title: abdominal; EVD; F42

city: Stanford

first: Heather

last: Clemons

state: CA

address: Beckman Center

department: Dept of Biochemistry

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

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: abdominal; EVD; F42, 10 ug labeled aRNA

tag: age

tag: organism part

value: abdominal

tag: sample fraction

value: EVD

tag: Sex


title: eFL_Shox2trac_E145_REP1

status: Public on Mar 22 2024

type: SRA

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: entire forelimb (bulk) RNA-seq

library_source: transcriptomic

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

organism: Mus musculus

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. 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.

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: entire limb (not sorted)

tag: biological replicate


title: 034-9015-1

city: New York City

first: MacIntosh

middle: Grant

last: Cornwell

state: NY

department: School of Medicine

country: USA

institute: New York University

description:
034-9015-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

data_processing:
Fastq qualtiy assessed via FastQC 0.11.7
Sample contamination assessed via fastqscreen v0.13.0
Fastq files trimmed via Trimmomatic v0.36
Fastq files aligned to the HG38 human genome via STAR v2.7.3a
Reads counted via featurecounts v1.6.3
Assembly: hg38
Supplementary files format and content: Raw count table as a .txt file
Supplementary files format and content: Normalized count table as a .txt file

organism: Homo sapiens

source_name: whole blood

extract_protocol:
18mLs of whole blood was drawn into 3.2% sodium citrate tubes (BD Vacutainer). Blood was centrifuged to obtain platelet rich plasma, and then depleted of leukocytes and RBCs using StemCell EasySep CD45 and RBC magnetic depletion kits. Purified platelets were pelleted and lysed with 500uL of Qiazol lysis buffer and stored at -80 until ready for RNA extraction. RNA extraction was done by utilizing Zymo Microprep kits (R2062), and stored again at -80 until ready for sequencing.
Sequencing libraries were barcoded and prepared using the Clontech SMART-Seq HT with Nxt HT kit (Takara Bio USA), and libraries sequenced single end on an Illumina NovaSeq 6000

value: whole blood

tag: cell type

value: platelet

tag: cohort

value: control

value: F

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 025-5598-1

description:
025-5598-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

value: Hispanic/Latino

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

value: Inactive Disease and Either ds-DNA or Low Complement at Enrollment


title: eFL_Shox2Δearly_E105_REP5

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 17q_D0_1 [ATAC-Seq]

city: Vienna

first: Florian

last: Halbritter

address: Zimmermannplatz 10

country: Austria

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

library_source: genomic

data_processing:
Raw sequencing data were processed using PEPATAC (Smith et al. 2021; v0.9.5; default parameters) including alignment to the human genome (refdata-cell ranger-atac-GRCh38-1.2.0 assembly provided by 10x Genomics for maximum compatibility with scRNA-seq analyses).
Following initial data processing, all subsequent analyses were performed in R (v4.1.2) using Bioconductor packages.
We removed peaks overlapping blacklisted regions from ENCODE (http://mitra.stanford.edu/kundaje/akundaje/release/blacklists/hg38-human/hg38.blacklist.bed.gz) and merged overlapping peaks across all ATAC-seq datasets to create a common set of consensus genomic regions for subsequent analysis (peak_annot.csv.gz).
Next, we quantified for each input dataset the number of reads overlapping these consensus peaks using featureCounts (Rsubread v2.8.1), see read_counts_raw.csv.gz
Raw read counts were loaded into DESeq2 (v1.34.0; default parameters, design: ~lane+batch+sample_group) for normalization (variance-stabilizing transformation) and differential analysis. In doing so, we estimated count size factors for normalization excluding regions on chromosomes with known chromosomal aberrations (i.e., chr1, chr17) to avoid overcompensation due to differences in global signal strength. Normalized counts are available in read_counts_norm.csv.gz
Assembly: GRCh38
Supplementary files format and content: Comma-separated text files (raw and normalized read counts per peak, annotation of peaks)
Supplementary files format and content: BigWig files summarizing read coverage in genomic bins per sample

molecule: genomic DNA

growth_protocol: hESCs were cultured routinely in feeder-free conditions at 37°C and 5% CO2 in E8 media (made in house adapted from Chen et al 2011) 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 a modified version described in Frith et al. (2018) and Frith & Tsakiridis (2019).

extract_protocol:
20,000 to 50,000 cells were lysed in the transposase reaction mix (12.5 μl 2xTD buffer, 2 μl TDE1 [Illumina], 10.25 μl nuclease-free water, and 0.25 μl 1% digitonin [Promega]) for 30 min at 37 °C.
Following DNA purification with the MinElute kit (Qiagen) eluting in 12 μl, 1 μl of eluted DNA was used in a quantitative PCR (qPCR) reaction to estimate the optimum number of amplification cycles. The remaining 11 μl of each library were amplified for the number of cycles corresponding to the Cq value (i.e., the cycle number at which fluorescence has increased above background levels) from the qPCR using custom Nextera primers. Library amplification was followed by SPRI (Beckman Coulter) size selection to exclude fragments larger than 1,200 bp. Libraries concentration was measured with a Qubit fluorometer (Life Technologies), and libraries were quality checked using a 2100 Bioanalyzer (Agilent Technologies). Libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform in 1x50bp single-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 "17q1qMYCN".

tag: cell line

tag: cell type

value: embryonic stem cells (hESC)

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: Responder 9 to Adalimumab

type: RNA

city: Rouen cedex

first: Celine

last: Derambure

address: 22 Bvd Gambetta

country: France

institute: INSERM U905

hyb_protocol: Hybridization was performed according to the Agilent instructions for Gene Expression Hybridization Kit (catalog number 5188-5242). Samples were applied to microarrays enclosed in Agilent SureHyb hybridization chambers (65°C, 17H). After hybridization, slides were washed and dried in acetonitril.

scan_protocol: Scanned on an Agilent G2565CA scanner. Images were quantified using Agilent Feature Extraction Software (v 10.5.1.1)

data_processing: Agilent Feature Extraction Software (v 10.5.1.1) was used for LOWESS normalization.

molecule: total RNA

source_name: PBMCs

label_protocol: Agilent QuickAmp Labeling kit was used according to the manufacturer instructions (catalog number 5190-0443) with 500ng of total RNA.

extract_protocol: Total RNA from PBMC were extracted using Trizol following manufacturer's instructions.

treatment_protocol: PBMCs from total blood for each patient were isolated by Ficoll and preserved in RNA later at -20°C until total RNA extraction.

tag: gender

value: PBMC

tag: disease state

value: rheumatoid arthritis

tag: treatment

value: methotrexate +  adalimumab

tag: efficacy

value: response

source_name: PBMCs from 10 healthy donnors

value: healthy

tag: sample type

value: Pool from 5 women and 5 men


title: 17q1q_D9_3 [ATAC-Seq]

value: hESC-derived trunk neural crest cells


title: 021-5848-1

description:
021-5848-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

value: whole blood

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: Responder 8 to Adalimumab

tag: gender

tag: cell type

tag: disease state

tag: treatment

tag: efficacy

tag: sample type


title: eFL_Shox2Δearly_E105_REP4

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: entire limb (not sorted)

tag: biological replicate


title: 020-5568-1

description:
020-5568-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: platelet

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

value: Predominately Active Cutaneous Disease


title: 17q1q_D9_2 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: eFL_Shox2Δearly_E105_REP3

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: Responder 7 to Adalimumab

tag: gender

tag: disease state

tag: treatment

tag: efficacy

tag: sample type


title: 018-5867-1

description:
018-5867-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cell type

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Inactive Disease

tag: progression status

tag: upcr clean


title: Responder 6 to Adalimumab

tag: gender

tag: cell type

value: PBMC

tag: disease state

value: rheumatoid arthritis

tag: treatment

tag: efficacy

tag: sample type


title: Responder 5 to Adalimumab

value: methotrexate +  adalimumab

value: response


title: Responder 4 to Adalimumab

value: healthy

value: Pool from 5 women and 5 men


title: eFL_Shox2trac_E145_REP2

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 026-5689-1

description:
026-5689-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

value: whole blood

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai


title: 017-9044-1

description:
017-9044-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

tag: cohort

value: control

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: sledai avail

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: Responder 3 to Adalimumab

tag: gender

value: M

tag: cell type

tag: disease state

tag: treatment

tag: efficacy

tag: sample type


title: eFL_Shox2Δearly_E105_REP1

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: entire limb (not sorted)

tag: biological replicate


title: eFL_Shox2Δearly_E105_REP2

description: entire forelimb (bulk) RNA-seq


title: 17q1q_D3_2 [ATAC-Seq]

tag: cell line

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 015-5769-1

description:
015-5769-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cell type

value: platelet

tag: cohort

tag: age

tag: Sex

value: F

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

tag: predominant disease_category

value: Inactive Disease and Either ds-DNA or Low Complement at Enrollment

tag: progression status

tag: upcr clean


title: eFL_Shox2trac_E105_REP5

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 17q1q_D3_1 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 013-5073-1

