title: Pat_946_visit1_NO_response

description: Gene expression of Patient 946, visit1, response: NO, MMF

source_name: SLE, Patient 946, visit1, response: NO, MMF

value: Whole Blood


title: RGI1_DMSO3

status: Public on Dec 21 2023

type: SRA

city: Gwangju

first: Jungmook

last: Kim

address: 77, yongbong-ro

department: Bioenergy science and technology

country: South Korea

institute: Chonnam national university

description: mock

library_source: transcriptomic

data_processing:
The quantification of transcript expression was performed using Salmon
Differential expression analysis was performed using DESeq2
Genome_build: Araport11
Supplementary_files_format_and_content: abundance measurements

molecule: polyA RNA

organism: Arabidopsis thaliana

growth_protocol: Seedlings were grown for 7 days after germination.

extract_protocol:
Total RNA from each samples was isolated using an RNeasy Plant Mini Kit (Qiagen, Japan)
The isolated total RNA was processed for preparing mRNA sequencing library using the Illumina TruSeq Stranded mRNA Sample preparation kit (Illumina) accoding to the manufacturer’s protocol.

treatment_protocol: Each plant was transferred on a filter paper containing 1/2 MS solution with mock, 100 nM rapamycin (RiD-RGI5/BAK1) or 1 µM rapamycin (RiD-RGI1/BAK1) and incubated for 4 hours with gentle shaking in light at 23°C. WT plants were treated with 100 nM RGF1 peptide for 4 hours.

tag: ecotype

tag: genotype

tag: tissue

value: root from 7-day-old-germination

tag: agent

value: mock


title: Pat_903_visit2_YES_response

type: RNA

city: GRANADA

first: Daniel

last: Toro

state: Spain

address: Avenida de la Ilustracion

department: Bioinformatics

country: Spain

institute: GENYO

description: Gene expression of Patient 903, visit2, response: YES, HC

hyb_protocol: Standard Affymetrix protcol

scan_protocol: HTAPS scan was used

data_processing: Data was normalized using rma R package

label: Biotin

molecule: total RNA

organism: Homo sapiens

source_name: SLE, Patient 903, visit2, response: YES, HC

label_protocol: NuGEN Ovation

growth_protocol: Whole Blood samples in collected fom PAXgene tubes

extract_protocol: The RNA was extracted with Trizol reagent (Life Technologies) and cleaned up with RNA easy

treatment_protocol: Standard

tag: diagnosis

value: SLE

tag: Sex

value: Female

tag: race

value: W

value: HC

value: YES

tag: sledai

tag: pga

tag: plaquenil


title: Pat_965_visit1_YES_response

description: Gene expression of Patient 965, visit1, response: YES, HC

source_name: SLE, Patient 965, visit1, response: YES, HC


title: Pat_903_visit4_YES_response

description: Gene expression of Patient 903, visit4, response: YES, HC

source_name: SLE, Patient 903, visit4, response: YES, HC


title: ovi_rep2_scRNA seq

city: Madison

first: Fei

last: Zhao

state: WI

address: 2015 Linden Drive, Room 4206/4210

department: CBS

country: USA

institute: School of Veterinary Medicine, University of Wisconsin Madison

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
Sequences were aligned with CellRanger with default setting
Data were filtered, clustered, visualized, and analyzed with Seurat V4.2.3
Data were analyzed with Seurat for oviduct and uterus (combined)
Mesenchyme and epithelial clusters data was extracted from oviduct and uterus combined Seurat object and processed with R futher.
Supplementary_files_format_and_content: barcode, feature, and matrix files exported from CellRanger
Supplementary_files_format_and_content: sheet of assigned clusters for each step of analysis
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

organism: Mus musculus

source_name: Neonatal oviduct

extract_protocol:
Oviduct or uterus were disassociated with 250µL dissociation media (0.04% BSA , 1.2 U/mL Dispase II , 1 mg/mL Collagenase B, 5 U/mL DNase I  in 1mL of 1× PBS).
Single cell sequencing libraries were prepared using Chromium Single Cell 3’ v3.1 Reagents Kits (10x Genomics) according to manufacturer’s instructions

value: Neonatal oviduct

tag: strain

value: CD1 (ICR, Strain Code:022)

tag: cell type

value: mesenchymal &epithelial cells

value: wild type

tag: treatment

value: no


title: ute_rep1_scRNA seq

description: 10x Genomics

source_name: Neonatal uterus

value: Neonatal uterus


title: ute_rep2_scRNA seq

description: 10x Genomics


title: ovi_rep1_scRNA seq

description: 10x Genomics


title: Pat_1034_visit1_NO_response

description: Gene expression of Patient 1034, visit1, response: NO, HC

source_name: SLE, Patient 1034, visit1, response: NO, HC

value: NO


title: Pat_903_visit1_YES_response

description: Gene expression of Patient 903, visit1, response: YES, HC

source_name: SLE, Patient 903, visit1, response: YES, HC


title: RGI1_DMSO1

description: mock


title: scRNAseq_mouse_progenitors_2

city: San Francisco

first: Rachel

middle: Klapper

last: Zwick

address: 513 Parnassus Ave.

institute: University of California, San Francisco

description: 10x Chromium single cell data

data_processing:
10x Genomics cellranger count used to produce the filtered gene count matrix files from fastq files
deMULTIplex v 1.0.2 was used to align MULTIseq barcodes and demultiplex the datasets from the "BAR" fastq files
Assembly: mouse mm10-3.0.0 reference (10x Genomics)
Supplementary files format and content: Matrix, barcodes, and features tables with raw gene counts for every gene and every sample

source_name: small intestine

extract_protocol:
The intestine was washed, cut into 30 pieces of equal length, and incubated with media supplemented with 5mM EDTA and 10mM DTT at 37°C with 5% CO2. Cells were triturated, strained, washed, and labelled with barcodes unique to each segment using the MULTIseq method. The target population was FACS sorted.
10x libraries were prepared for sequencing using standard 10x genomics protocols adaoted for MULTIseq as described in McGinnis et al. Nat Methods 2019.
Chromium Single Cell 3'

value: Intestinal progenitor cell sample

value: FACS sorted intestinal epithelial progenitor cells (CD45-, EpCAM+, CD44+, Lgr5-DTR+)

value: small intestine

tag: age

value: adult


title: scRNAseq_mouse_progenitors_1

description: 10x Chromium single cell data


title: col1_Rap4

description: 1 μM of rapamycin

value: WT

value: root from 7-day-old-germination

value: 1 microM of rapamycin


title: RGI1_DMSO4

description: mock

value: mock


title: scRNAseq_mouse_totalIEC_1

description: 10x Chromium single cell data

value: Total intestinal epithelial cell sample


title: Pat_881_visit1_YES_response

description: Gene expression of Patient 881, visit1, response: YES, PHC

source_name: SLE, Patient 881, visit1, response: YES, PHC

value: Whole Blood

value: SLE

value: Female

value: B

value: PHC

value: YES


title: col1_Rap2

description: 1 μM of rapamycin


title: Pat_877_visit2_NO_response

description: Gene expression of Patient 877, visit2, response: NO, HC

source_name: SLE, Patient 877, visit2, response: NO, HC

value: Male

value: W

value: HC


title: scRNAseq_mouse_Diet_9

description: 10x Chromium single cell data

value: Intestine Diet Types

value: FACS sorted intestinal epitheilal cells (CD45-, EpCAM+)


title: Pat_841_visit2_YES_response

description: Gene expression of Patient 841, visit2, response: YES, HC

source_name: SLE, Patient 841, visit2, response: YES, HC


title: Pat_881_visit2_YES_response

description: Gene expression of Patient 881, visit2, response: YES, PHC

source_name: SLE, Patient 881, visit2, response: YES, PHC


title: scRNAseq_mouse_Diet_5

description: 10x Chromium single cell data

value: small intestine

value: adult


title: scRNAseq_mouse_totalIEC_2

description: 10x Chromium single cell data

value: FACS sorted intestinal epithelial progenitor cells (CD45-, EpCAM+, CD44+, Lgr5-DTR+)


title: Pat_877_visit1_NO_response

description: Gene expression of Patient 877, visit1, response: NO, HC

source_name: SLE, Patient 877, visit1, response: NO, HC

value: NO


title: Pat_841_visit1_YES_response

description: Gene expression of Patient 841, visit1, response: YES, HC

source_name: SLE, Patient 841, visit1, response: YES, HC


title: col1_DMSO2

description: mock

value: WT

value: root from 7-day-old-germination

value: mock


title: scRNAseq_mouse_Diet_2

description: 10x Chromium single cell data


title: col1_Rap1

description: 1 μM of rapamycin

value: 1 microM of rapamycin


title: scRNAseq_mouse_Diet_8

description: 10x Chromium single cell data


title: scRNAseq_mouse_Diet_7

description: 10x Chromium single cell data


title: scRNAseq_mouse_Diet_3

description: 10x Chromium single cell data


title: scRNAseq_mouse_Diet_1

description: 10x Chromium single cell data


title: col1_DMSO1

description: mock


title: 80ng E14 mESC, 6-letter, Technical Rep2

city: Cambridge

first: Páidí

last: Creed

address: B400, The Trinity Building Chesterford Business Park, Saffron Walden

country: United Kingdom

institute: biomodal limited

library_source: genomic

data_processing:
Adapter and quality trimming: cutadapt v4.1 Read resolution: proprietary Python package Alignment:  bwa v0.7.17 Sorting and Indexing: samtools v1.15 Merging BAMs across lanes: samtools v1.15 Duplicate Marking: Picard MarkDuplicates v2.23.8 BAM splitting: samtools v1.15 Methylation quantification: proprietary Python package
Assembly: GRCm38
Supplementary files format and content: CG_quant.CXreport.txt.gz: TSV file with methylation and hybroxymethylation for each CpG.  Columns are Chromosome, Position (1-based), Strand, Count methylated (5mC), Count hydroxymethylated (5hmC), Count unmethylated, C-context, and Trinucleotide context.  This extends the commonly-used Bismark Cytosine report format to represent data with separate measurement of 5mC and 5hmC
Library strategy: 6-letter sequencing

molecule: genomic DNA

source_name: Embryo

growth_protocol: SAM mouse embryonic stem cells (ESCs) were generated by lentiviral transduction of lenti dCas9-VP64_Blast (Addgene 61425) and lenti MS2-p65-HSF1_Hygro (Addgene 61426) into E14 mouse ESCs, followed by antibiotic selection and manual subcloning. Clones were checked by genomic PCR and one clone was used for consecutive experiments.

