

growth_protocol: MaleES cells were grown on plates coated with 0.2% gelatin and 3.5 ug/mL laminin in serum-free 2i/LIF media composed as follows: 1:1 mix of DMEM/F-12 (Gibco) and Neurobasal (Gibco) supplemented with 1X N2 (Gibco), 0.5X B-27 (Gibco 17504-044), 2 mg/mL bovine insulin (Gemini BioSciences), 1.37 ug/mL progesterone (Sigma), 5 mg/mL BSA Fraction V (Gibco), 0.1 mM 2-mercaptoethanol (Sigma), 5 ng/mL murine LIF (GlobalStem), 0.1 uM PD0325901 (Axon Medchem 1408) and 0.3 uM CHIR99021 (University of Dundee Division of Signal Transduction Therapy).

extract_protocol:
Total RNA was harvested using RNeasy Minikit (QIAGEN). 5EU-labeled RNA was biotinylated by mixing samples with water, 100mM HEPES , 1 mM biotin picolyl azide (Click Chemistry Tools), Ribo Rnase Inhibitor, premixed 2mM CuSO4 and 10mM THPTA, and finally 12mM sodium ascorbate. Biotinylated RNA was then captured as follows: MyOne Streptavidin C1 Dynabeads (ThermoFisher Scientific) were first washed three times in Urea buffer (10mM HEPES, pH 7.5, 10mM EDTA, 0.5M LiCl, 0.5% Triton X-100, 0.2% SDS, 0.1% sodium deoxycholate, 2.5mM TCEP, 4M Urea) followed by three additional washes in M2 buffer (20mM Tris, pH 7.5, 50mM NaCl, 0.2% Triton X-100, 0.2% sodium deoxycholate, 0.2% NP-40). Washed beads were mixed with 3 parts 4M Urea buffer and 1 part biotinylated RNA and incubated for 60 min with 900rpm thermomixer shaking at room temperature. After magnetic separation, beads were washed 3 times with M2 buffer followed by 3 washes with Urea buffer at 37 C at 750rpm for 5 min. RNA was eluted from beads in 2 sequential elutions by incubating with elution buffer (5.7M guanidine thiocyanate, 1% N-lauroylsarcosine; both Sigma) at 65 C for 2 minutes, repeating with more elution buffer for a second elution. The elutions were pooled, diluted with Urea buffer, incubated with pre-washed streptavidin beads, washed, and eluted for 2 additional rounds exactly as described above for a total of 3 sequential captures. Final elutions were pooled, cleaned with Zymo RNA Clean and Concentrate following manufacturer’s protocols (Banerjee et al., 2020).
Captured RNA was used for library construction as previously described in Banerjee et al. 2020.

treatment_protocol: Cells were lifted with TVP (), washed and suspended in 2i/LIF media supplemented with 1mM 5EU (vendor) for 10 minutes shaking at 750 rpm on a Thermomixer (Eppendorf). Cells were then pelleted for extraction.

value: mouse embryonic stem cells

tag: treatment

value: 5EU Feed, 10 minutes


title: ARID1A_WT_1

description: CnR Run B

value: Arid1a WT


title: AR

value: treatment naïve patients with de novo FLT3 ITD driven-AML diagnosis

value: PBMCs


title: HL_Shox2trac_E105_INACTIVE_rep2

description: sorted cells RNA-seq


title: WT-Male-2_S1

city: Clayton

first: Wei

last: Shi

state: Victoria

address: 15 Innovation Walk

department: Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute

country: Australia

institute: Monash University

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.14.1. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 1 in at least one library. Counts were quantile normalized, precision weighted with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
A linear model was fitted to each gene. Empirical Bayes moderated t-statistics were used to assess differences in expression. Raw p values were adjusted to control the global FDR across all comparisons using the ‘global’ option in decideTests function in the limma package. Genes were called differentially expressed (DE) if they achieved a False Discovery Rate (FDR) of 20% or less.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2-FPKM values for each library. The supplementary file, count_table.txt, includes raw read counts for genes in all the libraries.

source_name: Total VAT Treg cells from male Foxp3cre mice, replicate 1

extract_protocol:
RNA extraction from VAT Treg cells was performed following the manufacturer's instructions using the Picopure RNA isolation kit
Libraries were generated following the manufacturer's protocol using the SMART-Seq mRNA LP, Takara Bio

value: male

value: Foxp3cre mice

value: VAT Treg cells, TCRb+CD4+Foxp3YFP+

value: 20-30  week old


title: ATAC_G401_dTAGDCAF5_V1_4h_rep3

city: Memphis

first: Jacquelyn

middle: A

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

description: G401 cells engineered with dTAG system treated with V-1 to degrade DCAF5

data_processing:
Sequenced reads were processed with Trim-Galore tool v0.4.4 and first 15 bp of each read were clipped to avoid GC bias
Reads were then mapped to the human reference genome GRCh37p19 (hg19) with bwa sampe v0.7.17-r119, duplicated reads identified with the bamsormadup tool from biobambam2, and and properly paired and uniquely mapped reads were extracted in BAM format with samtools v1.2
Using bedtools v2.24.0  nucleosome free fragments (defined as fragments <100 bp), were extracted, and MACS2 tool v2.1.1.20160309  was used to call peaks in narrow format with --extsize 200 ---nomodel -q 0.05 flags
Supplementary files format and content: GRCh37p19
Supplementary files format and content: peak (narrowPeak) and normalized coverage bigwig