description:
013-5073-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

value: sle

tag: age

tag: Sex

tag: ethnicity

value: Hispanic/Latino

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail


title: eFL_Shox2trac_E105_REP4

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: eFL_Shox2trac_E105_REP3

description: entire forelimb (bulk) RNA-seq


title: 17q1q_D19_3 [ATAC-Seq]

tag: cell line

tag: cell type

value: hESC-derived mature sympathoadrenal progenitors

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 009-5062-1

description:
009-5062-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

value: White

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: predominant disease_category

tag: progression status

tag: upcr clean


title: 17q1q_D19_2 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: 17q1q_D9_1 [ATAC-Seq]

value: hESC-derived trunk neural crest cells


title: 17q1q_D3_3 [ATAC-Seq]


title: eFL_Shox2trac_E105_REP2

description: entire forelimb (bulk) RNA-seq

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

tag: biological replicate


title: 17q1q_D19_1 [ATAC-Seq]


title: 008-5438-1

description:
008-5438-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: cohort

tag: age

tag: Sex

tag: ethnicity

tag: race

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail

value: Active Lupus Nephritis


title: Responder 1 to Adalimumab

tag: gender

tag: cell type

value: PBMC

tag: disease state

value: rheumatoid arthritis

tag: treatment

value: methotrexate +  adalimumab

tag: efficacy

value: response

tag: sample type


title: Responder 2 to Adalimumab

value: healthy

value: Pool from 5 women and 5 men


title: 005-5427-1

description:
005-5427-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

value: whole blood

tag: cohort

tag: age

tag: Sex

tag: ethnicity

value: Non-Hispanic/Latino

tag: race

value: Black or African American

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

value: IV

tag: seizure sledai

tag: psychosis sledai

tag: organic brain_syndrome_sledai

tag: visual disturbance_sledai

tag: cranial nerve_disorder_sledai

tag: lupus headache_sledai

tag: cerebrovascular accident_sledai

tag: vasculitis _sledai

tag: arthritis sledai

tag: myositis sledai

tag: hematuria sledai

tag: proteinuria sledai

tag: pyuria sledai

tag: rash sledai

tag: predominant disease_category

value: Predominately Hematologic Activity

tag: progression status

tag: upcr clean


title: 012-5650-1

description:
012-5650-1
platelet_sle_raw_counttable.txt
platelet_sle_normalized_counttable.txt

tag: tissue

tag: cell type

value: platelet

tag: cohort

value: sle

tag: age

tag: Sex

value: F

tag: ethnicity

tag: race

value: Asian

tag: fcgr2a genotype

tag: prednisone

tag: prednisone dosage

tag: hydroxychloroquine

tag: hydroxychloroquine dosage

tag: azathioprine

tag: azathioprine dosage

tag: mycophenolate mofetil

tag: mycophenolate mofetil_dosage

tag: methotrexate

tag: methotrexate dosage

tag: benlysta

tag: benlysta dosage

tag: seizure sledai

tag: alopecia sledai

tag: mucosal ulcers_sledai

tag: pleurisy sledai

tag: pericarditis sledai

tag: low complement_sledai

tag: increased dna_binding_sledai

tag: fever sledai

tag: thrombocytopenia sledai

tag: leukopenia sledai

tag: sledai avail


title: FL_Shox2trac_E135_MAINTAIN_rep2

description: sorted cells RNA-seq

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: dmCherry+/EYFP+

tag: biological replicate


title: 17q1q_D14_2 [ATAC-Seq]

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: batch

tag: flowcell

tag: lane


title: Moderate Responder 7 to Adalimumab

tag: gender

value: PBMC

tag: disease state

tag: treatment

tag: efficacy

value: moderate response

tag: sample type


title: MG63 cells, siLARP4B rep 2

city: Cambridge

first: Jennifer

last: Coleman

state: Cambridgeshire

address: Li Ka Shing Centre, Robinson Way

department: CRUK CI

country: United Kingdom

institute: University of Cambridge

data_processing:
FastQC - quality control checks of fastq files
HISAT2 - short read aligner to map to reference genome
featureCounts - generating count files
EdgeR - Normalisation and differential expression testing
Assembly: Hg38
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

growth_protocol: PC3 cells cultured in RPMI 1640 + 10% FBS supplemented with L-Glutamine; MG63 cells cultured in Alpha-MEM with GlutaMAX +10% FBS; both cell lines cultured in a humidified incubator 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Approximately 2µg of total RNA was submitted to GeneWiz for poly(A) selection, library preparation and sequencing
RNA libraries for RNAseq were constructed at GENEWIZ following submission of RNA to GENEWIZ

treatment_protocol: Cells were transfected with 10nM final concentration of siRNAs using Lipofectamine RNAiMAX in media without antibiotics, and incubated for 72h to ensure efficient knockdown prior to extraction of RNA

value: Osteosarcoma

value: WT

value: Transfection with siRNA targeting LARP4B


title: Moderate Responder 8 to Adalimumab

value: rheumatoid arthritis

value: methotrexate +  adalimumab

value: healthy

value: Pool from 5 women and 5 men


title: MG63 cells, siLARP4B rep 1


title: 17q1q_D14_1 [ATAC-Seq]


title: 17q1q_D14_3 [ATAC-Seq]


title: Moderate Responder 9 to Adalimumab


title: Moderate Responder 4 to Adalimumab


title: FL_Shox2trac_E135_INACTIVE_rep2

description: sorted cells RNA-seq

tag: background

tag: tissue

value: dmCherry-/EYFP-


title: MG63 cells, siLARP4A rep 2

tag: genotype

value: Transfection with siRNA targeting LARP4A


title: 17q1q_D0_1 [ATAC-Seq]

value: embryonic stem cells (hESC)


title: FL_Shox2trac_E135_INACTIVE_rep1

description: sorted cells RNA-seq

tag: embryonic stage

tag: facs-sorted status


title: Moderate Responder 5 to Adalimumab


title: eFL_Shox2trac_E105_REP1

description: entire forelimb (bulk) RNA-seq

value: entire limb (not sorted)

tag: biological replicate


title: MG63 cells, siLARP4A rep 1

tag: cell line

tag: cell type


title: FL_Shox2trac_E135_DECOM_rep2

description: sorted cells RNA-seq

value: dmCherry-/EYFP+


title: 17q1qMYCN_D9_3 [ATAC-Seq]

value: hESC-derived trunk neural crest cells

tag: day

value: dox at D5

tag: sample group


title: Moderate Responder 3 to Adalimumab

value: F


title: MG63 cells, siControl rep 2

value: Transfection with non-targeting siControl


title: DLNCD127highTregs_2

city: Westmead

first: Brian

middle: S

last: Gloss

state: NSW

address: 176 Hawkesbury Rd

department: Scientific Platforms

country: Australia

institute: Westmead Institute of Medical Research

description:
SMART-Seq v4 Ultra Low Input RNA Kit
The transplant tolerant model: Porcine-NICC were isolated from pancreases and propagated in culture for 6 days as described previously and in method details. DEREG-mice were transplanted with 4000 IEQ porcine-NICC under their renal capsules as described previously. The DEREG-mice received an intraperitoneal (i.p) dose (500 µg/mouse) of MR-1 (Bioexpress) at days 0, 2, 4 and 6; and a single intraperitoneal dose (500 µg/mouse) of CTLA4-Fc (NS-1, WEHI Antibody Facility, Australia) at day 0 as tolerant-group.

data_processing:
Library sequencing quality was determined using FastQC. Illumina adaptor sequence and low quality read trimming (read pair removed if < 20 base pairs) was performed using Trim Galore. STAR was used to align reads to mouse genome mm10 using ENSEMBL gene annotations as a guide. Read counts data corresponding to ENSEMBL gene annotations were generated using the star flag --quantMode GeneCounts
Assembly: mm10
Supplementary files format and content: text, unstranded, forward and reverse stranded gene counts

source_name: Mus kidney lymph node

extract_protocol:
Amplified cDNA for each sample was generated directly from sorted-Tregs using the SMART-Seq v4 Ultra Low Input RNA Kit for sequencing (Takara/Clontech) according to the manufacturer's instructions
Barcoded cDNA libraries were generated with the Nextera XT DNA Library Preparation kit (Illumina) following manufacturer's protocols.
cDNA sequenced with a 2 × 75 bp paired-end protocol with a v3 reagent kit on the Miseq (samples of DLN) and Nextseq 500 instruments (Illumina) (samples of spleen and graft) according to the manufacturer's instructions

tag: time

value: Day 100 post transplantation

value: Mus kidney lymph node


title: FL_Shox2trac_E135_DECOM_rep1

description: sorted cells RNA-seq

value: Embryonic Forelimb


title: 17q1qMYCN_D9_2 [ATAC-Seq]