extract_protocol:
DNA extracted using commerical Qiagen kit follow manufacturers instructions
80ng of sonicated genomic DNA was processed with 6-letter sequencing by biomodal

treatment_protocol: Mouse embryonic stem cells (mESCs) were grown under serum/LIF conditions: DMEM (Gibco, 11995-040), 15% fetal bovine serum, 1 U/ml penicillin - 1 mg/ml streptomycin (Gibco, 15140-122), 0.1 mM nonessential amino acids (Gibco, 11140-050), 4 mM GlutaMAX (Gibco, 35050-061), 50 mM β-mercaptoethanol (Gibco, 31350-010), and 103 U/ml LIF (Stem Cell Institute, Cambridge), and cultured at 37 ̊C in 5% CO2 on gelatinized tissue-culture plates. The media was refreshed every day and the cells passaged every other day with Trypsin EDTA (Thermo Fisher Scientific, 25200056).

value: Embryo

tag: cell line

value: embryonic stem cell , blastocyst-derived


title: 80ng E14 mESC, 6-letter, Technical Rep4


title: 80ng E14 mESC, 6-letter, Technical Rep3


title: col_RGF1_4

description: 100 nM RGF1

value: 100 nM RGF1


title: 80ng E14 mESC, 6-letter, Technical Rep1


title: col_RGF1_3

description: 100 nM RGF1


title: col1_DMSO3

description: mock


title: scRNAseq_mouse_Diet_4

description: 10x Chromium single cell data


title: Pat_834_visit2_YES_response

description: Gene expression of Patient 834, visit2, response: YES, HC

source_name: SLE, Patient 834, visit2, response: YES, HC

value: Whole Blood

value: SLE

value: Female

value: O

value: YES


title: col_RGF1_2

description: 100 nM RGF1


title: Pat_830_visit2_YES_response

description: Gene expression of Patient 830, visit2, response: YES, AZA

source_name: SLE, Patient 830, visit2, response: YES, AZA

value: B

value: AZA


title: Pat_802_visit2_YES_response

description: Gene expression of Patient 802, visit2, response: YES, HC

source_name: SLE, Patient 802, visit2, response: YES, HC

value: W

value: HC


title: Control_3

city: shanghai

first: Zhang

last: JIwei

address: 1200 Cai Lun Road

country: China

institute: Shanghai University of Traditional Chinese Medicine

data_processing:
fastqc0.11.5, STAR2.7.9, featureCounts2.0.1
Sequence reads were trimmed for adptor squence/low-quality sequence using fastqc0.11.5.
Trimmed sequence reads were mapped GRCm38/mm10 using STAR2.7.9.
Read count extraction and quantification were performed using featureCounts2.0.1.
Assembly: GRCm38
Supplementary files format and content: table-delimited txt file includes raw counts for each samples.

source_name: Tumor tissue

extract_protocol:
mRNA was purified from total RNA using poly-T oligo-attached magnetic beads
Fragmentation was carried out using divalent cations under elevated temperature in First Strand Synthesis Reaction Buffer(5X). First strand cDNA was synthesized using random hexamer primer and M-MuLV Reverse Transcriptase(RNase H-). Second strand cDNA synthesis was subsequently performed using DNA Polymerase I and RNase H.

value: Tumor tissue

value: Tumor cells


title: col_mock3

description: mock

value: WT

value: root from 7-day-old-germination


title: NFKB_3

value: NFKB overexpression


title: NFKB_2


title: NFKB_1


title: Pat_834_visit1_YES_response

description: Gene expression of Patient 834, visit1, response: YES, HC

source_name: SLE, Patient 834, visit1, response: YES, HC


title: Pat_802_visit1_YES_response

description: Gene expression of Patient 802, visit1, response: YES, HC

source_name: SLE, Patient 802, visit1, response: YES, HC


title: Control_1

value: Tumor  cells


title: col_mock2

description: mock

value: mock


title: col_mock1

description: mock


title: Pat_830_visit1_YES_response

description: Gene expression of Patient 830, visit1, response: YES, AZA

source_name: SLE, Patient 830, visit1, response: YES, AZA


title: Control_2


title: AB10792 [Lung]

city: Rehovot

first: Ido

last: Amit

address: 234 Herzl st.

department: Immunology

country: Israel

institute: Weizmann Institute of Science

description:
MARSseq
3' RNA

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed. well-barcode N7 followed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q27_annotated.txt

source_name: Lung

growth_protocol: GL261 cells were grown in full DMEM medium.

extract_protocol:
Isolation of tumor cells and tumor-infiltrating immune cells was performed from tumor-bearing brain hemispheres. Briefly mice were perfused with PBS and the tumor-bearing brain hemisphere was collected in Roswell Park Memorial Institute (RPMI) medium containing 0.4 mg/ml Collagenase IV and 0.1 mg/ml DNase I (both Sigma-Aldrich). The tissue was then incubated for 40 min at 37°C and further homogenize using a 18G needle. Myelin was removed using a 30% Percoll centrifugation step (Sigma-Aldrich). Blood samples were processed with RBC lysis solution, colon and lung tissue was digested with the enzymatic digestion mix.
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single-cell RNA-sequencing for gene expression quantitation

treatment_protocol:
Groups of tumor bearing mice were treated with anti-TREM2 antibodies or isotype control (anti-hILT1) at days 2 and 7 post tumor implantation. See Molgora et al 2020, Cell. Some groups did not receive tumor nor treatment.
Some mice were implanted with 2x10^4 GL261 cells intracerebrally, some did not. 11-12 days later mice received i.v. fluorescent CD45 antibody time stamps. On day 13 mice were sacrificed and tumors were extracted for single cell processing.

value: Lung

value: 5 weeks

tag: day of tissue harvest

tag: biological replicate

value: Mouse 4


title: AB10791 [Lung]

description:
MARSseq
3' RNA


title: AB10790 [Lung]

description:
MARSseq
3' RNA


title: AB10789 [Lung]

description:
MARSseq
3' RNA


title: AB10788 [Lung]

description:
MARSseq
3' RNA


title: AB10786 [Lung]

description:
MARSseq
3' RNA

value: Mouse 3


title: Pat_784_visit2_NO_response

description: Gene expression of Patient 784, visit2, response: NO, MMF

source_name: SLE, Patient 784, visit2, response: NO, MMF

value: Whole Blood

value: SLE

value: Female

value: MMF

value: NO


title: Pat_784_visit1_NO_response

description: Gene expression of Patient 784, visit1, response: NO, MMF

source_name: SLE, Patient 784, visit1, response: NO, MMF

value: B


title: AB10785 [Lung]

description:
MARSseq
3' RNA


title: Pat_783_visit2_YES_response

description: Gene expression of Patient 783, visit2, response: YES, HC

source_name: SLE, Patient 783, visit2, response: YES, HC

value: HC

value: YES


title: AB10784 [Lung]

description:
MARSseq
3' RNA


title: AB10782 [Lung]

description:
MARSseq
3' RNA

value: Mouse 2


title: Pat_765_visit2_YES_response

description: Gene expression of Patient 765, visit2, response: YES, MMF

source_name: SLE, Patient 765, visit2, response: YES, MMF

value: W


title: AB10781 [Lung]

description:
MARSseq
3' RNA


title: HAES_IGFPG

city: Setagaya-ku

first: Akihiro

last: Umezawa

state: Tokyo

department: Center for Regenerative Medicine

country: Japan

institute: National Center for Child Health and Development

hyb_protocol: Hybridization and washing were performed according to Agilent's standard manual, and a Gene Expression Wash Pack (5188-5327: Agilent) was used for washing.

scan_protocol: An Agilent DNA Microarray Scanner was used to scan the microarrays.

data_processing: Agilent's Feature Extraction was used to quantify the scan results. Instructions for use followed the Agilent manual.

source_name: ESC derived Hepatocytes, replicate #2

label_protocol: Cyanine-3 (Cy3)-labeled cRNA was prepared from 0.1 ug RNA using the One-Color Low Input Quick Amp Labeling Kit (5190-2305, Agilent) and the QIAGEN RNeasy mini kit (74104 : QIAGEN) according to the manufacturer's instructions. The amount of dye uptake and cRNA The quality of the labeled cRNA was monitored by Agilent 2100 Bioanalyzer, and the amount of dye incorporation and the yield of cRNA were confirmed by NanoDrop ND-1000 Spectrophotometer.