growth_protocol: McCoy's Medium + 10% FBS

extract_protocol: Active Motif ATAC-Seq Kit Cat # 53150 as per manufacturer instructions

treatment_protocol: 1ug/ml puromycin selection

value: human malignant rhabdoid tumor

value: G401 dTag DCAF5


title: HL_Shox2trac_E105_INACTIVE_rep1

description: sorted cells RNA-seq

value: dmCherry-/EYFP-


title: ATAC_G401_dTAGDCAF5_V1_4h_rep2


title: WT-Female-2_S3

source_name: Total VAT Treg cells from female Foxp3cre mice, replicate 2

value: female


title: ATAC_G401_dTAGDCAF5_DMSO_4h_rep3

description: G401 cells engineered with dTAG system to express tagged-DCAF5, control

value: DMSO (matched to V-1)


title: ATAC_G401_dTAGDCAF5_DMSO_4h_rep2


title: CHiC_HL_Shox2trac_E125_MAINTAIN

description: Shox2 Agilent probes C-HiC

data_processing:
Sequencing reads were mapped to reference genome mm9, filtered and deduplicated using the HiCUP pipeline v0.6.1. The pipeline was set up with Bowtie2 v2.3.4.2 for short read mapping.  In case replicates were available, they were combined before the processing with the HiCUP pipeline. Juicer command line tools v1.9.9 was used to generate binned contact maps from valid and unique reads pairs with MAPQ≥30 and to normalize maps by Knights and Ruiz matrix balancing. For binning and normalization, only the genomic region chr3: 65,000,001-68,500,000 was considered.  Afterwards, KR normalized maps, as well as raw count maps, were exported for 5 kb resolution. Subtraction maps were produced from theKR normalized maps and scaled together across their subdiagonals. CHiC maps of count values, as well as subtraction maps, were visualized as heatmaps in which values above the 99-th  percentile were truncated for visualization purposes.
Assembly: mm9
Supplementary files format and content: Text files indicating interaction frequency of valid pairs of the binned contact map

growth_protocol: Forelimbs and Hindlimbs from E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS. After producing cell suspention, cells were FACS sorted based on the dmCherry and EYFP fluorescent signal.

extract_protocol:
Tissues were homogenized in typsin-EDTA solution, fixed with 2% PFA at room temperature 10 min. Then fixation was halted with 1M glycine and the cells were lysed in custom-made lysis buffer (10mM Tris pH7.5, 10mM NaCl, 5mM MgCl2, 1mM EGTA, Protease Inhibitor, #04693159001). Upon PBS wash, samples were frozen and stored at -80°C. Samples were then digested with DpnII, re-ligated, de-crosslinked and purified.
The 3C-library was then sheared and adaptors were added to the sheared DNA and amplified according to Agilent instructions for Illumina sequencing. The library was hybridized to the custom-designed SureSelect beads and indexed for sequencing (50 to 100 bp paired-end) following Agilent instructions. Libraries were sequenced an Illumina HiSeq 4000 or Illumina NovaSeq 6000 sequencer.

value: dmCherry+/EYFP+


title: HL_Shox2trac_E115_DECOM_rep1

description: sorted cells RNA-seq

value: dmCherry-/EYFP+


title: WT-Female-1_S2


title: ATAC_G401_dTAGDCAF5_DMSO_4h_rep1


title: G401_ATAC_shDCAF5_BRMo14_rep2

description: loss of DCAF5 with ATPase inhibitor BRM014


title: CHiC_HL_Shox2trac_E125_DECOM

description: Shox2 Agilent probes C-HiC

value: Embryonic Hindlimb


title: G401_ATAC_shDCAF5_BRM014_rep1


title: CHiC_FL_Shox2trac_E125_MAINTAIN

description: Shox2 Agilent probes C-HiC

value: Embryonic Forelimb


title: G401_ATAC_shDCAF5_DMSO_rep3

description: loss of DCAF5 with control for ATPase inhibitor BRM014

value: DMSO


title: TbetKO-Male-2_S9

source_name: Total VAT Treg cells from male Tbet/Foxp3cre mice, replicate 2


title: CHiC_FL_Shox2trac_E125_DECOM

description: Shox2 Agilent probes C-HiC


title: G401_ATAC_shCTRL_BRM014_rep3

description: control for loss of DCAF5 with ATPase inhibitor BRM014

value: shCTRL


title: TbetKO-Female-2_S11

source_name: Total VAT Treg cells from female Tbet/Foxp3cre mice, replicate 2


title: G401_ATAC_shDCAF5_DMSO_rep2


title: G401_ATAC_shDCAF5_BRM014_rep3


title: ATAC_G401_dTAGDCAF5_V1_4h_rep1


title: G401_ATAC_shDCAF5_DMSO_rep1


title: TbetKO-Female-1_S10

source_name: Total VAT Treg cells from female Tbet/Foxp3cre mice, replicate 1


title: scMm_Shox2trac_HL_E125_rep2

description: 10x Single cell kit v3.0

data_processing:
10× Genomics Cell Ranger 6.1.2 software was used for Demultiplexing, alignment, filtering barcode, and UMI counting
Assembly: custom genome: mm39_dsmCherry_P2A_CRE_EYFP
Supplementary files format and content: hdf5 read count matrix containing per-molecule information

growth_protocol: Hindlimbs from E10.5, E11.5, E12.5 and E13.5 Shox2trac embryos were microdissected in PBS.