tag: batch

tag: flowcell

tag: lane


title: MG63 cells, siControl rep 1

value: Osteosarcoma

value: WT

tag: treatment


title: Moderate Responder 1 to Adalimumab

tag: gender

value: M

value: PBMC

tag: disease state

value: rheumatoid arthritis

value: methotrexate +  adalimumab

tag: efficacy

value: moderate response


title: PC3 cells, siLARP4B rep 2

value: Prostate adenocarcinoma

value: Transfection with siRNA targeting LARP4B


title: DLNCD127highTregs_1

tag: tissue


title: Moderate Responder 6 to Adalimumab

value: healthy

tag: sample type

value: Pool from 5 women and 5 men


title: FL_Shox2trac_E125_MAINTAIN_rep2

description: sorted cells RNA-seq

tag: background

tag: embryonic stage

tag: genotype

value: dmCherry+/EYFP+


title: Moderate Responder 2 to Adalimumab

value: F


title: FL_Shox2trac_E125_MAINTAIN_rep1

description: sorted cells RNA-seq

tag: facs-sorted status

tag: biological replicate


title: 17q1qMYCN_D19_2 [ATAC-Seq]

tag: cell line

tag: cell type

value: hESC-derived mature sympathoadrenal progenitors

tag: day

value: dox at D5


title: 17q1qMYCN_D19_3 [ATAC-Seq]

tag: sample group

tag: batch


title: DLN/CD127-Tregs_3

tag: time

value: Day 100 post transplantation

value: Mus kidney lymph node


title: 17q1q_D0_2 [ATAC-Seq]

value: embryonic stem cells (hESC)

tag: flowcell

tag: lane


title: PC3 cells, siLARP4B rep 1

value: WT

tag: treatment


title: 17q1qMYCN_D14_3 [ATAC-Seq]


title: DLN/CD127-Tregs_2


title: 17q1qMYCN_D19_1 [ATAC-Seq]


title: FL_Shox2trac_E125_INACTIVE_rep2

description: sorted cells RNA-seq

value: Embryonic Forelimb

value: dmCherry-/EYFP-


title: DLN/CD127-Tregs_1


title: PC3 cells, siLARP4A rep 2

value: Transfection with siRNA targeting LARP4A


title: PC3 cells, siControl rep 2

value: Transfection with non-targeting siControl


title: FL_Shox2trac_E125_INACTIVE_rep1

description: sorted cells RNA-seq


title: PC3 cells, siLARP4A rep 1


title: DLNCD127highTregs_3


title: FL_Shox2trac_E115_MAINTAIN_rep2

description: sorted cells RNA-seq


title: DLN/Naïve-Tregs_1

value: No transplantation

value: No


title: wt_D9_3

data_processing:
Quant-seq adapter fragments were trimmed using bbduk (from bbmap v38.87) prior to alignment to the human reference genome (refdata-gex-GRCh38-2020-A assembly provided by 10x Genomics for maximum compatibility with scRNA-seq analyses) using STAR v2.7.3a.
Read counts per gene were calculated using mmquant v1.3.
Assembly: GRCh38
Supplementary files format and content: Comma-separated text files (raw and normalized read count)

extract_protocol:
Total RNA was extracted using RNA Clean-Up and Concentration Kit (NORGEN BIOTEK CORP) following the instructions of the manufacturer
The amount of total RNA was quantified using the Qubit 4.0 Fluorometric Quantitation system (Thermo Fisher Scientific) and the RNA integrity number (RIN) was determined using the 2100 Bioanalyzer instrument (Agilent). RNA-seq libraries were prepared with the QuantSeq 3‘mRNA-Seq Library Prep Kit (FWD) for Illumina (Lexogen). Library concentrations were quantified with the Qubit 4.0 Fluorometric Quantitation system (Life Technologies) and the size distribution was assessed using the 2100 Bioanalyzer instrument (Agilent). For sequencing, samples were diluted and pooled into libraries in equimolar amounts. Libraries were sequenced by the Biomedical Sequencing Facility at CeMM using the Illumina HiSeq 4000 platform in 1x50bp single-end mode.

value: hESC-derived trunk neural crest cells

value: lanes 7+8


title: FL_Shox2trac_E115_MAINTAIN_rep1

description: sorted cells RNA-seq


title: 17q1qMYCN_D14_2 [ATAC-Seq]


title: wt_D9_4


title: Tumor from PBS Treated Mouse Rep3

city: Washington

first: Lu

last: Jin

address: 3970 Reservoir Rd NW

department: Oncology

institute: Georgetown University

data_processing:
RNAseq Raw data quality was checked using FastQC (v0.11.9), and adapter trimming on raw data was performed using Cutadapt (v3.5).
The reference genome was downloaded from Ensembl mm10 release 101, and the reference genome index was built using Star (v2.7.9a) software.
Paired end trimmed read alignment and raw read count calculations were performed using RSEM software (v1.3.1).
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

source_name: Tumor

growth_protocol: All mice were palpated for mammary tumors beginning at age of 7 months.

extract_protocol:
Total RNA was isolated from tissues using Qiagen kit and purity of the DNAse-treated RNA was measured by Agilent Tapestation
RNA libraries were prepared for sequencing using standard illumina protocols.

treatment_protocol: Once a measurable primary tumor was detected in age matched mice (n=16-17/group), mice were randomly assigned to one of two groups to receive a single intravenous injection of either PBS or BP (5 mg Fe/mouse). Tumors were measured twice weekly and a subset of animals from each group (n=5-6/group) was sacrificed after 31 days of treatment to collect tumors and organs for analysis

value: Tumor

value: Bulk Tissue

value: PBS


title: DLN/Naïve-Tregs_2


title: FL_Shox2trac_E125_DECOM_rep2

description: sorted cells RNA-seq

value: dmCherry-/EYFP+


title: FL_Shox2trac_E135_MAINTAIN_rep1

description: sorted cells RNA-seq

value: dmCherry+/EYFP+


title: FL_Shox2trac_E115_INACTIVE_rep2

description: sorted cells RNA-seq


title: wt_D9_2


title: FL_Shox2trac_E115_INACTIVE_rep1

description: sorted cells RNA-seq


title: FL_Shox2trac_E125_DECOM_rep1

description: sorted cells RNA-seq


title: BC12

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G12_GEX_features.tsv.gz
G12_GEX_barcodes.tsv.gz
G12_GEX_matrix.mtx.gz

library_source: transcriptomic single cell

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.
genome build/assembly GRCh38
processed data files format and content Tab-separated values files, matrix files, binary serialised R file containing a Seurat object

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)
Single-cell suspensions were barcoded using oligo-conjugated lipids following the MULTI-seq workflow and frozen live . Frozen, barcoded samples were thawed and 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 three 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.

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

tag: multiseq barcodes_per_sample_group

value: CACTGTAG, TGCATACG, CACGTATG, AGCATCAC

tag: sample pool


title: Spleen from PBS Treated Mouse Rep3

source_name: Spleen

tag: tissue

value: Spleen


title: BC13

description:
Three samples were pooled in this scRNA-seq reaction using MULTI-seq
G13_GEX_features.tsv.gz
G13_GEX_barcodes.tsv.gz
G13_GEX_matrix.mtx.gz

value: embryonic stem cells (hESC)

value: TAAGGCTC, TTACGGTG, GCATGTAC


title: BC11

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G11_GEX_features.tsv.gz
G11_GEX_barcodes.tsv.gz
G11_GEX_matrix.mtx.gz

value: hESC-derived mature sympathoadrenal progenitors

value: GGAGAAGA, TCACAGCA, CTAGCTGA, TTCCTTCC


title: Lung from PBS Treated Mouse Rep3

source_name: Lung

value: Lung


title: 17q1qMYCN_D14_1 [ATAC-Seq]

value: dox at D5


title: Lymph Nodes from PBS Treated Mouse Rep3

source_name: Lymph Nodes

value: Lymph Nodes


title: wt_D3_4


title: DLN/Naïve-Tregs_3

value: No transplantation

value: No

value: Mus kidney lymph node


title: FL_Shox2trac_E115_DECOM_rep2

description: sorted cells RNA-seq

tag: background

value: Embryonic Forelimb


title: FL_Shox2trac_E115_DECOM_rep1

description: sorted cells RNA-seq

tag: embryonic stage


title: wt_D9_1

value: hESC-derived trunk neural crest cells

value: lanes 7+8


title: PC3 cells, siControl rep 1

value: Prostate adenocarcinoma

tag: genotype

value: WT

value: Transfection with non-targeting siControl


title: BC9

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G9_GEX_features.tsv.gz
G9_GEX_barcodes.tsv.gz
G9_GEX_matrix.mtx.gz