growth_protocol: Human pluripotent stem cells derived mesenchymal stromal cells (LONG) were cultured in DMEM. Human pluripotent stem cells derived intestinal epithelial cells (RYU) were cultured on LONG and ESTEM-HE medium.

extract_protocol: Total RNA was isolated using the miRNeasy mini kit (Qiagen, Hilden, Germany) following the manufacturer's instructions. RNA was quantified using a NanoDrop-1000 spectrophotometer and monitored for quality using an Agilent 2100 Bioanalyzer (Agilent, CA, USA).

value: Hepatocytes

tag: derived

value: hESC


title: Pat_783_visit1_YES_response

description: Gene expression of Patient 783, visit1, response: YES, HC

source_name: SLE, Patient 783, visit1, response: YES, HC


title: AB10779 [Lung]

description:
MARSseq
3' RNA


title: Pat_765_visit1_YES_response

description: Gene expression of Patient 765, visit1, response: YES, MMF

source_name: SLE, Patient 765, visit1, response: YES, MMF


title: AB10780 [Lung]

description:
MARSseq
3' RNA


title: AB10787 [Lung]

description:
MARSseq
3' RNA


title: AB10778 [Lung]

description:
MARSseq
3' RNA


title: AB10783 [Lung]

description:
MARSseq
3' RNA


title: HAES_Somaz

source_name: ESC derived Hepatocytes, replicate #3


title: HAES_IGFS

source_name: ESC derived Hepatocytes, replicate #1


title: AB10777 [Gut]

description:
MARSseq
3' RNA

source_name: Gut

value: Gut


title: AB10776 [Gut]

description:
MARSseq
3' RNA


title: AB10775 [Gut]

description:
MARSseq
3' RNA


title: Pat_759_visit4_YES_response

description: Gene expression of Patient 759, visit4, response: YES, MMF

source_name: SLE, Patient 759, visit4, response: YES, MMF


title: AB10774 [Gut]

description:
MARSseq
3' RNA


title: Pat_759_visit3_YES_response

description: Gene expression of Patient 759, visit3, response: YES, MMF

source_name: SLE, Patient 759, visit3, response: YES, MMF


title: AB10773 [Gut]

description:
MARSseq
3' RNA


title: LONG05_P5

source_name: ESC derived mesenchymal stromal cells, LONG05, P5

value: mesenchymal stromal cells


title: LONG07_P5

source_name: iPSC derived mesenchymal stromal cells, LONG07, P5

value: hiPSC


title: Pat_759_visit2_YES_response

description: Gene expression of Patient 759, visit2, response: YES, MMF

source_name: SLE, Patient 759, visit2, response: YES, MMF


title: LONG04_P5

source_name: ESC derived mesenchymal stromal cells, LONG04, P5


title: Pat_759_visit1_YES_response

description: Gene expression of Patient 759, visit1, response: YES, MMF

source_name: SLE, Patient 759, visit1, response: YES, MMF


title: JUN01P4Pu

source_name: human small intestine derived intestinal epithelial cells, P4, puromycin treatment

value: intestinal epithelial cells

value: tissue


title: Pat_749_visit2_NO_response

description: Gene expression of Patient 749, visit2, response: NO, HC

source_name: SLE, Patient 749, visit2, response: NO, HC

value: Whole Blood


title: RYU05P12Pu

source_name: ESC derived intestinal epithelial cells, RYU05, P12, puromycin treatment


title: RYU05P6Pu

source_name: ESC derived intestinal epithelial cells, RYU05, P6, puromycin treatment


title: AB10771 [Gut]

description:
MARSseq
3' RNA

value: 5 weeks

value: Mouse 3


title: AB10769 [Gut]

description:
MARSseq
3' RNA


title: AB10767 [Gut]

description:
MARSseq
3' RNA


title: AB10766 [Gut]

description:
MARSseq
3' RNA


title: AB10765 [Gut]

description:
MARSseq
3' RNA


title: AB10763 [Gut]

description:
MARSseq
3' RNA


title: AB10770 [Gut]

description:
MARSseq
3' RNA


title: AB10764 [Gut]

description:
MARSseq
3' RNA


title: AB10768 [Gut]

description:
MARSseq
3' RNA


title: AB10772 [Gut]

description:
MARSseq
3' RNA


title: AB10760 [Blood]

description:
MARSseq
3' RNA

source_name: Blood

value: Blood

value: Mouse 4


title: AB10759 [Blood]

description:
MARSseq
3' RNA


title: AB10758 [Blood]

description:
MARSseq
3' RNA


title: RYU04P12Pu

source_name: ESC derived intestinal epithelial cells, RYU04, P12, puromycin treatment


title: Pat_749_visit1_NO_response

description: Gene expression of Patient 749, visit1, response: NO, HC

source_name: SLE, Patient 749, visit1, response: NO, HC

value: SLE

value: Female

value: NO


title: Pat_742_visit2_NO_response

description: Gene expression of Patient 742, visit2, response: NO, PHC

source_name: SLE, Patient 742, visit2, response: NO, PHC

value: B

value: PHC


title: AB10761 [Blood]

description:
MARSseq
3' RNA


title: AB10757 [Blood]

description:
MARSseq
3' RNA


title: RYU04_P2

source_name: ESC derived intestinal epithelial cells, RYU04, P2


title: AB10756 [Blood]

description:
MARSseq
3' RNA


title: RYU04P3Pu

source_name: ESC derived intestinal epithelial cells, RYU04, P3, puromycin treatment


title: Pat_725_visit5_NO_response

description: Gene expression of Patient 725, visit5, response: NO, PHC

source_name: SLE, Patient 725, visit5, response: NO, PHC

value: W


title: RYU05_P5

source_name: ESC derived intestinal epithelial cells, RYU05, P5

value: hESC


title: RYU04_P12

source_name: ESC derived intestinal epithelial cells, RYU04, P12


title: Pat_742_visit1_NO_response

description: Gene expression of Patient 742, visit1, response: NO, PHC

source_name: SLE, Patient 742, visit1, response: NO, PHC


title: Pat_725_visit3_NO_response

description: Gene expression of Patient 725, visit3, response: NO, PHC

source_name: SLE, Patient 725, visit3, response: NO, PHC


title: Pat_725_visit6_NO_response

description: Gene expression of Patient 725, visit6, response: NO, PHC

source_name: SLE, Patient 725, visit6, response: NO, PHC


title: Pat_725_visit4_NO_response

description: Gene expression of Patient 725, visit4, response: NO, PHC

source_name: SLE, Patient 725, visit4, response: NO, PHC


title: AB10753 [Blood]

description:
MARSseq
3' RNA

value: Mouse 2


title: RYU05_P12

source_name: ESC derived intestinal epithelial cells, RYU05, P12


title: JUN01_P4

source_name: human small intestine derived intestinal epithelial cells, P4


title: Pat_725_visit1_NO_response

description: Gene expression of Patient 725, visit1, response: NO, PHC

source_name: SLE, Patient 725, visit1, response: NO, PHC


title: human_SI

source_name: adult human small intestine (whole)


title: AB10755 [Blood]

description:
MARSseq
3' RNA

source_name: Blood


title: AB10754 [Blood]

description:
MARSseq
3' RNA


title: AB10751 [Blood]

description:
MARSseq
3' RNA


title: AB10752 [Blood]

description:
MARSseq
3' RNA


title: AB10750 [Blood]

description:
MARSseq
3' RNA


title: AB10745 [Lung]

description:
MARSseq
3' RNA

source_name: Lung

value: Lung

value: Mouse 1


title: AB10746 [Lung]

description:
MARSseq
3' RNA


title: AB10744 [Lung]

description:
MARSseq
3' RNA


title: Pat_699_visit5_YES_response

description: Gene expression of Patient 699, visit5, response: YES, HC

source_name: SLE, Patient 699, visit5, response: YES, HC

value: HC

value: YES


title: AB10743 [Gut]

description:
MARSseq
3' RNA

source_name: Gut

value: Gut


title: RYU02_5653

source_name: ESC derived intestinal epithelial cells, RYU02, P4, puromycin treatment

value: intestinal epithelial cells


title: AB10742 [Gut]

description:
MARSseq
3' RNA

value: 5 weeks


title: RYU03_5653

source_name: ESC derived intestinal epithelial cells, RYU03, P5, puromycin treatment


title: Pat_699_visit4_YES_response

description: Gene expression of Patient 699, visit4, response: YES, HC

source_name: SLE, Patient 699, visit4, response: YES, HC

value: Whole Blood


title: Pat_725_visit2_NO_response

description: Gene expression of Patient 725, visit2, response: NO, PHC

source_name: SLE, Patient 725, visit2, response: NO, PHC


title: Pat_699_visit3_YES_response

description: Gene expression of Patient 699, visit3, response: YES, HC

source_name: SLE, Patient 699, visit3, response: YES, HC


title: AB10739 [Blood]

description:
MARSseq
3' RNA

value: Blood


title: AB10741 [Gut]

description:
MARSseq
3' RNA


title: AB10738 [Blood]

description:
MARSseq
3' RNA


title: AB10740 [Blood]

description:
MARSseq
3' RNA


title: HFD_TNO [104398-001-016]

city: Leiden

first: Martine

middle: C

last: Morrison

address: Sylviusweg 71

department: MHR

country: Netherlands

institute: TNO

data_processing:
Quality filtering and adapter-trimming of the Illumina NovaSeq6000 fastq files was performed by TRIMMOMATIC software
Trimmed Fastq files were merged (in case of Paired-end reads) and aligned to the reference genome using the STAR 2.5 algorithm with default settings (https://github.com/alexdobin/STAR).
Based on the mapped read locations and the gene annotation, Htseq-count 0.6.1p1 was used to count the read mapping frequency/gene (transcript region) resulting in count.files.
Assembly: Mus_musculus.GRCm38.gencode.vM19
Supplementary files format and content: The count files contain the # reads mapped per gene (not normalised per sample). These counts serve as input for the statistical analysis using DEseq2 package.