extract_protocol:
Two replicates of hindlimb buds of E10.5, E11.5, and E12.5 and one replicate of E13.5 Shox2trac embryos were micro-dissected and incubated for 8, 9, 12 or 15 min respectively in 400ul of trypsin-EDTA 0.25% (Thermo Fischer Scientific, 25300062),supplemented with 40ul of 5% BSA. During incubation tissues were disrupted by pipetting after the first 6 minutes of incubation and at the end of the rest of the incubation time. Trypsin was then inactivated by adding 2x volume of 5% BSA and single cell suspension was obtained by passing cells in a 40um cell strainer. Cells were then spun at 250g for 5 minutes at 4° and resuspended in 1%BSA in PBS. Cells were then counted using an automatized cell counter and a 1% BSA 700cells/ul suspension was prepared.
Single-cell libraries were prepared using the Chromium Single Cell 3’ GEM, Library & Gel Bead Kit v3.0 or v3.1 following the manufacture’s protocol (10X Genomics, PN-1000075 or PN-1000121). In brief, Single-Cell 3’ Gel Beads were combined with the Master Mix containing single cells, and Partitioning Oil onto Chromium Chip B, to generate Gel Beads in Emulsion (GEMs). Full-length cDNA was produced, during beads incubation, from the poly-adenylated mRNA barcoded. Right after, gel beads were dissolved, cDNA was amplified via PCR. This cDNA was used to construct the library and then sequenced on an Illumina HiSeq 4000 or an Illumina NovaSeq 6000. On average, 7000 cells were loaded on the Chromium Chip and between 25000-35000 mean reads were obtained.

value: entire limb (not sorted)


title: scMm_Shox2trac_HL_E115_rep2

description: 10x Single cell kit v3.0


title: G401_ATAC_shCTRL_BRM014_rep2


title: scMm_Shox2trac_HL_E125_rep1

description: 10x Single cell kit v3.0


title: ST2-2_S13

source_name: ST2+ VAT Treg cells sorted from male Foxp3RFP mice, replicate 2

value: Foxp3RFP mice

value: VAT Treg cells, TCRb+CD4+Foxp3+ST2+


title: G401_ATAC_shCTRL_BRM014_rep1


title: G401_ATAC_shCTRL_DMSO_rep1

description: control sample for loss of DCAF5 and ATPase inhibitor BRM014


title: G401dTAGDCAF5 DMSO 4h H3K27ac AbCam rep2 [2585564]

description:
dTag DCAF5 DMSO 4h ChIP for H3K27ac
2585564_G401dTAGDCAF5_DMSO_4h_H3K27ac_AbCam_rep2_hg19

data_processing:
Raw reads in fastq format were processed with Trim-Galore tool (v0.4.4, Krueger F. (2012)
Reads were mapped to human-drosophila reference hybrid genome (merged hg19/GRCh37.p13 and dm6 genomes) with bwa aln, followed by bwa samse (v0.7.12-r1039, PMID: 19451168)
Reads mapping to human reference genome were extracted for further analysis using samtools, duplicated reads were marked with bamsormadup tool from biobambam2 (v2.0.87, DOI: 10.1186/1751-0473-9-13) and Cross-Correlation analysis was conducted with SPP (v1.11, PMID: 19029915)
Uniquely mapped reads were then extracted with samtools, extended with bedtools (v2.24.0, PMID: 20110278) using the fragment size value previously estimated with Cross-Correlation analysis, and then converted to bigwig track files by UCSC tools (v4, PMID: 22908213).
Peaks were called using MACS2 (PMID: 18798982) program with –nomodel -q 0.05 flags (high confidence peaks).
Assembly: merged hg19/GRCh37.p13 and dm6
Supplementary files format and content: bigWig, narrowPeak (except for Input sample)

growth_protocol: McCoy's Media + 10% FBS

extract_protocol:
Covaris truCHIP Chromatin Shearing Kit
KAPA Library Prep Kit


title: G401dTAGDCAF5 V1 4h H3K27ac AbCam rep2 [2585566]

description:
Degredation of DCAF5 at 4h ChIP for H3K27ac
2585566_G401dTAGDCAF5_V1_4h_H3K27ac_AbCam_rep2_hg19


title: scMm_Shox2trac_HL_E105_rep2

description: 10x Single cell kit v3.0


title: G401_ATAC_shCTRL_DMSO_rep3


title: Gata3KO-Male-2_S5

source_name: Total VAT Treg cells from male Gata3/Foxp3cre mice, replicate 2

value: male


title: G401_ATAC_shCTRL_DMSO_rep2


title: scMm_Shox2trac_HL_E105_rep1

description: 10x Single cell kit v3.0


title: TbetKO-Male-1_S8

source_name: Total VAT Treg cells from male Tbet/Foxp3cre mice, replicate 1

value: VAT Treg cells, TCRb+CD4+Foxp3YFP+


title: G401dTAGDCAF5 V1 4h H3K27ac AbCam rep1 [2585565]