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

value: TTCTCCTC, GACACTAC, CTCTCTCT


title: Liver Form PBS Treated Mouse Rep3

source_name: Liver

value: Liver

value: Bulk Tissue

value: PBS


title: wt_D3_3


title: wt_D3_2


title: FL_Shox2trac_E105_MAINTAIN_rep2

description: sorted cells RNA-seq

tag: facs-sorted status

value: dmCherry+/EYFP+


title: Tumor from PBS Treated Mouse Rep2

value: Tumor


title: Bone Marrow from PBS Treated Mouse Rep3

source_name: Bone Marrow

value: Bone Marrow


title: BC6

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G6_GEX_features.tsv.gz
G6_GEX_barcodes.tsv.gz
G6_GEX_matrix.mtx.gz

value: GTAGCACT, TTAGCCAG, TGACCGAT, CAATCGGT


title: wt_D3_1


title: BC10

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G10_GEX_features.tsv.gz
G10_GEX_barcodes.tsv.gz
G10_GEX_matrix.mtx.gz

value: CTCGGAAT, TCCAGAGT, GACTGATC, AACTGGCT


title: wt_D19_3

value: hESC-derived mature sympathoadrenal progenitors


title: BC5

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G5_GEX_features.tsv.gz
G5_GEX_barcodes.tsv.gz
G5_GEX_matrix.mtx.gz

value: GAAGGAAG, AGAAGAGG, GTACGCAT, ACATGCGT


title: wt_D19_2


title: FL_Shox2trac_E105_INACTIVE_rep1

description: sorted cells RNA-seq

value: Embryonic Forelimb

value: dmCherry-/EYFP-

tag: biological replicate


title: FL_Shox2trac_E105_INACTIVE_rep2

description: sorted cells RNA-seq


title: BC4

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G4_GEX_features.tsv.gz
G4_GEX_barcodes.tsv.gz
G4_GEX_matrix.mtx.gz

tag: cell line

value: TAACTGGC, CCAGTTAG, GGCTAACT, TGCTACAG


title: Lung from PBS Treated Mouse Rep2

value: Lung

tag: cell type


title: Lymph Nodes from PBS Treated Mouse Rep2

value: Lymph Nodes


title: FL_Shox2trac_E105_DECOM_rep2

description: sorted cells RNA-seq

value: dmCherry-/EYFP+


title: wt_D19_1

tag: day

value: lanes 7+8


title: FL_Shox2trac_E105_DECOM_rep1

description: sorted cells RNA-seq


title: BC8

description:
Three samples were pooled in this scRNA-seq reaction using MULTI-seq
G8_GEX_features.tsv.gz
G8_GEX_barcodes.tsv.gz
G8_GEX_matrix.mtx.gz

value: embryonic stem cells (hESC)

tag: sample group

value: ACCGATTG, GTCTCAAG, AACACCGT


title: wt_D14_3


title: BC1

description:
Three samples were pooled in this scRNA-seq reaction using MULTI-seq
G1_GEX_features.tsv.gz
G1_GEX_barcodes.tsv.gz
G1_GEX_matrix.mtx.gz

value: TCCTTCCT, CCACAATG, TGAGACCT


title: Bone Marrow from PBS Treated Mouse Rep2

value: Bulk Tissue

value: PBS


title: Liver from PBS Treated Mouse Rep2

value: Liver


title: HL_Shox2trac_E135_MAINTAIN_rep2

description: sorted cells RNA-seq

source_name: Embryonic Hindlimb

value: Embryonic Hindlimb

value: dmCherry+/EYFP+


title: BC7

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G7_GEX_features.tsv.gz
G7_GEX_barcodes.tsv.gz
G7_GEX_matrix.mtx.gz

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

value: ATAGCGTC, GAATCTCG, ACCTTGAG, AGACCTTG


title: wt_D14_2


title: GEX13

value: TAAGGCTC, TTACGGTG, GCATGTAC


title: FL_Shox2trac_E105_MAINTAIN_rep1

description: sorted cells RNA-seq

value: Embryonic Forelimb


title: Spleen from PBS Treated Mouse Rep2

value: Spleen


title: Tumor from PBS Treated Mouse Rep1

value: Tumor


title: wt_D14_1


title: HL_Shox2trac_E135_MAINTAIN_rep1

description: sorted cells RNA-seq


title: HL_Shox2trac_E135_INACTIVE_rep2

description: sorted cells RNA-seq

value: dmCherry-/EYFP-


title: GEX12

value: CACTGTAG, TGCATACG, CACGTATG, AGCATCAC


title: Spleen from PBS Treated Mouse Rep1


title: wt_D0_4

value: lanes 7+8


title: Lung from PBS Treated Mouse Rep1

value: Lung


title: Lymph Nodes from PBS Treated Mouse Rep1

value: Lymph Nodes


title: wt_D0_2

value: embryonic stem cells (hESC)


title: HL_Shox2trac_E135_DECOM_rep2

description: sorted cells RNA-seq

value: dmCherry-/EYFP+


title: GEX10

value: hESC-derived trunk neural crest cells

value: CTCGGAAT, TCCAGAGT, GACTGATC, AACTGGCT


title: wt_D0_3


title: BC3

description:
Four samples were pooled in this scRNA-seq reaction using MULTI-seq
G3_GEX_features.tsv.gz
G3_GEX_barcodes.tsv.gz
G3_GEX_matrix.mtx.gz

value: AGATTCCG, GAACTCTG, CGATTGAC, ACAGTGCT


title: Liver from PBS Treated Mouse Rep1

value: Liver

value: Bulk Tissue

value: PBS


title: GEX9

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

value: TTCTCCTC, GACACTAC, CTCTCTCT


title: HL_Shox2trac_E115_LowEYFP_rep3

description: sorted cells RNA-seq

value: Embryonic Hindlimb


title: HL_Shox2trac_E135_DECOM_rep1

description: sorted cells RNA-seq


title: HL_Shox2trac_E135_INACTIVE_rep1

description: sorted cells RNA-seq


title: wt_D0_1


title: GEX8

value: ACCGATTG, GTCTCAAG, AACACCGT


title: 17q_D9_4


title: Tumor from BP Treated Mouse Rep3

value: Tumor

value: BP


title: Spleen from BP Treated Mouse Rep3

value: Spleen


title: HL_Shox2trac_E115_LowEYFP_rep2

description: sorted cells RNA-seq


title: 17q_D9_3

value: lanes 7+8


title: HL_Shox2trac_E105_DECOM_rep1

description: sorted cells RNA-seq


title: GEX5

value: hESC-derived mature sympathoadrenal progenitors

value: GAAGGAAG, AGAAGAGG, GTACGCAT, ACATGCGT


title: 17q_D9_2


title: GEX6

value: GTAGCACT, TTAGCCAG, TGACCGAT, CAATCGGT


title: Nanoparticle Associated Cells in Spleen from BP Treated Mouse Rep3

value: Nanoparticle Associated Cells


title: CHiC_HL_Shox2trac_E135_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: GEX4

value: TAACTGGC, CCAGTTAG, GGCTAACT, TGCTACAG


title: 17q_D3_4


title: Nanoparticle Associated Cells in Tumor from BP Treated Mouse Rep3


title: 17q_D3_3


title: 17q_D9_1

value: hESC-derived trunk neural crest cells


title: GEX3

value: AGATTCCG, GAACTCTG, CGATTGAC, ACAGTGCT


title: CHiC_HL_Shox2trac_E135_DECOM

description: Shox2 Agilent probes C-HiC

value: dmCherry-/EYFP+


title: Bone Marrow from PBS Treated Mouse Rep1

value: Bone Marrow

value: Bulk Tissue

value: PBS


title: Nanoparticle Associated Cells in Liver from BP Treated Mouse Rep3

value: Liver


title: CHiC_HL_Shox2trac_E115_MAINTAIN

description: Shox2 Agilent probes C-HiC

value: Embryonic Hindlimb


title: 17q_D3_2


title: CHiC_HL_Shox2trac_E115_INACTIVE

description: Shox2 Agilent probes C-HiC

value: dmCherry-/EYFP-


title: GEX7

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

value: ATAGCGTC, GAATCTCG, ACCTTGAG, AGACCTTG


title: TCMR4

city: Pittsburgh

first: Elodie

last: Bailly

state: PA

address: BST 200 lothrop street

department: Surgery

institute: Starzl Transplant Institute

description: 10x Genomics 3Pv3

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.0 multi (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger).
Assembly: GRCh38
Supplementary files format and content: sample_feature_bc_matrix h5 files.

source_name: Circulating NK cells

extract_protocol:
NK cells were FACS-sorted from frozen PBMC, with the following gating strategy: viable cells, CD3 negative, CD19 negative, CD14 negative, CD7 positive, CD56 positive. Samples were labeled with TotalSeq-A Cell Hashing HTO Ab (BioLegend), then resuspended in PBS+0.04% BSA.
Ready-to sequence Illumina libraries were generated using the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry; 10× Genomics; Pleasanton, CA) per manufacturer’s protocol. Single Cell chips were loaded to retrieve 3000 cells. Sequencing single-indexed libraries (5 nM) were pooled. The resulting pooled library was loaded on a NovaSeq S2-100. The following parameters of sequencing were used: Read 1: 28 cycles; i7 Index 8 cycles; Read 2: 91 cycles, as specified by the 10× Genomics guidelines.