source_name: liver

growth_protocol: All animal experiments were carried out in accordance with European guidelines for the care and use of laboratory animals (European Directive 2010/63/EU) and the Norwegian national guidelines for animal welfare, and the protocol was ethically reviewed and approved by the Norwegian Food Safety Authority (ID 21501). Animal welfare was monitored by daily assessment of water and food intake, stool and fur quality, activity level and behavior. Male Ldlr-/-.Leiden mice (genetic background 94% C57BL/6J and 6% 129S) were obtained from the breeding stock in the AAALAC-accredited SPF animal facility at TNO Metabolic Health Research (Leiden, the Netherlands). The animal experiment was performed in the animal facility at the Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, (NMBU; Ås, Norway). Animals where group-housed (n=3/cage) in individually ventilated cages (IVC; Innovive, San Diego, CA, USA) in a temperature- and humidity-controlled room (24-26°C, RH 45-60%) on a 12-hour light-dark cycle with free access to food and water. Until the start of the experiment all mice were kept on a standard rodent chow diet (Rat/Mouse Maintenance; Ssniff Spezialdïaten, Soest, Germany).

extract_protocol:
For next generation sequencing the RNA-Bee total-RNA isolation kit (Campro Scientific, Veenendaal, the Netherlands) was used to isolate total RNA from individual liver samples and RNA integrity was determined with the RNA 6000 Nano Lab-on-a-Chip kit and bioanalyzer 2100 (Agilent Technologies, Amstelveen, The Netherlands). Total RNA's were processed into tagged random sequence libraries.
Next Generation Sequencing was performed at Genome Scan (Leiden, the Netherlands). For this, strand-specific cDNA libraries were generated from total-RNA using oligo-dT magnetic beads, mRNA fragmentation, NEBNext Ultra Directional RNA Library Prep Kit from Illumina, NEB #E7760S/L resulting in 300–500 bp amplified libraries/sample. Libraries were multiplexed, clustered, and sequenced on a NovaSeq6000 v1.5 system (Illumina, New England Biolabs, Inc. Ipswich, MA, USA), with a paired-end, 2x150 bp sequencing protocol, 20 million (min-max=11-38 million) reads per sample and indexing.
Clustering and DNA sequencing using the NovaSeq6000 v1.5 was performed according to manufacturer's protocols. A concentration of 1.1 nM of DNA was used yielding paired end reads (2x 150bp). NovaSeq control software NCS v1.7 was used. Image analysis, base calling, and quality check was performed with the Illumina data analysis pipeline RTA3.4.4 and Bcl2fastq v2.20.

treatment_protocol: At 15-18 weeks of age, mice were randomized and divided into 6 experimental groups. One group (n=9) was kept on the chow diet as a healthy/ageing reference group (chow). The other 5 groups were fed an energy-dense high-fat diet (HFD) that contained 45 kcal% fat from either plant or animal origin: olive and rapeseed oil (olive : rapeseed, 20:80 ratio); n=13), sunflower oil (n=13), pork fat (n=13), beef fat (n=14) or milk fat (n=14). The HFDs were iso-energetic (4,75 kcal/g) and differed only in fat source. The carbohydrate source of the HFDs was fine grained whole oat flour (Norgesmøllene, Skien, Norway) and the protein source was casein (Dyets Inc., Betlehem, PA, USA). The vitamin mix and mineral mix were based on the AIN76A vitamin mix and a DIO mineral mix (Dyets Inc.). The vitamin A in the vitamin mix added to the milk fat diet was reduced by 50% to adjust for higher vitamin A naturally present in milk fat. All diets were made in-house by mixing all the ingredients followed by manual pelleting and freeze drying. The full diet composition is provided in Supplement 1. All diets were vacuum packed to prohibit oxidation and stored at -20 °C until use and cages were provided with fresh feed weekly.   Body weight and food intake were monitored throughout the study. Blood samples for EDTA plasma isolation were collected via leg vein after a 4 hour fast, in week 17 and 24 of the study. After 28 weeks, animals were euthanized by cervical dislocation under deep anesthesia with a cocktail of Zoletil Forte® (Virbac, Carros, France), Rompun® (Bayer, Oslo, Norway), and Fentadon® (Eurovet Animal Health, Gaziantep, Turkey) (ZRF; intraperitoneally 0.01 mL ZRF/g body weight), with the following active ingredients: zolazepam (32 mg/kg), tiletamine (32 mg/kg), xylazine (4.5 mg/kg), and fentanyl (26 μg/kg). Blood for EDTA plasma isolation was collected via heart puncture and organs were isolated. Hearts with aortic roots were fixed in formalin and embedded in paraffin for atherosclerosis analysis. Livers were weighed, snap-frozen in liquid N2 and then stored at -80 °C for RNA isolation. Epidydimal fat pads were weighed and fixed in formalin and embedded in paraffin for analysis of adipocyte hypertrophy and adipose tissue inflammation.

value: liver

tag: group

value: High Fat Diet (TNO, dept. MHR, Leiden, NL)

tag: mouse number


title: HFD_TNO [104398-001-024]

tag: tissue


title: Pat_699_visit2_YES_response

description: Gene expression of Patient 699, visit2, response: YES, HC

source_name: SLE, Patient 699, visit2, response: YES, HC

tag: diagnosis

value: SLE

value: Female


title: HFD_TNO [104398-001-056]


title: HFD_TNO [104398-001-052]


title: RYU01_5653

source_name: iPSC derived intestinal epithelial cells, RYU01, P6, puromycin treatment

value: hiPSC


title: RYU01_P6

source_name: iPSC derived intestinal epithelial cells, RYU01, P6


title: Pat_676_visit2_YES_response

description: Gene expression of Patient 676, visit2, response: YES, MMF

source_name: SLE, Patient 676, visit2, response: YES, MMF

tag: Sex

value: W

value: MMF


title: RYU02_P4

source_name: ESC derived intestinal epithelial cells, RYU02, P4

value: hESC


title: Pat_676_visit1_YES_response

description: Gene expression of Patient 676, visit1, response: YES, MMF

source_name: SLE, Patient 676, visit1, response: YES, MMF

tag: race


title: Pat_699_visit1_YES_response

description: Gene expression of Patient 699, visit1, response: YES, HC

source_name: SLE, Patient 699, visit1, response: YES, HC

tag: sledai


title: Trigeminal ganglion, ctrl, scRNAseq

city: Los Angeles

last: Pei

state: CA

address: 2250 Alcazar St

institute: USC

data_processing:
Quality control, mapping, and count table assembly of the library were performed using the CellRanger pipeline version 3.1.0.
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, features.tsv, matrix.mtx)

source_name: trigeminal ganglion

growth_protocol: Mice were housed in pathogen-free conditions.

extract_protocol: cDNA libraries were prepared for sequencing using standard 10X Genomics protocols

treatment_protocol: trigeminal ganglion samples from wild-type mice were collected at PN3.5 and single cells were collected

value: trigeminal ganglion

tag: genotype

value: wild type


title: HFD_TNO [104398-001-040]


title: RYU03_P5

source_name: ESC derived intestinal epithelial cells, RYU03, P4


title: Pat_675_visit1_NO_response

description: Gene expression of Patient 675, visit1, response: NO, AZA

source_name: SLE, Patient 675, visit1, response: NO, AZA

value: B

value: AZA

value: NO

tag: pga

tag: plaquenil


title: HFD_TNO [104398-001-044]


title: Pat_646_visit2_YES_response

description: Gene expression of Patient 646, visit2, response: YES, MMF

source_name: SLE, Patient 646, visit2, response: YES, MMF

value: YES


title: TBK1i_KLA rep1

city: La Jolla

first: Christopher

last: Glass

address: 9500 Gilman Dr.