description:
Degredation of DCAF5 at 4h ChIP for H3K27ac
2585565_G401dTAGDCAF5_V1_4h_H3K27ac_AbCam_rep1_hg19


title: G401dTAGDCAF5 DMSO 4h H3K27ac AbCam rep1 [2585563]

description:
dTag DCAF5 DMSO 4h ChIP for H3K27ac
2585563_G401dTAGDCAF5_DMSO_4h_H3K27ac_AbCam_rep1_hg19


title: ST2-Darya_s_S14

source_name: ST2+ VAT Treg cells sorted from male Foxp3RFP mice, replicate 3

value: 20-30  week old


title: ST2-1_S12

source_name: ST2+ VAT Treg cells sorted from male Foxp3RFP mice, replicate 1


title: Gata3KO-Male-1_S4

source_name: Total VAT Treg cells from male Gata3/Foxp3cre mice, replicate 1


title: G401 dTAG DCAF5 V1 4h BRG1 abcam rep1 [2574946]

description:
Degredation of DCAF5 at 4h ChIP for BRG1
2574946_g401_dTAG_DCAF5_V1_4h_BRG1_abcam_hg19

value: human malignant rhabdoid tumor


title: G401 dTAG DCAF5 DMSO 4h BRG1 abcam rep1 [2574943]

description:
dTag DCAF5 DMSO 4h treated for BRG1
2574943_g401_dTAG_DCAF5_DMSO_4h_BRG1_abcam_hg19

value: G401 dTag DCAF5


title: G401 dTAG DCAF5 V1 4h BAF155 thermo rep1 [2574945]

description:
Degredation of DCAF5 at 4h ChIP for BAF155
2574945_g401_dTAG_DCAF5_V1_4h_BAF155_thermo_hg19


title: G401 dTAG DCAF5 V1 4h ARID1A sigma rep1 [2574944]

description:
Degredation of DCAF5 at 4h ChIP ARID1A
2574944_g401_dTAG_DCAF5_V1_4h_ARID1A_sigma_hg19


title: Gata3KO-Female-1_S6

source_name: Total VAT Treg cells from female Gata3/Foxp3cre mice, replicate 1


title: Synovial macrophage, sham surgical control, 12-week post surgery, rep 4

city: London

first: Tom

last: Appleton

state: Ontario

address: 1151 Richmond Street

country: Canada

institute: Western University

data_processing:
Rstudio Version: 1.2.5001
The program fastp (version 0.20.0) was used to collect QC metrics of the raw reads.
RNA sequences were aligned and sorted by coordinates, to the NCBI rat genome Rattus_Rnor6_V102, using STAR aligner (STAR-2.7.6a).
The removal of alignment duplicates was done with Sambamba (version 0.8.0).
Quantification of genes was performed using featureCounts (v2.0.0).
DESeq2 (v 1.24.0) was used to normalize feature counts and to test for differentially expressed genes.
The HGNC symbols were extracted and added to the DESeq2 results data frame using biomaRt (version 2.40.4) using the rat "rnorvegicus_gene_ensemb" BioMart version "Ensembl Release 102 (November 2020)".
Assembly: NCBI rat genome Rattus_Rnor6_V102
Supplementary files format and content: Comma seperated values format containing normalized count values, statistics, gene ID's and symbols

organism: Rattus norvegicus

source_name: synovial tissue

extract_protocol:
RNA was collected with TRIzol and purified using the Direct-zol RNA MicroPrep Kit (Zymo Research, R2062) as per the manufacturer’s protocol. RNA was analysed using a Qubit 1.0 fluorimeter (Thermo Fisher Scientific) using the Qubit RNA high sensitivity kit (Thermo Fisher Scientific, Q32852); 500ug of RNA with RNA integrity numbers (RIN) of 7.8-9.3 were used for sequencing.
RNA libraries for RNA-seq were prepared using the Illumina stranded total RNA prep kit with Ribo-Zero plus following the manufacturer's protocols.

tag: strain

value: Sprague Dawley

value: wild type

value: Male

tag: disease

value: Sham surgical control

tag: study length

value: 12-weeks post surgery

value: synovial tissue

value: macrophage (CD11b/c+)


title: G401 dTAG DCAF5 DMSO 4h ARID1A sigma rep1 [2574941]

description:
dTag DCAF5 DMSO 4h treated for ARID1A
2574941_g401_dTAG_DCAF5_DMSO_4h_ARID1A_sigma_hg19

value: DMSO (matched to V-1)


title: Synovial macrophage, sham surgical control, 12-week post surgery, rep 3


title: G401 dTAG DCAF5 DMSO 4h BAF155 thermo rep1 [2574942]

description:
dTag DCAF5 DMSO 4h treated for BAF155
2574942_g401_dTAG_DCAF5_DMSO_4h_BAF155_thermo_hg19


title: scMm_Shox2trac_HL_E115_rep1

description: 10x Single cell kit v3.0

source_name: Embryonic Hindlimb

tag: background

value: Embryonic Hindlimb

tag: embryonic stage

tag: facs-sorted status


title: Foxp3Cre-WT-female-3_S18

source_name: Total VAT Treg cells from female Foxp3cre mice, replicate 1

value: female

value: Foxp3cre mice


title: Gata3KO-Female-2_S7

source_name: Total VAT Treg cells from female Gata3/Foxp3cre mice, replicate 2


title: G401 dTAG DCAF5 V1 input [2574939]