value: Circulating NK cells

tag: developmental stage

value: adult

value: M

tag: time post transplant(months)

tag: anti-hla donor specific antibodies

value: no

tag: disease state

tag: g (glomerulitis)

tag: ptc (peritubular capillaritis)

tag: i (interstitial inflammation)

tag: t (tubulitis)

tag: v (intimal arteritis)

tag: cg (transplant glomerulopathy)

tag: ci (interstitial fibrosis)

tag: ct (tubular atrophy)

tag: cv (chronic vasculopathy)

tag: ah (arteriolar hyaline thickening)

tag: mm (mesangial matrix increase)

tag: ptc c4d

value: yes

tag: tacrolimus

tag: mmf

tag: prednisone


title: Nanoparticle Associated Cells in Bone Marrow from BP Treated Mouse Rep3

tag: tissue

tag: cell type

value: Nanoparticle Associated Cells

tag: treatment

value: BP


title: GEX1

tag: cell line

value: embryonic stem cells (hESC)

tag: day

tag: sample group

tag: multiseq barcodes_per_sample_group

value: TCCTTCCT, CCACAATG, TGAGACCT

tag: sample pool

tag: flowcell

tag: lane


title: Lung from BP Treated Mouse Rep3

value: Lung


title: CHiC_FL_Shox2trac_E135_MAINTAIN

description: Shox2 Agilent probes C-HiC

tag: background

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: dmCherry+/EYFP+

tag: biological replicate


title: Lymph Nodes from BP Treated Mouse Rep3

value: Lymph Nodes

value: Bulk Tissue


title: 17q_D3_1

value: lanes 7+8


title: TCMR3

description: 10x Genomics 3Pv3

tag: developmental stage

tag: time post transplant(months)

tag: anti-hla donor specific antibodies

tag: disease state

tag: g (glomerulitis)

tag: ptc (peritubular capillaritis)

tag: i (interstitial inflammation)

tag: t (tubulitis)

tag: v (intimal arteritis)

tag: cg (transplant glomerulopathy)

tag: ci (interstitial fibrosis)

tag: ct (tubular atrophy)

tag: cv (chronic vasculopathy)

tag: ah (arteriolar hyaline thickening)

tag: mm (mesangial matrix increase)

tag: ptc c4d

value: FOCAL

tag: tacrolimus

tag: mmf


title: CHiC_FL_Shox2trac_E135_INACTIVE

description: Shox2 Agilent probes C-HiC

tag: background

tag: tissue

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: dmCherry-/EYFP-

tag: biological replicate


title: Liver From BPTreated Mouse Rep3

value: Liver

tag: cell type

tag: treatment


title: CHiC_FL_Shox2trac_E135_DECOM

description: Shox2 Agilent probes C-HiC

value: dmCherry-/EYFP+


title: CHiC_FL_Shox2trac_E115_MAINTAIN

description: Shox2 Agilent probes C-HiC


title: Bone Marrow from BP Treated Mouse Rep3

value: Bone Marrow


title: TCMR1

description: 10x Genomics 3Pv3

value: Circulating NK cells

tag: developmental stage

value: adult

value: M

tag: time post transplant(months)

tag: anti-hla donor specific antibodies

value: no

tag: disease state

tag: g (glomerulitis)

tag: ptc (peritubular capillaritis)

tag: i (interstitial inflammation)

tag: t (tubulitis)

tag: v (intimal arteritis)

tag: cg (transplant glomerulopathy)

tag: prednisone


title: 17q_D19_1

tag: cell line

value: hESC-derived mature sympathoadrenal progenitors

tag: day

tag: sample group

tag: flowcell

tag: lane


title: 17q_D14_3

tag: cell type


title: MixedABMR4

description: 10x Genomics 3Pv3

extract_protocol:
NK cells were FAC-sorted from frozen PBMC, with the following gating strategy: viable cells, CD3 negative, CD19 negative, CD14 negative, CD7 positive, CD56 positive. Samples were labeled with TotalSeq-A Cell Hashing HTO Ab (BioLegend), then resuspended in PBS+0.04% BSA.
Ready-to sequence Illumina libraries were generated using the Chromium Single Cell 3′ Reagent Kit (v3 Chemistry; 10× Genomics; Pleasanton, CA) per manufacturer’s protocol. Single Cell chips were loaded to retrieve 3000 cells. Sequencing single-indexed libraries (5 nM) were pooled. The resulting pooled library was loaded on a NovaSeq S2-100. The following parameters of sequencing were used: Read 1: 28 cycles; i7 Index 8 cycles; Read 2: 91 cycles, as specified by the 10× Genomics guidelines.

tag: developmental stage

value: yes

tag: ci (interstitial fibrosis)

tag: ct (tubular atrophy)

tag: cv (chronic vasculopathy)

value: ND

tag: ah (arteriolar hyaline thickening)

tag: mm (mesangial matrix increase)

tag: ptc c4d

tag: tacrolimus

tag: mmf


title: Tumor from BP Treated Mouse Rep2

tag: tissue

value: Tumor

tag: treatment

value: BP


title: 17q_D19_2

tag: cell line


title: Spleen from BP Treated Mouse Rep2

value: Spleen


title: CHiC_ESCs_Shox2trac

description: Shox2 Agilent probes C-HiC

source_name: mESC

tag: background

value: mESC

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: Not sorted

tag: biological replicate


title: MixedABMR3

description: 10x Genomics 3Pv3

tag: cell type

tag: developmental stage

value: F

tag: time post transplant(months)

tag: anti-hla donor specific antibodies

tag: disease state

tag: g (glomerulitis)

tag: ptc (peritubular capillaritis)

tag: i (interstitial inflammation)

tag: t (tubulitis)

tag: v (intimal arteritis)

tag: cg (transplant glomerulopathy)

value: DIFFUSE

tag: prednisone


title: MixedABMR2

description: 10x Genomics 3Pv3

tag: ci (interstitial fibrosis)

tag: ct (tubular atrophy)

tag: cv (chronic vasculopathy)

tag: ah (arteriolar hyaline thickening)

tag: mm (mesangial matrix increase)

tag: ptc c4d

tag: tacrolimus

tag: mmf


title: CHiC_FL_Shox2trac_E115_INACTIVE

description: Shox2 Agilent probes C-HiC

tag: background

tag: tissue

value: Embryonic Forelimb

tag: embryonic stage

tag: genotype

tag: facs-sorted status

value: dmCherry-/EYFP-

tag: biological replicate


title: 17q_D14_2

tag: cell line

tag: cell type

tag: day

tag: sample group

tag: flowcell

tag: lane

value: lanes 7+8


title: Nanoparticle Associated Cells in Tumor from BP Treated Mouse Rep2

value: Nanoparticle Associated Cells

tag: treatment


title: 17q_D14_1


title: scMm_Shox2trac_HL_E135

description: 10x Single cell kit v3.1

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: Embryonic Hindlimb

value: entire limb (not sorted)


title: 17q_D0_4

value: embryonic stem cells (hESC)


title: TCMR2

description: 10x Genomics 3Pv3

value: Circulating NK cells

tag: developmental stage

value: adult

value: M

tag: time post transplant(months)

tag: anti-hla donor specific antibodies

value: no

tag: disease state

tag: g (glomerulitis)

tag: ptc (peritubular capillaritis)

tag: i (interstitial inflammation)

tag: t (tubulitis)

tag: v (intimal arteritis)

tag: cg (transplant glomerulopathy)

tag: ci (interstitial fibrosis)

tag: ct (tubular atrophy)

tag: cv (chronic vasculopathy)

tag: ah (arteriolar hyaline thickening)

tag: mm (mesangial matrix increase)

tag: thymoglobulin induction

tag: prednisone


title: 17q_D19_3

tag: cell line

tag: cell type

value: hESC-derived mature sympathoadrenal progenitors

tag: day

tag: sample group

tag: flowcell

tag: lane


title: MixedABMR1

description: 10x Genomics 3Pv3

tag: developmental stage

tag: time post transplant(months)

tag: anti-hla donor specific antibodies

value: yes

tag: disease state

tag: g (glomerulitis)

tag: ptc (peritubular capillaritis)

tag: i (interstitial inflammation)

tag: ptc c4d

value: MINIMAL

tag: tacrolimus

tag: mmf


title: Nanoparticle Associated Cells in Lymph Nodes from BP Treated Mouse Rep2

tag: tissue

value: Lymph Nodes

tag: treatment

value: BP


title: G401_SB1_shdcaf5_rep3

city: Memphis

first: Jacquelyn

middle: A

last: Myers

state: TN

address: 262 Danny Thomas Pl

institute: St. Jude Children’s Research Hospital

data_processing:
trim_galore v0.6.3 remove adapter sequences
alignment with STAR2.7.3a --twopassMode Basic
read counts quantified by RSEMv1.3.1
Assembly: hg19/GRCh37.p13
Supplementary files format and content: quantified read counts are provided in the txt format for every sample for gencode v19

source_name: human malignant rhabdoid tumor

growth_protocol: McCoy's Medium + 10% tet-free FBS

extract_protocol:
ZymoResearch Direct-zol™ RNA MiniPrep Plus Cat # R2070 according to manufacturer instructions
TruSeq Stranded mRNA Library Prep Kit, Illumina, PN 20020595

treatment_protocol: 1ug/ml puromycin + 1ug/ml doxycycline

value: human malignant rhabdoid tumor

tag: cell line

tag: genotype

tag: time


title: GEX11

tag: cell type

tag: day

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

tag: sample group

tag: multiseq barcodes_per_sample_group

value: GGAGAAGA, TCACAGCA, CTAGCTGA, TTCCTTCC

tag: sample pool

tag: flowcell


title: 17q_D0_3

tag: lane

value: lanes 7+8


title: BV2 cells, BV2-col-2 (biol rep 2)

city: Guangzhou

first: Li

last: Wang

address: 1023 S Shatai Rd, Life Science BLDG 15B03

department: Department of Cell Biology

country: China

institute: Southern Medical University

data_processing:
FastQC (v 0.11.9) was utilized to assess the sequencing quality of the fastq files and ensure that all samples exhibited high quality.
Illumina adapter sequences were trimmed using Trim galore (v 0.6.7).
150 bp paired-end reads were aligned to mouse reference genome (GRCm39) using hisat2 (v2.2.1) method.
Comparative analysis of differentially expressed genes based on reads was performed using DEseq2 (v1.40.2).
Assembly: mm10
Supplementary files format and content: all.fpkm_anno excel file includes FPKM values for each Sample.