department: CMM

institute: University of California, San Diego

description:
mouse_C57Bl6_KLA6h_BMDM_RNA_TBK1inh_rep1_YA_l20210323_CGTACG
DMSO_KLA_merged_allRawTags.txt

data_processing:
FASTQ files were processed to assess quality by determining general sequencing bias, clonality and adapter sequence contamination.  RNA sequencing reads were aligned to the mm10 mouse reference genome using STAR.  Gene expression levels were calculated using HOMER by counting all strand specific reads within exons.  Only the most abundant transcripts, including multiple alternative variants, were selected for each gene, and the genes with a length smaller than 250 bp were removed.  Transcripts per million (TPM) were used to evaluate the correlation among replicates.  Differential gene expression was calculated using DESeq2 to assess both biological and technical variability between experiments.
Assembly: mm10

source_name: Bone marrow-derived macrophages

extract_protocol:
Total RNA was isolated from culture cells and purified using a Direct-zol RNA MicroPrep Kit (Zymo Research) as described by the manufacture.  mRNAs were enriched by incubation with Oligo d(T) Magnetic Beads (NEB).
To fragment Poly A-enriched mRNA, mRNAs were incubated in 2X Superscript III first-strand buffer (Invitrogen) with 10 mM DTT at 94°C for 9 minutes.  The 10 µ l of fragmented mRNAs were incubated with 0.5 µl of Random primers (3 µg/µl) (Invitrogen), 0.5 µl of Oligo dT primer (50 µM) (Invitrogen), 0.5 µl of SUPERase-In (Ambion), and 1 µl of dNTPs (Invitrogen) at 50°C for 1 min.  After the incubation, 5.8 µl of water, 1 µl of DTT (100 mM), 0.1 µl of Actinomycin D (2 µg/µL), 0.2 µl of 1% Tween-20 and 0.5 µl of Superscript III (Invitrogen) were added and incubated on the following conditions: 25°C for 10 min, 50°C for 50 min, and 4°C hold.  The mixture was purified with RNAClean XP beads (Beckman Coulter) as described by the manufacture and eluted with 10 µl of water.  For second-strand synthesis with dUTP, the RNA/cDNA double-stranded hybrid was then added to 1.5 µl of Blue Buffer (Enzymatics), 1.1 µl of dUTP mix (10 mM dATP, dCTP, dGTP and 20 mM dUTP), 0.2 µl of RNAse H (5 U/µl) (Enzymatics), 1.05 µl of water, 1 µl of DNA polymerase I (Enzymatics), and 0.15 µl of 1% Tween-20.  The mixture was incubated at 16°C for 2.5 hr.  The resulting dUTP-marked dsDNA was purified with 2 µl of SpeedBeads (GE Healthcare) in 20% PEG 8000/2.5M NaCl (final 13% PEG 8000), and eluted with 40 µl of EB (Zymo Research).  The eluted dsDNA was carried out end repair by blunting, A-tailing and adapter ligation as previously described (Heinz et al., 2010) using barcoded adapters (Bioo Scientific).  The end repaired dsDNA was amplified for 16 cycles using 0.05 U/µl KAPA High Fidelity HotStart (Kapa Biosystems) and 1 µM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction.

tag: cell type

value: Bone marrow-derived macrophages

value: Wild type

tag: time


title: TBK1i_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_RNA_TBK1inh_rep2_YA_l20210323_GAGTGG
DMSO_KLA_merged_allRawTags.txt

tag: treatment


title: HFD_TNO [104398-001-036]


title: HFD_TNO [104398-001-020]


title: HFD_TNO [104398-001-012]


title: HFD_TNO [104398-001-004]


title: Pat_675_visit2_NO_response

description: Gene expression of Patient 675, visit2, response: NO, AZA

source_name: SLE, Patient 675, visit2, response: NO, AZA

value: Whole Blood


title: DMSO_KLA rep1

description:
mouse_C57Bl6_KLA6h_BMDM_RNA_rep1_YA_l20210323_GTCCGC
DMSO_KLA_merged_allRawTags.txt

value: KLA


title: Pat_646_visit1_YES_response

description: Gene expression of Patient 646, visit1, response: YES, MMF

source_name: SLE, Patient 646, visit1, response: YES, MMF


title: HFD_TNO [104398-001-048]

value: liver

value: High Fat Diet (TNO, dept. MHR, Leiden, NL)


title: Milk [104398-001-094R]

value: High Fat Diet with Milk fat


title: DMSO_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_RNA_rep2_YA_l20210323_GGCTAC
DMSO_KLA_merged_allRawTags.txt

value: Veh


title: DMSO_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_RNA_rep2_YA_l20210323_GTGGCC
DMSO_KLA_merged_allRawTags.txt


title: Milk [104398-001-090]


title: LONG01_P5

source_name: iPSC derived mesenchymal stromal cells, LONG01, P5

value: mesenchymal stromal cells

value: hiPSC


title: Pat_641_visit2_YES_response

description: Gene expression of Patient 641, visit2, response: YES, PHC

source_name: SLE, Patient 641, visit2, response: YES, PHC

value: SLE

value: Female

value: W

value: PHC


title: Pat_641_visit1_YES_response

description: Gene expression of Patient 641, visit1, response: YES, PHC

source_name: SLE, Patient 641, visit1, response: YES, PHC


title: Milk [104398-001-086]

source_name: liver


title: DMSO_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_RNA_rep1_YA_l20210323_TAGCTT
DMSO_KLA_merged_allRawTags.txt


title: Pat_623_visit2_YES_response

description: Gene expression of Patient 623, visit2, response: YES, AZA

source_name: SLE, Patient 623, visit2, response: YES, AZA

value: B

value: AZA


title: Milk [104398-001-058]


title: Milk [104398-001-082]


title: Milk [104398-001-078]


title: Pat_623_visit1_YES_response

description: Gene expression of Patient 623, visit1, response: YES, AZA

source_name: SLE, Patient 623, visit1, response: YES, AZA

value: YES


title: Pgc1b_flox_Cre_KLA rep2

description:
mouse_C57Bl6_KLA_BMDM_RNA_PGC1bfloxLysMCre_rep2_YA_l20210617_CCGTCC
Pgc1b_flox_merged_allRawTags.txt

value: Bone marrow-derived macrophages

value: Pgc1b flox/flox, LysMCre


title: Milk [104398-001-039]


title: Pgc1b_flox_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_RNA_PGC1bflox_rep2_YA_l20210617_GTGGCC
Pgc1b_flox_merged_allRawTags.txt

value: Pgc1b flox/flox


title: Milk [104398-001-074]


title: Milk [104398-001-050]


title: Milk [104398-001-031]


title: Milk [104398-001-023]


title: Pgc1b_flox_KLA rep1

description:
mouse_C57Bl6_KLA6h_BMDM_RNA_PGC1bflox_rep1_YA_l20210617_GTCCGC
Pgc1b_flox_merged_allRawTags.txt

value: KLA


title: Pgc1b_flox_Cre_KLA rep1

description:
mouse_C57Bl6_KLA_BMDM_RNA_PGC1bfloxLysMCre_rep1_YA_l20210617_GGCTAC
Pgc1b_flox_merged_allRawTags.txt


title: Pgc1b_flox_Cre_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_RNA_PGC1bfloxLysMCre_rep2_YA_l20210617_CTTGTA
Pgc1b_flox_merged_allRawTags.txt


title: Milk [104398-001-011]

value: liver


title: Milk [104398-001-019]


title: Beef [104398-001-062]

value: High Fat Diet with Beef fat


title: Pgc1b_flox_Cre_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_RNA_PGC1bfloxLysMCre_rep1_YA_l20210617_CAGATC
Pgc1b_flox_merged_allRawTags.txt


title: Milk [104398-001-003R]

value: High Fat Diet with Milk fat


title: Beef [104398-001-046]


title: Beef [104398-001-054]


title: Pgc1b_flox_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_RNA_PGC1bflox_rep2_YA_l20210617_TGACCA
Pgc1b_flox_merged_allRawTags.txt

value: Veh


title: Pat_600_visit3_YES_response

description: Gene expression of Patient 600, visit3, response: YES, AZA

source_name: SLE, Patient 600, visit3, response: YES, AZA

value: Whole Blood


title: Pat_600_visit2_YES_response

description: Gene expression of Patient 600, visit2, response: YES, AZA

source_name: SLE, Patient 600, visit2, response: YES, AZA


title: Pat_615_visit2_NO_response

description: Gene expression of Patient 615, visit2, response: NO, HC

source_name: SLE, Patient 615, visit2, response: NO, HC

value: HC

value: NO


title: Pat_615_visit1_NO_response

description: Gene expression of Patient 615, visit1, response: NO, HC

source_name: SLE, Patient 615, visit1, response: NO, HC

value: SLE

value: Female


title: Pat_598_visit2_YES_response

description: Gene expression of Patient 598, visit2, response: YES, PHC

source_name: SLE, Patient 598, visit2, response: YES, PHC

value: W

value: PHC


title: Beef [104398-001-042R]


title: Pgc1b_flox_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_RNA_PGC1bflox_rep1_YA_l20210617_CGATGT
Pgc1b_flox_merged_allRawTags.txt


title: RGFP966_KLA rep2

description:
mouse_C57Bl6_RGFP_BMDM_RNA_KLA6h_rep2_YA_l20201221_TGACCA
RGFP966_KLA_Veh_merged_allRawTags.txt

value: Wild type


title: KLA rep2

description:
mouse_C57Bl6_BMDM_RNA_KLA6h_rep2_YA_l20201207_TCGAAG
RGFP966_KLA_Veh_merged_allRawTags.txt


title: Beef [104398-001-014]


title: Beef [104398-001-026]


title: RGFP966_KLA rep1

description:
mouse_C57Bl6_RGFP_BMDM_RNA_KLA6h_rep1_YA_l20201207_CGATGT
RGFP966_KLA_Veh_merged_allRawTags.txt


title: Pat_584_visit2_NO_response

description: Gene expression of Patient 584, visit2, response: NO, HC

source_name: SLE, Patient 584, visit2, response: NO, HC


title: Beef [104398-001-030]


title: Beef [104398-001-022]


title: Beef [104398-001-018]


title: Beef [104398-001-034]


title: Pat_598_visit1_YES_response

description: Gene expression of Patient 598, visit1, response: YES, PHC

source_name: SLE, Patient 598, visit1, response: YES, PHC

value: YES


title: KLA rep1

description:
mouse_C57Bl6_BMDM_RNA_KLA6h_rep1_YA_l20201207_TAATCG
RGFP966_KLA_Veh_merged_allRawTags.txt

value: Bone marrow-derived macrophages


title: Beef [104398-001-006R]


title: Beef [104398-001-038]


title: Beef [104398-001-002]