description:
V-1 treated input control
2574939_G401_dTAG_DCAF5_V1_input_hg19


title: G401 shDCAF5 p300 AbCam rep2 [2516873]

description:
ChIP enriched for p300 in shDCAF5
2516873_G401_shDCAF5_p300_AbCam_n2_hg19


title: G401 dTAG DCAF5 DMSO input [2574938]

description:
DMSO treated input control
2574938_G401_dTAG_DCAF5_DMSO_input_hg19


title: G401 shDCAF5 p300 AbCam rep1 [2516872]

description:
ChIP enriched for p300 in shDCAF5
2516872_G401_shDCAF5_p300_AbCam_n1_hg19


title: Synovial macrophage, post traumatic osteoarthritis, 12-week post surgery, rep 3

value: Post traumatic osteoarthritis


title: CXCR3-2_S16

source_name: CXCR3+ VAT Treg cells sorted from male Foxp3RFP mice, replicate 2

value: male

value: Foxp3RFP mice

value: VAT Treg cells, TCRb+CD4+Foxp3+CXCR3+


title: CXCR3-Darya_s_S17

source_name: CXCR3+ VAT Treg cells sorted from male Foxp3RFP mice, replicate 3

value: 20-30  week old


title: G401 shDCAF5 p300 AbCam rep3 [2516874]

description:
ChIP enriched for p300 in shDCAF5
2516874_G401_shDCAF5_p300_AbCam_n3_hg19

value: human malignant rhabdoid tumor


title: Synovial macrophage, post traumatic osteoarthritis, 12-week post surgery, rep 4

value: Sprague Dawley


title: G401 shCTRL p300 AbCam rep1 [2516869]

description:
ChIP enriched for p300 in shCTRL
2516869_G401_shCTRL_p300_AbCam_n1_hg19

value: shCTRL


title: G401 shCTRL p300 AbCam rep3 [2516871]

description:
ChIP enriched for p300 in shCTRL
2516871_G401_shCTRL_p300_AbCam_n3_hg19


title: Synovial macrophage, post traumatic osteoarthritis, 12-week post surgery, rep 2

value: wild type

value: Male


title: CXCR3-1_S15

source_name: CXCR3+ VAT Treg cells sorted from male Foxp3RFP mice, replicate 1


title: Pseudomonas fluorescens SBW25, MHPP rep 3

city: Richland

first: Joshua

last: Elmore

state: WA

address: 902 Battelle Blvd

institute: PNNL

data_processing:
Pseudoalignment of reads to the SBW25 CDS sequences was performed with Salmon 1.9.0
Count normalization and differential expression analyses were performed with DESeq2 1.36.0
Assembly: NC_012660
Supplementary files format and content: DEseq2 output comparing samples grown on glucose vs. those grown on MHPP.

organism: Pseudomonas fluorescens

growth_protocol: Pseudomonas fluorescens SBW25 were cultivated in MME medium containing either 10 mM glucose or 2.5 mM MHPP, until they reached mid-log phase growth, at a OD600 1cm pathlength of 0.2.

extract_protocol:
Total RNA was isolated, digested using Dnase I treatment, and depleted of rRNA using the Illumina Ribo-Zero kit by third party vendor Genewiz.
RNA was isolated and non-strand specific RNAseq libraries prepared by third party vendor Genewize.

treatment_protocol: Cultures were rapidly centrifuged at 4 C, media decanted, and cell pellets immediately flash frozen for storage at -80 C

value: MHPP


title: G401 shDCAF5 input [2516868]

description:
input control for shDCAF5
2516868_G401_shDCAF5_input_hg19


title: LNZ308 72h C

city: Tübingen

first: Bianca

last: Walter

state: Deutschland

address: Otfried-Müller-Str. 27

country: Germany

institute: Hertie Institut für klinische Hirnforschung

data_processing:
To align the reads to the GRCh38 we used STAR v2.7.3a
alignment quality was analyzed using ngs-bits
Normalized read counts for all genes were obtained using Subread (v2.0.0) and edgeR (v3.26.6)
Lastly we used R package “DESeq2”
Assembly: GRCh38
Supplementary files format and content: count file matrix

source_name: Brain

extract_protocol:
Qiagen RNeasy Mini Kit; enrichment of the mRNA fraction using polyA capture from 200 ng of total RNA using the NEBNext Poly(A) mRNA Magnetic Isolation Module (NEB)
NEB Next Ultra II Directional RNA Library Prep Kit for Illumina (NEB)

treatment_protocol: LN229 cells were treated with 1.6 µM AZD6738, LNZ308 cells were treated with 3.5 µM AZD6738; DMSO was used as vehicle and applied in equal amounts as AZD6738

value: Brain

value: cell line

value: p53 del, PTEN mut, p16 wt, p14ARF wt


title: Synovial macrophage, sham surgical control, 12-week post surgery, rep 2

value: Sham surgical control

value: 12-weeks post surgery

value: synovial tissue

value: macrophage (CD11b/c+)


title: LNZ308 72h A


title: G401 shCTRL p300 AbCam rep2 [2516870]

description:
ChIP enriched for p300 in shCTRL
2516870_G401_shCTRL_p300_AbCam_n2_hg19


title: LNZ308 72h B


title: G401 shCTRL input [2516867]