source_name: Brain

growth_protocol: Mouse microglia cell line BV2 were grown in DMEM (Gibco) supplemented with 10% FBS and incubated at 37°C in a 95% humidified air and 5% CO2 incubator.

extract_protocol:
RNA was extracted using the RNeasy Mini Kit (Qiagen). 1 μg total RNA was used for following library preparation.
The poly(A) mRNA isolation was performed using Oligo(dT) beads. The mRNA fragmentation was performed using divalent cations and high temperature. Priming was performed using Random Primers. First strand cDNA and the second-strand cDNA were synthesized. The purified double-stranded cDNA was then treated to repair both ends and add a dA-tailing in one reaction, followed by a T-A ligation to add adaptors to both ends. Size selection of Adaptor-ligated DNA was then performed using DNA Clean Beads. Each sample was then amplified by PCR using P5 and P7 primers and the PCR products were validated. Then libraries with different indexs were multiplexed and loaded on an Illumina Novaseq instrument for sequencingaccording to manufacturer’s instructions.

treatment_protocol: BV2 cells were treated with 4 mg/ml COL1 for 24 hours.

value: Brain

value: mouse microglia

value: WT

value: 3D COL1 gel


title: BV2 cells, BV2-col-3 (biol rep 3)


title: G401_SB1_shdcaf5_rep2


title: Nanoparticle Associated Cells in Liver from BP Treated Mouse Rep2

value: Liver

value: Nanoparticle Associated Cells


title: G401_SB1_shdcaf5_rep1


title: 17q_D0_2

value: embryonic stem cells (hESC)


title: BV2 cells, BV2-col-1 (biol rep 1)


title: Nanoparticle Associated Cells in Bone Marrow from BP Treated Mouse Rep2

value: Bone Marrow


title: Lung from BP Treated Mouse Rep2

value: Lung

value: Bulk Tissue


title: BV2 cells, BV2-3 (biol rep 3)

value: control


title: G401_SB1_shctrl_rep3


title: Nanoparticle Associated Cells in Spleen from BP Treated Mouse Rep2

value: Spleen


title: BV2 cells, BV2-2 (biol rep 2)


title: 17q_D0_1


title: Lymph Nodes from BP Treated Mouse Rep2

value: Lymph Nodes

value: BP


title: G401_SB1_shctrl_rep1

value: human malignant rhabdoid tumor


title: 17q1q_D9_4

value: hESC-derived trunk neural crest cells


title: Liver from BP Treated Mouse Rep2


title: 17q1q_D9_2

value: lanes 7+8


title: 17q1q_D9_3


title: BV2 cells, BV2-1 (biol rep 1)

value: Brain


title: Bone Marrow from BP Treated Mouse Rep2


title: 17q1q_D9_1


title: G401_GFP_shdcaf5_rep3


title: G401_GFP_shdcaf5_rep2


title: 17q1q_D3_4


title: Spleen from BP Treated Mouse Rep1


title: Tumor from BP Treated Mouse Rep1

value: Tumor


title: G401_GFP_shdcaf5_rep1


title: 17q1q_D3_3


title: G401_GFP_shctrl_rep3

value: shCTRL


title: G401_GFP_shctrl_rep2


title: 17q1q_D3_1


title: Nanoparticle Associated Cells in Spleen from BP Treated Mouse Rep1


title: G401_GFP_shctrl_rep1


title: G401_SB1_shctrl_rep2


title: 17q1q_D19_3

value: hESC-derived mature sympathoadrenal progenitors


title: G401_shDCAF5_Input_rep1 [2432991]

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

tag: chip antibody


title: Nanoparticle Associated Cells in Liver from BP Treated Mouse Rep1

value: Liver


title: Nanoparticle Associated Cells in Bone Marrow from BP Treated Mouse Rep1

value: Nanoparticle Associated Cells


title: 17q1q_D19_2


title: Lung from BP Treated Mouse Rep1


title: 17q1q_D19_1


title: G401_shDCAF5_BRD9_rep2 [2433000]


title: Lymph Nodes from BP Treated Mouse Rep1


title: 17q1q_D14_3


title: 17q1q_D14_2


title: Liver From BPTreated Mouse Rep1


title: Bone Marrow from BP Treated Mouse Rep1


title: 17q1q_D14_1


title: G401_shCTRL_BRD9_rep2 [2432994]


title: G401_shCTRL_BRD9_rep1 [2432992]


title: Nanoparticle Associated Cells in Tumor from BP Treated Mouse Rep1


title: G401_shDCAF5_BRG1_rep1 [2403660]


title: 17q1q_D3_2


title: AB1

city: hangzhou

first: wenzheng

last: qu

address: Kaixuan Road

institute: Zhejiang University

description: Adult astrocyte-Aβ_rep1

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to mm10 whole genome.
Fragments Per Kilobase of transcript sequence per  Millions (FPKM) were calculated based on the length of the gene and reads count mapped  to this gene.FPKM considers the effect of sequencing depth and gene length for  the reads count at the same time, and is currently the most commonly used method for  estimating gene expression levels.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text file include FPKM values for each Sample and genes.

source_name: Adult astrocyte

growth_protocol: Adult mice were scarified by cervical dislocation and quakily decapitated. Hippocampal and cortical tissues were dissected in pre-cold PBS. Single cells were isolated by 0.125% trypsin and 1000 U/mg papain in EBSS. After washed with cold PBS, tissues were minced finely with scalpel and pipetted followed by the digestion with 0.125% trypsin for 15 minutes at 37°C on a rotator. Precipitates were mechanically dissociated by a pipette. Cell suspension was neutralized with 2 ml DMEM with 10% FBS. After centrifuging at 1600 rpm for 3 minutes, cell pellet was resuspended within astrocyte growth medium. Suspension was centrifuged at 1600 rpm for 20 minutes then washed once with 2 ml astrocyte growth medium and centrifuged at 1600 rpm for 3 minutes. Cells were resuspended with 4 ml astrocyte growth medium and or slided in 24-well plates. Adult astrocytes were cultured at 37°C in 5% CO2.

extract_protocol:
The total RNA of cells was extracted by TRIzol reagent according to the manufacture’s protocol and the concentration was determined with a Nanodrop
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: For Aβ treated adult astrocytes, Aβ 1-42 was added to purified adult astrocytes with the working concentration of 20 μM for 72 hours.

value: cortex+hippocampus

value: astrocyte

tag: strain

value: A-beta 1-42 was added to purified adult astrocytes with the working concentration of 20 μM for 72 hours.

value: wild type

tag: age

value: 2 months old


title: 17q1q_D0_4

value: embryonic stem cells (hESC)


title: 17q1q_D0_3


title: AB2

description: Adult astrocyte-Aβ_rep2

value: A-beta 1-42 was added to purified adult astrocytes with the working concentration of 20 μM for 73 hours.