title: Pat_582_visit6_YES_response

description: Gene expression of Patient 582, visit6, response: YES, MMF

source_name: SLE, Patient 582, visit6, response: YES, MMF

value: MMF


title: Veh rep2

description:
mouse_C57Bl6_BMDM_RNA_Veh6h_rep2_YA_l20201207_CTCAGA
RGFP966_KLA_Veh_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages


title: Pork [104398-001-085]

value: High Fat Diet with Pork fat


title: Pork [104398-001-093]


title: Pork [104398-001-065]


title: Veh rep1

description:
mouse_C57Bl6_BMDM_RNA_Veh6h_rep1_YA_l20201207_CTATAC
RGFP966_KLA_Veh_merged_allRawTags.txt


title: Pat_600_visit1_YES_response

description: Gene expression of Patient 600, visit1, response: YES, AZA

source_name: SLE, Patient 600, visit1, response: YES, AZA

value: AZA


title: Pat_584_visit1_NO_response

description: Gene expression of Patient 584, visit1, response: NO, HC

source_name: SLE, Patient 584, visit1, response: NO, HC


title: Pat_582_visit4_YES_response

description: Gene expression of Patient 582, visit4, response: YES, MMF

source_name: SLE, Patient 582, visit4, response: YES, MMF


title: Pork [104398-001-057]

value: liver


title: Pat_582_visit5_YES_response

description: Gene expression of Patient 582, visit5, response: YES, MMF

source_name: SLE, Patient 582, visit5, response: YES, MMF


title: Beef [104398-001-010]

value: High Fat Diet with Beef fat


title: Pork [104398-001-053]


title: NKO_IL4 rep2

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_IL46h_rep2_YA_l20210209_CTCAGA
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: NCoR flox/flox, LysMCre


title: WT_IL4 rep2

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_IL46h_rep2_YA_l20210209_GTGGCC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: NCoR flox/flox


title: Pork [104398-001-049]


title: NKO_IL4 rep1

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_IL46h_rep1_YA_l20210209_CTATAC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Pork [104398-001-041]


title: Pork [104398-001-025]


title: Pork [104398-001-037]


title: Pork [104398-001-045]


title: WT_IL4 rep1

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_IL46h_rep1_YA_l20210209_GTCCGC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Pork [104398-001-017]


title: NKO_IFNb rep2

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_INFb6h_rep2_YA_l20210209_CATGGC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: IFNb


title: NKO_IFNb rep1

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_INFb6h_rep1_YA_l20210209_CACTCA
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Pork [104398-001-009R]


title: Pat_582_visit2_YES_response

description: Gene expression of Patient 582, visit2, response: YES, MMF

source_name: SLE, Patient 582, visit2, response: YES, MMF

value: Whole Blood


title: Sunf [104398-001-083]

source_name: liver

value: High Fat Diet with Sunflower oil


title: Sunf [104398-001-091]


title: Pat_572_visit3_YES_response

description: Gene expression of Patient 572, visit3, response: YES, MMF

source_name: SLE, Patient 572, visit3, response: YES, MMF

value: SLE


title: Pork [104398-001-033]


title: Sunf [104398-001-063R]


title: Pat_572_visit1_YES_response

description: Gene expression of Patient 572, visit1, response: YES, MMF

source_name: SLE, Patient 572, visit1, response: YES, MMF

value: Female


title: Pat_582_visit3_YES_response

description: Gene expression of Patient 582, visit3, response: YES, MMF

source_name: SLE, Patient 582, visit3, response: YES, MMF

value: W


title: Pat_572_visit2_YES_response

description: Gene expression of Patient 572, visit2, response: YES, MMF

source_name: SLE, Patient 572, visit2, response: YES, MMF


title: Sunf [104398-001-075]


title: Pat_458_visit2_NO_response

description: Gene expression of Patient 458, visit2, response: NO, PHC

source_name: SLE, Patient 458, visit2, response: NO, PHC

value: PHC

value: NO


title: Pat_582_visit1_YES_response

description: Gene expression of Patient 582, visit1, response: YES, MMF

source_name: SLE, Patient 582, visit1, response: YES, MMF

value: YES


title: WT_IFNb rep1

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_INFb6h_rep1_YA_l20210209_TAGCTT
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: Bone marrow-derived macrophages


title: Pat_458_visit3_NO_response

description: Gene expression of Patient 458, visit3, response: NO, PHC

source_name: SLE, Patient 458, visit3, response: NO, PHC


title: Sunf [104398-001-059]


title: Sunf [104398-001-047]


title: Sunf [104398-001-055]


title: Sunf [104398-001-008]


title: WT_IFNb rep2

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_INFb6h_rep2_YA_l20210209_GGCTAC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Sunf [104398-001-095]


title: NKO_PolyIC rep1

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_PolyIC6h_rep1_YA_l20210209_TAATCG
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: PolyIC


title: Oliv_Rape [104398-001-092]

value: High Fat Diet with olive and rapeseed oil


title: Oliv_Rape [104398-001-081]


title: Pat_439_visit2_YES_response

description: Gene expression of Patient 439, visit2, response: YES, HC

source_name: SLE, Patient 439, visit2, response: YES, HC

value: B

value: HC


title: WT_PolyIC rep2

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_PolyIC6h_rep2_YA_l20210209_GAGTGG
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Oliv_Rape [104398-001-089]

value: liver


title: WT_PolyIC rep1

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_PolyIC6h_rep1_YA_l20210209_CGTACG
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: NKO_PolyIC rep2

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_PolyIC6h_rep2_YA_l20210209_TCGAAG
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: NCoR flox/flox, LysMCre


title: Oliv_Rape [104398-001-073R]


title: Pat_458_visit1_NO_response

description: Gene expression of Patient 458, visit1, response: NO, PHC

source_name: SLE, Patient 458, visit1, response: NO, PHC


title: Pat_439_visit1_YES_response

description: Gene expression of Patient 439, visit1, response: YES, HC

source_name: SLE, Patient 439, visit1, response: YES, HC


title: Pat_429_visit2_NO_response

description: Gene expression of Patient 429, visit2, response: NO, HC

source_name: SLE, Patient 429, visit2, response: NO, HC


title: Oliv_Rape [104398-001-071]


title: Pat_429_visit1_NO_response

description: Gene expression of Patient 429, visit1, response: NO, HC

source_name: SLE, Patient 429, visit1, response: NO, HC


title: NKO_RANKL rep2

description:
mouse_NCoRKO_Osteoclast_RNA_RANKL12h_rep2_YA_l20190823_GATCAG
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages

value: RANKL


title: Oliv_Rape [104398-001-069]


title: NKO_RANKL rep1

description:
mouse_NCoRKO_Osteoclast_RNA_RANKL12h_rep1_YA_l20190823_ACTTGA
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Oliv_Rape [104398-001-068]


title: WT_RANKL rep2

description:
mouse_NCoRWT_Osteoclast_RNA_RANKL12h_rep2_YA_l20190823_ATTCCT
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: NCoR flox/flox


title: WT_RANKL rep1

description:
mouse_NCoRWT_Osteoclast_RNA_RANKL12h_rep1_YA_l20190823_ATGAGC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Oliv_Rape [104398-001-061]


title: Oliv_Rape [104398-001-060]


title: Oliv_Rape [104398-001-015]


title: Oliv_Rape [104398-001-007R]


title: Pat_408_visit2_YES_response

description: Gene expression of Patient 408, visit2, response: YES, AZA

source_name: SLE, Patient 408, visit2, response: YES, AZA

value: Whole Blood

value: A

value: AZA


title: Oliv_Rape [104398-001-005]


title: Oliv_Rape [104398-001-079]


title: NKO_KLA rep2

description:
NCoRKO_BMDM_RNA_polyA_KLA_6hour_LN243bM_JSS_TDT_16_12_16
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: KLA


title: Pat_408_visit1_YES_response

description: Gene expression of Patient 408, visit1, response: YES, AZA

source_name: SLE, Patient 408, visit1, response: YES, AZA

value: SLE

value: Female


title: Chow [104398-001-096]

value: Chow diet (Healthy control)


title: Chow [104398-001-072]


title: Pat_399_visit1_YES_response

description: Gene expression of Patient 399, visit1, response: YES, MMF

source_name: SLE, Patient 399, visit1, response: YES, MMF

value: MMF

value: YES


title: Chow [104398-001-088]

source_name: liver


title: WT_KLA rep1

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_KLA6h_rep1_YA_l20201017_CACTCA
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: Bone marrow-derived macrophages


title: WT_KLA rep2

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_KLA6h_rep2_YA_l20201017_CATGGC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Pat_376_visit2_YES_response

description: Gene expression of Patient 376, visit2, response: YES, PHC

source_name: SLE, Patient 376, visit2, response: YES, PHC

value: W

value: PHC


title: Chow [104398-001-076]


title: AB6520

description: MARSseq

data_processing:
bcl2fastq/2.15.0.4
Sequences with RMT of low quality (defined as RMT with minimum Phred score of less than 27) were filtered out.
Pool-barcode used i5+i7 barcodes each of them is unique in run, 1 error was allowed.  well-barcode N7 folowed by UMI N8 in read 2.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include mRNA molecule count values for each Sample
Supplementary files format and content: metadata_q_annotated.txt

source_name: GL261 tumor

extract_protocol:
Isolation of tumor cells and tumor-infiltrating immune cells was performed from tumor-bearing brain hemispheres. Briefly mice were perfused with PBS and the tumor-bearing brain hemisphere was collected in Roswell Park Memorial Institute (RPMI) medium containing 0.4 mg/ml Collagenase IV and 0.1 mg/ml DNase I (both Sigma-Aldrich). The tissue was then incubated for 40 min at 37°C and further homogenize using a 18G needle. Myelin was removed using a 30% Percoll centrifugation step (Sigma-Aldrich).
3' end mRNA libraries were prepared for sequencing using MARS-seq (Jaitin et al, Science 2014)
single-cell RNA-sequencing for gene expression quantitation

treatment_protocol:
Groups of mice were treated with anti-TREM2 antibodies or isotype control (anti-hILT1) at days 2 and 7 post tumor implantation. See Molgora et al 2020, Cell.
All mice were implanted with 2x10^4 GL261 cells intracerebrally. 11-12 days later mice received i.v. fluorescent CD45 antibody time stamps. On day 13 mice were sacrificed and tumors were extracted for single cell processing.