description:
input control for shCTRL
2516867_G401_shCTRL_input_hg19


title: Synovial macrophage, post traumatic osteoarthritis, 12-week post surgery, rep 1

value: Post traumatic osteoarthritis


title: Synovial macrophage, sham surgical control, 12-week post surgery, rep 1


title: Synovial macrophage, sham surgical control, 4-week post surgery, rep 4

value: 4-weeks post surgery


title: LNZ308 24h B


title: LNZ308 2h C


title: Synovial macrophage, sham surgical control, 4-week post surgery, rep 3


title: Synovial macrophage, sham surgical control, 4-week post surgery, rep 5


title: LNZ308 2h B


title: Pseudomonas fluorescens SBW25, MHPP rep 2


title: Synovial macrophage, sham surgical control, 4-week post surgery, rep 2


title: LNZ308 24h C


title: LNZ308 UC C

value: UC


title: LNZ308 2h A


title: Pseudomonas fluorescens SBW25, MHPP rep 1


title: LNZ308 24h A


title: Pseudomonas fluorescens SBW25, MHPP rep 4


title: Pseudomonas fluorescens SBW25, Glucose rep 4

value: Glucose


title: Pseudomonas fluorescens SBW25, Glucose rep 3


title: LNZ308 UC B


title: Synovial macrophage, sham surgical control, 4-week post surgery, rep 1


title: Pseudomonas fluorescens SBW25, Glucose rep 1


title: Synovial macrophage, post traumatic osteoarthritis, 4-week post surgery, rep 4


title: Pseudomonas fluorescens SBW25, Glucose rep 2


title: LN229 72h A

value: p53 mut, PTEN wt, p16 del, p14ARF del


title: LN229 72h C


title: E18.5 cerebral cortex, CAP1-KO, Biolrep3

city: Marburg

first: Sharof

last: Khudayberdiev

state: Hessen

address: Karl-von-Frisch Str 2

institute: Inst. Phys. Chem. Marburg University

data_processing:
Raw sequencing reads were trimmed from 3ʹ-adapter (AGATCGGAAGAGC) and filtered according to quality and length using default parameters of Fastx-Toolkit for fastq data on Galaxy, a web-based genome analysis tool (https://usegalaxy.org)
Reads longer than 15 nt were mapped to the mouse genome (GRCm38-mm10) with STAR RNA-aligner software and differential expression of transcripts was performed using edgeR (FDR<0.05), both of which are integrated into https://usegalaxy.org.
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes edgeR's TMM normalised gene counts for all samples

source_name: Cerebral cortex

extract_protocol:
Total RNA from cerebral cortices of CAP1 flx/flx (n=3) and CAP1flx/flx,Nestin-Cre (n=3) E18 embryos were extracted using peqGOLD TriFast reagent (PeqLab) according to manufacturer’s instructions. DNA contamination was removed by treatment with DNaseI (Qiagen) and purified with MinElute kit (Qiagen).
Barcoded stranded mRNA-seq libraries were prepared from high quality total RNA samples (~150 ng/sample) using the NEBNext Poly(A) mRNA Magnetic Isolation Module and NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (New England Biolabs (NEB), Ipswich, MA, USA) implemented on the liquid handling robot Beckman i7.

value: Cerebral cortex


title: Synovial macrophage, post traumatic osteoarthritis, 4-week post surgery, rep 3

value: Sprague Dawley


title: LN229 24 h B


title: Synovial macrophage, post traumatic osteoarthritis, 4-week post surgery, rep 1

value: wild type


title: Synovial macrophage, post traumatic osteoarthritis, 4-week post surgery, rep 2

value: Male


title: E18.5 cerebral cortex, CAP1-KO, Biolrep2


title: LN229 2h A


title: LN229 24 h A


title: E18.5 cerebral cortex, CAP1-KO, Biolrep1


title: LN229 2h C


title: E18.5 cerebral cortex, Control, Biolrep3

value: Cap1 flx/flx


title: LN229 2h B

value: Brain


title: LN229 UC B

value: cell line


title: E18.5 cerebral cortex, Control, Biolrep2


title: LN229 72h B


title: LN229 UC A


title: PBMC_905_ImmEnrich_Healthy Control

city: Chicago

first: David

last: Gate

state: IL

address: 303 E Chicago Ave, Chicago, IL 60611

department: Neurology

institute: Northwestern University

data_processing:
Illumina RTA3 method for base-calling
10xGenomics cellranger pipeline for alignment and filtering (trimming 5' TSO sequence and 3' polyA tail, alignment with STAR, UMI counting, EmptyDrops method for empty droplet removal)
SoupX background contamination removal (S100A8 and S100A9 were used to estimate contamination fraction and counts were adjusted using SoupX::adjustCounts function)
DoubletFinder doublet removal (doublet formation rate of 5.4% based on 10xGenomics multiplet rate estimation, using 12 PCs and pN = 0.25)
Seurat filtering and normalization (filter out cells with >10% mitochondrial reads, retain cells with at least 200 mapped features, retain features with at least 3 mapped cells, counts were then normalized using Seurat's LogNormalize method)
Assembly: hg38
Supplementary files format and content: .rds object of raw gene count matrix for each gene and cell barcode
Supplementary files format and content: .rds object of log-normalized expression matrix for each gene and cell barcode
Library strategy: scRNA-seq + amplification using predesigned gene panel