title: WT2_AB

description: Adult astrocyte-Aβ Ctrl_rep2

value: untreated


title: WT1_AB

description: Adult astrocyte-Aβ Ctrl_rep1


title: G401_shDCAF5_ARID1A_rep1 [2403658]

value: human malignant rhabdoid tumor


title: AD2

description: Adult astrocyte-AD_rep2

value: 5X APP Alzheimer's mice model

value: 6 months old


title: G401_shDCAF5_BAF155_rep1 [2403659]


title: G401_shCTRL_BRG1_rep1 [2403657]


title: G401_shCTRL_Input_rep1 [2432990]


title: 17q1qMYCN_D9_4

value: hESC-derived trunk neural crest cells

value: dox at D5

value: lanes 7+8


title: 17q1q_D0_1


title: G401_shDCAF5_BRD9_rep1 [2432998]


title: G401_shCTRL_ARID1A_rep1 [2403655]

value: shCTRL


title: AD1

description: Adult astrocyte-AD_rep1


title: 17q1qMYCN_D9_2


title: WT1_AD

description: Adult astrocyte-AD Ctrl_rep1


title: 17q1qMYCN_D9_3


title: WT2_AD

description: Adult astrocyte-AD Ctrl_rep2


title: G401_shDCAF5_input_rep1 [2403654]


title: 17q1qMYCN_D19_3

value: hESC-derived mature sympathoadrenal progenitors


title: G401_shCTRL_BAF155_rep1 [2403656]


title: 17q1qMYCN_D9_1


title: G401_shCTRL_input_rep1 [2403653]


title: G401_shDCAF5_H3K4me1_rep2 [2418853]


title: 17q1q_D0_2


title: cKO2

description: Adult astrocyte-Ogt cKO_rep2

value: 4 months old


title: cKO1

description: Adult astrocyte-Ogt cKO_rep1

value: cortex+hippocampus


title: 17q1qMYCN_D19_2


title: G401_shDCAF5_H3K4me1_rep1 [2418852]


title: WT2_cKO

description: Adult astrocyte-Ogt cKO Ctrl_rep2

value: astrocyte


title: 17q1qMYCN_D19_1


title: WT1_cKO

description: Adult astrocyte-Ogt cKO Ctrl_rep1


title: 17q1qMYCN_D14_3


title: G401_shDCAF5_H3K4me3_rep2 [2418851]


title: G401_shDCAF5_H3K4me3_rep1 [2418850]


title: UVABCO92_TAM

city: Charlottesville

first: Kevin

middle: A.

last: Janes

state: VA

address: Box 800759 Health System

department: Department of Biomedical Engineering

institute: University of Virginia

data_processing:
RNA-seq data was aligned to the human assembly GRCh38.86 and quantified using STAR v2.5 {23104886}.
Gene counts were batch corrected using ComBat_seq R package {33015620} where each patient was considered as a batch.
Assembly: GRCh38.86
Supplementary files format and content: ReadsPerGene.out.tab - STAR aligned counts in column 4 #column1: geneID #column2: countsforunstrandedRNA-seq #column3: countsforthe1streadstrandalignedwithRNA(htseq-countoption-syes) #column4: countsforthe2ndreadstrandalignedwithRNA(htseq-countoption-sreverse)
Supplementary files format and content: Aligned.out.bam - alignment
Supplementary files format and content: allcounts_batchcorr.csv - batch corrected counts

source_name: breast cancer organoids

growth_protocol: Organoid initiation. The 50-ml conical tubes containing glass slides of tumor scrapes were centrifuged at 450 rcf for 5 minutes at 8ºC to detach and pellet cells. The slides and supernatant were removed, and the pellet was washed with DMEM GlutaMAX (Gibco, #10569010) containing penicillin–streptomycin (Gibco, #15140122; final concentration = 100 U/ml) and 0.1% (wt/vol) fatty acid-free BSA (Sigma, #A6003) (D-BSA). Pellets were washed with D-BSA three times in 15 ml or 1.5 ml tubes depending on pellet size to remove dead cells, debris, and fat. Next, the pellet was digested in Type 1 medium {33692550} containing collagenase II (Fisher, #17101015; final concentration = 1 mg/ml) and ROCK inhibitor (StemCell #72304; final concentration = 10 μM) for 15 minutes at 37ºC with shaking. 15 ml conical tubes were placed at a ~20° angle in the orbital shaker at 140 rpm (New Brunswick I26 Incubator Shaker) while 1.5ml were inserted in a small benchtop shaker at 350 rpm (Eppendorf Thermomixer 5350 Mixer). The digestion was stopped by adding 1/10th volume of FBS (Gibco, #16170086) directly to the tube and pipetting vigorously with a 1-ml micropipette. If large particulates were present, the sample was passed through a pre-wet 100 μm strainer (VWR, #76327102). To remove red blood cells, the cell pellet was mixed with RBC lysis buffer (Sigma, #11814389001) and incubated at RT for 2 min. After a final wash with D-BSA, the pellet was suspended in growth factor-reduced matrigel (Corning, #354230). The volume of matrigel depended on the cellular yield, with 40 μl matrigel used to resuspend a pellet of 10 μl and scaling linearly for larger pellets. The matrigel suspension was serially dispensed a one 5 μl drop per well in a 96-well plate. The first 20 cases were initiated as 20 µl drops in a 48-well plate according to published recommendations {33692550}, and volumes of 2 µl or 7 µl were tested in Fig. 3.The drops were solidified upside down in a 37ºC incubator for 30 minutes and then100 μl pre-warmed Type 2 medium {33692550} was added to each well. Organoid maintenance. Organoids were kept in a humidified 37ºC incubator with 5% CO2 and refed every 2–4 of days by gently removing old media and adding fresh Type 2 medium, which was prepared every 7 days. For the first 20 cases when passaging was attempted,TrypLE (Gibco, #12604013) was used to dissociate the matrigel and organoids were mechanically sheared by forcefully pipetting up and down. The cells were washed with ice-cold adDMEM+, and centrifuged at 300 rcf for 5 minutes. Matrigel-free dissociated organoids were resuspended in fresh ice-cold matrigel by carefully pipetting up and down. The matrigel-suspended cells were plated in one 20 μl drop per well in a 48-well plate. The drops were solidified upside down in a 37ºC incubator for 15 minutes and then 100 μl of pre-warmed Type 2 medium was added to each well. Cell culture. MCF7 (ATCC, #HTB-22) were cultured in EMEM (ATCC, #30-2003) supplemented with 10% FBS, 1% penicillin-streptomycin, and 0.01 mg/ml insulin (Gibco, #12585014). T47D (ATCC, #HTB-133) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% FBS, 1% penicillin-streptomycin, and 0.2 Units/ml insulin. CAMA1 (ATCC, #HTB-21) were cultured in EMEM (ATCC, #30-2003) supplemented with 10% FBS and 1% penicillin-streptomycin. EFM19 (DSMZ, #ACC231) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% heat-inactivated FBS and 1% penicillin-streptomycin. HCC1500 (ATCC, #CRL-2329) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% FBS and 1% penicillin-streptomycin. ZR-75-1 (ATCC, #CRL-1500) were cultured in RPMI-1640 (ATCC, #30-2001) supplemented with 10% heat-inactivated FBS and 1% penicillin-streptomycin. Cells were grown and passaged according to ATCC or DSMZ guidelines.

extract_protocol:
RNA from primary tumors, organoids, 2D cultures, and cell lines was isolated with TRIzol reagent (Life Technologies, #15596018) followed by purification with the Direct-zol RNA MicroPrep Plus Kit including DNase treatment (Zymo Research, #R2062).
RNA-seq was performed by Genome Sciences Laboratory at Center for Public Health Genomics on 50-550 ng total RNA (TruSeq® Stranded Total RNA Library Prep, Illumina, #20020596)

value: breast cancer organoids

value: 4-OHT 200nM


title: G401_shDCAF5_H3K27ac_rep2 [2418849]


title: UVABCO87_TAM


title: 17q1qMYCN_D14_1


title: UVABCO92_DMSO

value: DMSO


title: Esophagus, K5CreERT2, KEAP1fl/fl::K5CreERT2_3

city: Sendai

first: Takafumi

last: Suzuki

address: 2-1 Seiryo-machi, Aoba-ku

department: Department of Biochemistry and Molecular Biology

country: Japan

institute: Tohoku Medical Megabank Organization, Tohoku University

data_processing:
The raw reads were mapped to the mouse genome assembly GRCm39 using Galaxy.
Transcript per million (TPM) normalized read counts were generated using Salmon quant script (Galaxy version 1.5.1+galaxy0)
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes TPM for each sample

source_name: Esophagus

extract_protocol:
RNA was harvested using Sepasol-RNA I Super G (Nacalai Tesque). About 200 µg of total RNA used for cDNA library synthesis.
RNA library for RNA-seq were prepared using MGIEasy RNA Directional Library Prep Set (MGI).