value: GL261 tumor

tag: strain

tag: age

value: 10-12 weeks

tag: day of_tumor_harvest

value: Mouse 15


title: Chow [104398-001-080]

value: liver


title: Pat_345_visit3_NO_response

description: Gene expression of Patient 345, visit3, response: NO, AZA

source_name: SLE, Patient 345, visit3, response: NO, AZA

value: NO


title: NKO_Veh rep1

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_Veh6h_rep1_YA_l20210209_GGTAGC
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: NCoR flox/flox, LysMCre

value: Veh


title: AB6518

description: MARSseq

tag: biological replicate


title: AB6519

description: MARSseq


title: Pat_399_visit2_YES_response

description: Gene expression of Patient 399, visit2, response: YES, MMF

source_name: SLE, Patient 399, visit2, response: YES, MMF

value: Whole Blood

value: B


title: Chow [104398-001-084]

tag: group


title: AB6516

description: MARSseq

value: IgG

value: Mouse 14


title: Pat_345_visit1_NO_response

description: Gene expression of Patient 345, visit1, response: NO, AZA

source_name: SLE, Patient 345, visit1, response: NO, AZA

value: SLE

value: Female

value: AZA


title: AB6515

description: MARSseq


title: AB6514

description: MARSseq


title: Chow [104398-001-064]

value: Chow diet (Healthy control)

tag: mouse number


title: WT_Veh rep2

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_Veh6h_rep2_YA_l20210209_TGACCA
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: Bone marrow-derived macrophages

value: NCoR flox/flox


title: Pat_330_visit2_NO_response

description: Gene expression of Patient 330, visit2, response: NO, HC

source_name: SLE, Patient 330, visit2, response: NO, HC

tag: tissue

value: HC


title: WT_Veh rep1

description:
mouse_C57Bl6_NCoRWT_BMDM_RNA_Veh6h_rep1_YA_l20210209_CGATGT
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt


title: Pat_330_visit1_NO_response

description: Gene expression of Patient 330, visit1, response: NO, HC

source_name: SLE, Patient 330, visit1, response: NO, HC

tag: diagnosis


title: NKO_KLA rep1

description:
NCoRKO_BMDM_RNA_polyA_KLA_6hour_LN243aM_JSS_TDT_16_12_16
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: KLA


title: Pat_345_visit2_NO_response

description: Gene expression of Patient 345, visit2, response: NO, AZA

source_name: SLE, Patient 345, visit2, response: NO, AZA

tag: Sex

value: W


title: Chow [104398-001-021]

value: liver


title: AB6512

description: MARSseq

value: GL261 tumor

value: 10-12 weeks


title: AB6513

description: MARSseq


title: NKO_Veh rep2

description:
mouse_C57Bl6_NCoRKO_BMDM_RNA_Veh6h_rep2_YA_l20210209_ACTGAT
RANKL_KLA_IL4_IFNb_PolyIC_Veh_merged_allRawTags.txt

value: NCoR flox/flox, LysMCre

value: Veh


title: Pat_376_visit1_YES_response

description: Gene expression of Patient 376, visit1, response: YES, PHC

source_name: SLE, Patient 376, visit1, response: YES, PHC

value: Whole Blood

tag: race

value: PHC

value: YES


title: Pat_326_visit1_YES_response

description: Gene expression of Patient 326, visit1, response: YES, HC

source_name: SLE, Patient 326, visit1, response: YES, HC

value: SLE

tag: sledai


title: AB6517

description: MARSseq

value: IgG

value: Mouse 14


title: AB6511

description: MARSseq


title: AB6510

description: MARSseq


title: AB6509

description: MARSseq


title: Input_p300_WT_Day4 rep1

description:
mouse_C57Bl6_Osteoclast_ChIP_input_Day4_rep1_YA_l20190916_GACGAC
p300_WT_Day0_Day4_merged_allRawTags.txt

data_processing:
FASTQ files were mapped to the mm10 mouse reference genome with Bowtie2.  Peaks were called with HOMER (findPeaks) using parameters “-style factor -minDist 200 -size 200”.  After merging these peaks, correlations among replicates from the same cell subset/treatment were evaluated by correlation using tag counts.  The two most highly correlated samples were used for identifying the most robust peaks using the irreproducible discovery rate (IDR) method.  For this step, peaks were called with HOMER’s findPeaks, using parameters “-L 0 -C 0 -fdr 0.9 -minDist 200 -size 200”.  IDR peaks from different conditions involved in a comparison merged with HOMER’s mergePeaks and annotated with HOMER’s annotatePeaks.pl.  The raw tags of all samples which had reasonable correlation were quantified with HOMER (annotatePeaks.pl) using parameter “-noadj”.  Peaks which contained at least 4 tags in at least 1 sample were used to identify differentially bounded peaks (DBP) by DESeq2.  Peaks were categorized as distal peaks which are 2 kb away from known TSS and promotor peaks which are located within 2 kb region of known TSS sites.
ChIP peak single was normalized to the sequence depth.
Assembly: mm10

source_name: Bone marrow cell

extract_protocol:
Chromatin immunoprecipitation (ChIP) was performed in biological replicates as previously described (Heinz et al., 2018: Sakai et al., 2019) with modifications as follows.  For H3K27ac ChIP assays, cells were cross-linked with 1% (vol/vol) formaldehyde (Thermo Fisher Scientific) in PBS for 10 min at room temperature.  For NCoR, HDAC3, PU.1, p65, Fosl2, PGC1b, ERK1 and p300 ChIP assays, cells were cross-linked with 2 mM disuccinimidyl glutarate (DSG) (ProteoChem) in PBS for 30 min at room temperature, and then directly a second crosslinking was performed by the addition of 1% (vol/vol) formaldehyde in PBS for 10 min.  The crosslinking reaction was quenched by 0.125 M glycine (Thermo Fisher Scientific).  Cells were washed once with cold PBS and pelleted at 1,000 g for 5 min at 4°C.  Crosslinked cells were resuspended in ice-cold hypotonic buffer (10 mM HEPES-KOH (pH 7.9), 85 mM KCl, 1 mM EDTA, 1% NP-40, 1 mM PMSF (Sigma), 0.5 mM sodium butyrate (Sigma), 1X protease inhibitor cocktail (Sigma)), and centrifuged at 1,000 g for 5 min at 4°C to obtain a nuclear fraction.  Nuclear pellets were resuspended in 100 ml of either LB3 buffer (10 mM Tris-HCl (pH 7.5), 100 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.1% sodium deoxycholate, 0.5% N-laurosylsarcosine, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail for H3K27ac ChIP) or PIPA-NR buffer (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1 mM EDTA, 0.5 mM EGTA, 0.4% sodium deoxycholate, 0.1% SDS, 1% NP-40, 0.5 mM DTT, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail, for NCoR, HDAC3, PU.1, p65, Fosl2, PGC1b, ERK1 and p300 ChIP).  Chromatin DNA was sonicated in a 96 Place microTUBE Rack (Covaris) using a Covaris E220 for 12-18 cycles with the following setting: time, 60 seconds; duty, 5.0; PIP, 140; cycles, 200; amplitude, 0.0; velocity, 0.0; dwell, 0.0. Samples were centrifuged at 15,000 rpm for 10 min at 4°C, and the supernatant was used for immunoprecipitation.  LB3 lysate was diluted 1.1-fold with 10% Triton X-100.  1% of the lysate was kept as ChIP input.  The lysates were rotated with each antibody pre-bound to 20 ml of beads (10 ml of Dynabeads protein A (Invitrogen) + 10 ml of Dynabeads protein G (Invitrogen)) overnight at 4°C.  After the immunoprecipitation, beads were collected on a magnet and washed three times each with wash buffer I (20 mM Tris-HCl (pH 7.5), 150 mM NaCl, 1% Triton X-100, 0.1% SDS, 2 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), wash buffer III (10 mM Tris-HCl (pH 7.5), 250 mM LiCl, 1% Triton X-100, 0.7% sodium deoxycholate, 1 mM EDTA, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail) and twice with TET (10 mM Tris-HCl (pH 7.5), 1 mM EDTA, 0.2% Tween-20, 1 mM PMSF, 0.5 mM sodium butyrate, 1X protease inhibitor cocktail), and then resuspended in 25 ml of TT (10mM Tris-HCl (pH 7.5), 0.05% Tween-20).
The immunoprecipitated chromatin samples were used for library preparation with NEBNext Ultra II Library kit (NEB) according to the manufacturer’s instructions.  DNA in 46.5 ml of NEB reactions was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K (NEB) and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  DNA was purified with 2 ml of SpeedBeads (GE Healthcare) in 20% PEG 8000/1.5 M NaCl (Final 12% PEG 8000), and eluted with 25 ml of TT.  The eluted DNA was amplified for 14 cycles in 50 ml of PCR reactions using NEBNext High-Fidelity 2X PCR Master Mix and 0.5 mM each of primers Solexa 1GA and Solexa 1GB.  The amplified libraries were purified with 2 ml of SpeedBeads in 20% PEG 8000/2.5 M NaCl (Final 13% PEG 8000), eluted with 20 ml of TT, size selected using PAGE/TBE gel (Invitrogen) for 225-325 bp fragments by gel extraction, and single-end sequenced on HiSeq 4000.  ChIP input material (1% of sheared DNA) in 46.5 ml of TE was crosslinks reversed by adding 4 ml of 10% SDS, 4.5 ml of 5 M NaCl, 3 ml of 500 mM EDTA, 1 ml of 20 mg/ml proteinase K and 20 ml of water by incubation for 1 hr at 55°C, and then 30 min at 65°C.  The input DNA was purified with SpeedBeads as described above, and eluted with 25 ml of TT.  The eluted input DNA was prepared for libraries and amplified as described for ChIP samples.