source_name: Peripheral blood mononuclear cells

extract_protocol:
PBMCs were pelleted, frozen, and resuspended in PBS with 0.04% BSA before being sorted with Sytox blue live/dead dye
Chromium Next GEM Single Cell 5' v2 + Targeted Gene Expression, Human Immunology panel

value: Peripheral blood mononuclear cells

value: male

tag: disease state

value: Healthy Control


title: at-seed_RNAseq_replicate2_Col_4DAP

city: Uppsala

first: Juan

middle: C

last: Santos-González

state: Uppsala

address: Almas Allé 5

department: Department of Plant Biology and Forest Genetics

country: Sweden

institute: SLU

description:
Arabidopsis thaliana seed 4DAP of Columbia-0
TPM.genes.arf22.txt

data_processing:
Reads were trimmed by removing the 5 bp from the 5’ end and 20 bp from the 3' end and mapped in a paired-end mode to the Arabidopsis (TAIR10) genome  using using hisat2. Gene expression levels (TPM-transcript per million) were calculated using stringtie.
Assembly: TAIR10
Supplementary files format and content: RNA-seq: expression levels (TPM-transcript per million) are shown for genes in TAIR10 for each condition and replicate.

organism: Arabidopsis thaliana

source_name: AT 4DAP Seed Col

growth_protocol: Seeds were sown on plates containing Murashige and Skoog medium and stratified at 4°C for two days. The plates were transferred to a growth chamber for two weeks (16 h light/8 h dark; 60µmol/s/m²; 22°C). Seedlings were pricked onto soil and grown in phytotron chambers (16 h light/8 h dark; 150µmol/s/m²; 21°C; 70% humidity).

extract_protocol:
RNA extraction was performed using the plant RNeasy Kit from Qiagen. Total RNA was treated with DNAseI. mRNAs were specifically isolated using NEBNext® Poly(A) mRNA Magnetic Isolation Module from NEB (E7490S). The libraries were prepared using NEBNext® Ultra™ II DNA Library Prep Kit for Illumina (E7645S).
Library construction and sequencing were performed at Novogene on an Illumina Novaseq platform in paired-end mode and with 150bp read length.

treatment_protocol: Anthers were removed from the flowers two days before hand-pollination. Resulting siliques were opened at 4- or 7-DAP and seeds were carefully removed in RNAlater solution.

value: seed


title: at-seed_RNAseq_replicate1_Col_4DAP


title: at-seed_RNAseq_replicate2_pPHE1:ARF22#Line2_4DAP

description:
Arabidopsis thaliana seed 4DAP of Columbia-0 pPHE1:ARF22#Line2
TPM.genes.arf22.txt

source_name: AT 4DAP Seed wt pPHE1:ARF22#Line2


title: PBMC_970_ImmEnrich_Healthy Control

tag: age


title: LN229 24 h C


title: E18.5 cerebral cortex, Control, Biolrep1

tag: developmental stage


title: Male-Normal-Diet-rep3

description: Male mice fed with normal diet, replicate 3

data_processing:
The libraries were aligned to the GRCm38/mm10 genome using Rsubread_2.14.1. The mapped read-pairs in each library were assigned to the NCBI RefSeq gene annotation for mm10 (build 38.1) by using featureCounts.
Genes were excluded from downstream analysis if they failed to achieve a CPM (counts per million mapped reads) value of at least 2 in at least 2 libraries. Counts were quantile normalized with the “voom” function of the limma package and converted to log2 counts per kilobase per million(log2 FKPM).
The log2 FPKM values were provided to the CellPhoneDB program (version 4.1.0) for cell-cell communication analysis. The CellPhoneDB database version 4.0.0 was used for analysis, and interactors having p values less than 0.1 were called as significant.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include log2-FPKM values for each library. The supplementary file, count_table.txt, includes raw read counts for genes in all the libraries.

source_name: Total VAT tissue from normal diet fed male mice

extract_protocol:
RNA extraction from VAT Treg cells was performed following the manufacturer's instructions using the Qiagen Rneasy mini kit and Rneasy lipid tissue mini kit
Libraries were generated following the manufacturer's protocol using the SMART-Seq mRNA LP, Takara Bio

tag: diet

value: normal diet

value: 20-30  week old


title: PBMC_947_ImmEnrich_Alzheimers Disease

tag: Sex

value: Alzheimers Disease


title: LNZ308 UC A

tag: tissue

value: p53 del, PTEN mut, p16 wt, p14ARF wt

value: UC


title: PBMC_1200_ImmEnrich_Healthy Control


title: at-seed_RNAseq_replicate1_pPHE1:ARF22#Line2_4DAP


title: Male-Normal-Diet-rep2

description: Male mice fed with normal diet, replicate 2

value: Total VAT tissue from normal diet fed male mice


title: LN229 UC C

tag: cell line

value: p53 mut, PTEN wt, p16 del, p14ARF del


title: Synovial macrophage, post traumatic osteoarthritis, 4-week post surgery, rep 5

value: Sprague Dawley

value: Post traumatic osteoarthritis

value: 4-weeks post surgery

value: synovial tissue

tag: cell type

value: macrophage (CD11b/c+)