value: Esophagus


title: UVABCO87_DMSO


title: Esophagus, K5CreERT2, KEAP1fl/fl::K5CreERT2_4


title: G401_shCTRL_H3K4me1_rep1 [2418846]


title: UVABCO81_TAM


title: Esophagus, K5CreERT2, KEAP1fl/fl::K5CreERT2_2


title: UVABCO81_DMSO


title: Esophagus, K5CreERT2, KEAP1fl/fl::K5CreERT2_1


title: G401_shCTRL_H3K4me3_rep2 [2418845]


title: UVABCO80_TAM


title: 168 cells treated with PP2A inhibitor LB-100, 5uM, 24h, replicate 1

city: San Francisco

first: MARK

middle: ALAN

last: TAYLOR

department: Hellen Diller Family Comprehensive Cancer Center

institute: UCSF

data_processing:
Data quality check was done on Illumina SAV. Demultiplexing was performed with Illumina Bcl2fastq v2.19.1.403 software.
STAR aligner v2.7.11 was used to map reads to the mouse reference genome (mm10) with default settings
Sequencing QC reports were generated with QualiMap v2.3 with both bampqc and ranseq qc.  Quantification of mapped reads was performed with Salmon v1.10.2 with gcBias and seqBias enabled.  Read annotations was done with GenCode’s M31 basic annotation.  We then used DESeq2 to perform differential expression analysis between Pp2a-inhibitor treated samples and vehicle-treated samples.
Assembly: mm10
Supplementary files format and content: tab-delimited .sf files output from Salmon containing raw quantified transcript-level counts

growth_protocol: Cells were grown in 6cm petric dishes in a mdium of DMEM supplemented with 10% FBS for 24 hr

extract_protocol:
RNA was extracted using ISOLATE II RNA mini kit (Bioline) according to the manufacturer’s recommended protocol.
Libraries for RNA-Seq were prepared with KAPA Stranded mRNA-Seq Kit (Cat.KK8420), KAPA UDI Primersmix and KAPA Universal UMI Adapters

treatment_protocol: LB100 was added at 10 µM for 24 h

value: squamous cell carcinoma parenchyma

value: KO in Hras and G13R substitution in Kras


title: 168 cells treated with PP2A inhibitor LB-100, 5uM, 24h, replicate 3


title: G401_shCTRL_H3K4me3_rep1 [2418844]

value: human malignant rhabdoid tumor


title: 168 cells treated with PP2A inhibitor LB-100, 5uM, 24h, replicate 2


title: 17q1qMYCN_D14_2


title: Esophagus, K5CreERT2, NRF2L30F/L30F::K5CreERT2_4


title: 168 cells, untreated, replicate 3

value: control


title: UVABCO80_DMSO


title: G401_shDCAF5_BAF155_rep3 [2418841]


title: G401_shCTRL_H3K4me1_rep2 [2418847]


title: G401_shDCAF5_H3K27ac_rep1 [2418848]


title: Esophagus, K5CreERT2, NRF2L30F/L30F::K5CreERT2_2


title: Esophagus, K5CreERT2, NRF2L30F/L30F::K5CreERT2_3


title: G401_shCTRL_H3K27ac_rep2 [2418843]


title: Esophagus, K5CreERT2, NRF2L30F/L30F::K5CreERT2_1


title: 168 cells, untreated, replicate 1


title: G401_shDCAF5_BAF155_rep2 [2418840]


title: UVABCO78_TAM

value: 4-OHT 200nM, b-est


title: UVABCO78_DMSO

value: DMSO, b-est


title: 85 cells treated with PP2A inhibitor LB-100, 5uM, 24h, replicate 3

value: WT in Hras and Kras


title: Esophagus, K5CreERT2, NRF2L30F/+::K5CreERT2_4


title: UVABCO92_2D

source_name: breast cancer 2D culture

value: breast cancer 2D culture


title: Esophagus, K5CreERT2, NRF2L30F/+::K5CreERT2_3


title: G401_shDCAF5_ARID1A_rep2 [2418838]


title: 85 cells treated with PP2A inhibitor LB-100, 5uM, 24h, replicate 2


title: UVABCO78_TAM_3

value: 4-OHT 3uM, b-est


title: 168 cells, untreated, replicate 2


title: G401_shDCAF5_BRG1_rep3 [2418837]


title: UVABCO92_3D


title: 85 cells treated with PP2A inhibitor LB-100, 5uM, 24h, replicate 1


title: Esophagus, K5CreERT2, NRF2L30F/+::K5CreERT2_2


title: G401_shDCAF5_BRG1_rep2 [2418836]


title: G401_shCTRL_BAF155_rep3 [2418835]

value: shCTRL


title: 85 cells, untreated, replicate 3


title: Esophagus, K5CreERT2, Wild-Type_4

value: Wild-Type


title: Esophagus, K5CreERT2, Wild-Type_3


title: 85 cells, untreated, replicate 1


title: G401_shDCAF5_ARID1A_rep3 [2418839]


title: G401_shCTRL_BAF155_rep2 [2418834]


title: UVABCO87_2D


title: UVABCO87_3D


title: UVABCO87_TS

source_name: breast cancer tissue

value: breast cancer tissue


title: Esophagus, K5CreERT2, Wild-Type_2


title: UUO6_day21_biol_rep_3

city: Guadalajara

first: Raquel

last: Echavarria

state: Jalisco

address: Sierra Mojada 800

department: Surgical research

country: Mexico

institute: CONACYT- Centro de Investigacion Biomedica de Occidente, IMSS

description:
gene_count_matrix1.txt
transcript_count_matrix1.txt
genes_fpkm_expression.txt
transcripts_fpkm_expression.txt

data_processing:
Cutadapt v1.10 and in-house perl scripts were used to remove low-quality reads.
Sequence quality was verified with FastQC 0.10.1
HISAT2 2.0 was used to map reads to the genome of ftp://ftp.ensembl.org/pub/release-101/fasta/mus_musculus/dna/.
The mapped reads of each sample were assembled using StringTie.
Transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare. Transcript expression levels were estimated with StringTie 1.3.4 and ballgown.
Assembly: GRCm39
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (gene)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample (transcript)
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample (gene)
Supplementary files format and content: tab-delimited text file includes fpkm values for each sample (transcript)

source_name: Heart

extract_protocol:
RNA was isolated using TRIzol reagent and ~4 ug was submitted to LC Sciences (Houston, TX, USA) for Sequencing
Poly(A) RNA-seq library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol (Illumina, San Diego, CA, USA) after passing RNA integrity checks (RIN>7).
Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads in two rounds.
Quality control and sequencing library quantification were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip.

treatment_protocol: C57BL/6 male mice were subjected to either sham surgery (n=3) or unilateral urinary obstruction (UUO) (n=3), and 21 days post-surgery, the whole heart was removed and processed for RNA extraction.

value: Heart

tag: Sex

value: male

value: UUO surgery

value: 21 days


title: 85 cells, untreated, replicate 2


title: G401_shCTRL_ARID1A_rep2 [2418832]


title: G401_shCTRL_ARID1A_rep3 [2418833]


title: Esophagus, K5CreERT2, Wild-Type_1

value: Esophagus


title: G401_shCTRL_BRG1_rep3 [2418831]


title: Esophagus, K5Cre, KEAP1fl/fl::K5Cre_E3


title: UVABCO92_TS


title: G401_shDCAF5_Input_rep2 [2418829]


title: UUO5_day21_biol_rep_2


title: SHAM3_day21_biol_rep_3

value: Sham surgery


title: UVABCO81_TS


title: UVABCO80_2D


title: G401_shCTRL_Input_rep2 [2418828]


title: Esophagus, K5Cre, KEAP1fl/fl::K5Cre_E2


title: Esophagus, K5Cre, KEAP1fl/fl::K5Cre_E1


title: SHAM2_day21_biol_rep_2


title: G401_ATAC_shDCAF5_rep3

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
Assembly: 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


title: G401_ATAC_shDCAF5_rep2


title: UVABCO81_2D


title: SHAM1_day21_biol_rep_1


title: Esophagus, K5Cre, NRF2L30F/L30F::K5Cre_E3


title: UVABCO80_3D

value: breast cancer organoids


title: Esophagus, K5CreERT2, NRF2L30F/+::K5CreERT2_1


title: Esophagus, K5Cre, NRF2L30F/L30F::K5Cre_E2


title: UVABCO78_2D


title: UVABCO80_TS


title: Esophagus, K5Cre, NRF2L30F/L30F::K5Cre_E1


title: G401_ATAC_shCTRL_rep3

value: human malignant rhabdoid tumor


title: G401_ATAC_shDCAF5_rep1


title: UVABCO81_3D


title: UUO4_day21_biol_rep_1


title: UVABCO78_3D


title: Esophagus, K5Cre, Wild-Type_E3


title: UVABCO78_TS


title: G401_ATAC_shCTRL_rep2


title: Esophagus, K5Cre, Wild-Type_E2


title: G401_ATAC_shCTRL_rep1


title: BP treated day31 rep1

hyb_protocol: Hybridiztion wes performed using standard Nanostring nCounter protocol

scan_protocol: samples were scanned following standard Nanostring nCounter protocol

data_processing: ruv package (v0.9.7.1) in R (v4.1) was used to normalize the raw count and the batch effect for Nanostring data

label: Biotin

source_name: primary mammary tumor

label_protocol: Labeling was performed using standard Nanostring nCounter protocol

extract_protocol: Total RNA was isolated from tissues using Qiagen kit and purity of the DNAse-treated RNA was measured by Agilent Tapestation

treatment_protocol: HuHER2 transgenic tumor bearing mice were treated with PBS or BP (5 mg Fe) on the day of tumor detection (n = 12/group). Three mice from each group were sacrificed on day 1, 3, 7, or 31 and primary tumors collected for RNA isolation

value: primary mammary tumor

value: BP


title: BP treated day31 rep3


title: BP treated day31 rep2


title: UVABCO37_2D


title: Esophagus, K5Cre, Wild-Type_E1