title: at-seed_RNAseq_replicate2_pPHE1:ARF22#Line1_4DAP

description:
Arabidopsis thaliana seed 4DAP of Columbia-0 pPHE1:ARF22#Line1
TPM.genes.arf22.txt

source_name: AT 4DAP Seed wt pPHE1:ARF22#Line1

tag: genotype


title: PBMC_1237_ImmEnrich_Alzheimers Disease


title: Male-Normal-Diet-rep1

description: Male mice fed with normal diet, replicate 1


title: PBMC_1236_ImmEnrich_Alzheimers Disease

value: female


title: PBMC_836_ImmEnrich_Healthy Control

value: Peripheral blood mononuclear cells


title: PBMC_230_ImmEnrich_Alzheimers Disease


title: Male-High-Fat-Diet-rep3

description: Male mice fed with high-fat diet, replicate 3

source_name: Total VAT tissue from HFD fed male mice

value: Total VAT tissue from HFD fed male mice

value: male

value: HFD


title: PBMC_921_ImmEnrich_Alzheimers Disease


title: PBMC_70_ImmEnrich_Alzheimers Disease


title: Male-High-Fat-Diet-rep2

description: Male mice fed with high-fat diet, replicate 2


title: at-seed_RNAseq_replicate1_pPHE1:ARF22#Line1_4DAP

value: seed


title: at-seed_RNAseq_replicate2_osd1xCol_4DAP

description:
Arabidopsis thaliana seed 4DAP of osd1 crossed with Columbia-0
TPM.genes.arf22.txt

source_name: AT 4DAP Seed osd1

value: osd1 x Col-0


title: Male-High-Fat-Diet-rep1

description: Male mice fed with high-fat diet, replicate 1

value: 20-30  week old


title: at-seed-RNAseq_replicate3 _arf13_arf20xCol_7DAP

description:
Arabidopsis thaliana seed 7DAP of Columbia-0 arf13 arf20 crossed with Col-0
TPM.genes.crispRarf.txt

source_name: AT 7DAP Seed arf13 arf20

value: crispR arf13 arf20 x Col-0


title: PBMC_820_ImmEnrich_Healthy Control

value: Healthy Control


title: PBMC_1162_ImmEnrich_Healthy Control


title: PBMC_1010_ImmEnrich_Healthy Control


title: PBMC_989_ImmEnrich_Healthy Control


title: PBMC_965_ImmEnrich_Alzheimers Disease

value: Alzheimers Disease


title: at-seed-RNAseq_replicate3_Colxosd1_7DAP

description:
Arabidopsis thaliana seed 7DAP of Columbia-0 crossed with osd-1
TPM.genes.crispRarf.txt

source_name: AT 7DAP Seed osd1

value: Col-0 x osd1


title: Female-Normal-Diet-rep2

description: Female mice fed with normal diet, replicate 2

source_name: Total VAT tissue from normal diet fed female mice

value: normal diet


title: PBMC_1282_ImmEnrich_Healthy Control


title: PBMC_978_ImmEnrich_Healthy Control


title: at-seed-RNAseq_replicate3_Col_7DAP

description:
Arabidopsis thaliana seed 7DAP of Columbia-0
TPM.genes.crispRarf.txt

source_name: AT 7DAP Seed Col


title: at-seed-RNAseq_replicate2 _arf13_arf20xCol_7DAP


title: PBMC_912_ImmEnrich_Healthy Control


title: PBMC_1111_ImmEnrich_Healthy Control


title: Female-Normal-Diet-rep1

description: Female mice fed with normal diet, replicate 1

value: Total VAT tissue from normal diet fed female mice


title: PBMC_781_ImmEnrich_Healthy Control


title: Female-High-Fat-Diet-rep3

description: Female mice fed with high-fat diet, replicate 3

source_name: Total VAT tissue from HFD fed female mice


title: at-seed-RNAseq_replicate2_Colxosd1_7DAP


title: PBMC_1147_ImmEnrich_Alzheimers Disease


title: at-seed_RNAseq_replicate1_osd1xCol_4DAP


title: at-seed-RNAseq_replicate2_Col_7DAP


title: PBMC_968_ImmEnrich_Healthy Control


title: PBMC_942_ImmEnrich_Alzheimers Disease


title: Female-Normal-Diet-rep3

description: Female mice fed with normal diet, replicate 3


title: PBMC_953_ImmEnrich_Alzheimers Disease


title: Female-High-Fat-Diet-rep1

description: Female mice fed with high-fat diet, replicate 1

value: Total VAT tissue from HFD fed female mice


title: Female-High-Fat-Diet-rep2

description: Female mice fed with high-fat diet, replicate 2


title: PBMC_1020_ImmEnrich_Healthy Control


title: at-seed-RNAseq_replicate1 _arf13_arf20xCol_7DAP


title: Male-Macrophages-rep1

source_name: Macrophages sorted from female VAT, replicate 1

value: CD45+TCRb-B220-CD11b+ cells from VAT


title: at-seed-RNAseq_replicate1_Colxosd1_7DAP


title: PBMC_932_ImmEnrich_Alzheimers Disease


title: PBMC_802_ImmEnrich_Alzheimers Disease


title: Male-Macrophages-rep2

source_name: Macrophages sorted from female VAT, replicate 2


title: PBMC_917_ImmEnrich_Alzheimers Disease