tag: genotype

value: Wild type

value: Bone marrow cell

tag: chip antibody


title: AB6505

description: MARSseq


title: Input_p300_WT_Day0 rep2

description:
mouse_C57Bl6_Osteoclast_ChIP_input_Day0_rep2_YA_l20190916_CTCAGA
p300_WT_Day0_Day4_merged_allRawTags.txt


title: Input_p300_WT_Day0 rep1

description:
mouse_C57Bl6_Osteoclast_ChIP_input_Day0_rep1_YA_l20190916_CTATAC
p300_WT_Day0_Day4_merged_allRawTags.txt


title: AB6496

description: MARSseq

value: Mouse 12


title: p300_WT_Day4 rep2

description:
mouse_C57Bl6_Osteoclast_ChIP_P300_Day4_rep2_YA_l20190916_CAAAAG
p300_WT_Day0_Day4_merged_allRawTags.txt


title: AB6495

description: MARSseq


title: Pat_317_visit7_YES_response

description: Gene expression of Patient 317, visit7, response: YES, MMF

source_name: SLE, Patient 317, visit7, response: YES, MMF

value: Female

value: MMF

tag: pga

tag: plaquenil


title: AB6494

description: MARSseq

tag: cell type


title: p300_WT_Day4 rep1

description:
mouse_C57Bl6_Osteoclast_ChIP_P300_Day4_rep1_YA_l20190916_ATTCCT
p300_WT_Day0_Day4_merged_allRawTags.txt

tag: treatment


title: Pat_317_visit8_YES_response

description: Gene expression of Patient 317, visit8, response: YES, MMF

source_name: SLE, Patient 317, visit8, response: YES, MMF

value: W


title: Pat_317_visit6_YES_response

description: Gene expression of Patient 317, visit6, response: YES, MMF

source_name: SLE, Patient 317, visit6, response: YES, MMF


title: AB6492

description: MARSseq

tag: strain


title: AB6493

description: MARSseq

tag: age


title: p300_WT_Day0 rep2

description:
mouse_C57Bl6_Osteoclast_ChIP_P300_Day0_rep2_YA_l20190916_ATGAGC
p300_WT_Day0_Day4_merged_allRawTags.txt


title: AB6491

description: MARSseq

tag: day of_tumor_harvest


title: AB6508

description: MARSseq

tag: biological replicate


title: AB6490

description: MARSseq


title: AB6506

description: MARSseq


title: AB6489

description: MARSseq


title: AB6507

description: MARSseq


title: p300_WT_Day0 rep1

description:
mouse_C57Bl6_Osteoclast_ChIP_P300_Day0_rep1_YA_l20190916_ACTGAT
p300_WT_Day0_Day4_merged_allRawTags.txt


title: Pat_317_visit3_YES_response

description: Gene expression of Patient 317, visit3, response: YES, MMF

source_name: SLE, Patient 317, visit3, response: YES, MMF


title: Input_p300_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA6h_rep2_YA_l20181031_GGCTAC
p300_WT_Veh_KLA_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages

value: KLA

value: Bone marrow-derived macrophages


title: AB6488

description: MARSseq

value: GL261 tumor

value: 10-12 weeks


title: AB6487

description: MARSseq


title: Pat_317_visit2_YES_response

description: Gene expression of Patient 317, visit2, response: YES, MMF

source_name: SLE, Patient 317, visit2, response: YES, MMF


title: AB6486

description: MARSseq


title: Input_p300_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA6h_rep1_YA_l20181031_TAGCTT
p300_WT_Veh_KLA_merged_allRawTags.txt


title: Pat_317_visit5_YES_response

description: Gene expression of Patient 317, visit5, response: YES, MMF

source_name: SLE, Patient 317, visit5, response: YES, MMF


title: Pat_317_visit4_YES_response

description: Gene expression of Patient 317, visit4, response: YES, MMF

source_name: SLE, Patient 317, visit4, response: YES, MMF


title: AB6485

description: MARSseq

source_name: GL261 tumor


title: Pat_317_visit1_YES_response

description: Gene expression of Patient 317, visit1, response: YES, MMF

source_name: SLE, Patient 317, visit1, response: YES, MMF


title: Pat_311_visit3_YES_response

description: Gene expression of Patient 311, visit3, response: YES, PHC

source_name: SLE, Patient 311, visit3, response: YES, PHC

value: B


title: AB6484

description: MARSseq


title: Input_p300_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA0h_rep2_YA_l20181031_CAGATC
p300_WT_Veh_KLA_merged_allRawTags.txt

value: Veh


title: AB6483

description: MARSseq


title: AB6478

description: MARSseq

value: Mouse 10


title: Input_p300_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA0h_rep1_YA_l20181031_ACAGTG
p300_WT_Veh_KLA_merged_allRawTags.txt


title: Pat_311_visit1_YES_response

description: Gene expression of Patient 311, visit1, response: YES, PHC

source_name: SLE, Patient 311, visit1, response: YES, PHC

value: Whole Blood

value: PHC

value: YES


title: AB6479

description: MARSseq

value: IgG


title: p300_WT_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_P300_KLA6h_rep2_YA_l20181031_TGACCA
p300_WT_Veh_KLA_merged_allRawTags.txt

value: Wild type


title: AB6474

description: MARSseq


title: Pat_311_visit2_YES_response

description: Gene expression of Patient 311, visit2, response: YES, PHC

source_name: SLE, Patient 311, visit2, response: YES, PHC

value: SLE


title: AB6475

description: MARSseq


title: p300_WT_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_P300_KLA6h_rep1_YA_l20181031_CGATGT
p300_WT_Veh_KLA_merged_allRawTags.txt


title: AB6473

description: MARSseq


title: AB6471

description: MARSseq


title: Pat_310_visit2_YES_response

description: Gene expression of Patient 310, visit2, response: YES, HC

source_name: SLE, Patient 310, visit2, response: YES, HC

value: HC


title: AB6472

description: MARSseq


title: AB6470

description: MARSseq

value: Mouse 9


title: p300_WT_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_P300_KLA0h_rep2_YA_l20181031_TACAGC
p300_WT_Veh_KLA_merged_allRawTags.txt


title: AB6477

description: MARSseq


title: p300_WT_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_P300_KLA0h_rep1_YA_l20181031_TAATCG
p300_WT_Veh_KLA_merged_allRawTags.txt


title: AB6469

description: MARSseq


title: Input_PGC1b_WT_DMSO_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA_rep2_YA_l20210719_TAATCG
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt


title: Pat_310_visit1_YES_response

description: Gene expression of Patient 310, visit1, response: YES, HC

source_name: SLE, Patient 310, visit1, response: YES, HC

value: Female


title: Pat_285_visit2_YES_response

description: Gene expression of Patient 285, visit2, response: YES, HC

source_name: SLE, Patient 285, visit2, response: YES, HC


title: AB6468

description: MARSseq


title: Pat_285_visit1_YES_response

description: Gene expression of Patient 285, visit1, response: YES, HC

source_name: SLE, Patient 285, visit1, response: YES, HC


title: Pat_131_visit2_YES_response

description: Gene expression of Patient 131, visit2, response: YES, PHC

source_name: SLE, Patient 131, visit2, response: YES, PHC

value: W


title: Input_PGC1b_WT_DMSO_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_KLA_rep1_YA_l20210719_CTCAGA
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt


title: Input_PGC1b_WT_DMSO_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_input_Veh_rep2_YA_l20210719_CTATAC
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt


title: AB6467

description: MARSseq


title: Pat_131_visit1_YES_response

description: Gene expression of Patient 131, visit1, response: YES, PHC

source_name: SLE, Patient 131, visit1, response: YES, PHC


title: Sunf [104398-001-051]

source_name: liver

value: liver

tag: group

value: High Fat Diet with Sunflower oil


title: Input_PGC1b_WT_DMSO_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_input_Veh_rep1_YA_l20210719_CATGGC
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt

value: Bone marrow-derived macrophages


title: Pat_113_visit4_YES_response

description: Gene expression of Patient 113, visit4, response: YES, HC

source_name: SLE, Patient 113, visit4, response: YES, HC


title: AB6422

description: MARSseq

value: GL261 tumor

value: 10-12 weeks

value: Mouse 5


title: PGC1b_WT_ERKi_KLA rep2

description:
mouse_C57Bl6_ERKi_BMDM_ChIP_PGC1b_KLA_rep2_YA_l20210719_CACTCA
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages


title: AB6466

description: MARSseq


title: AB6420

description: MARSseq


title: Pat_113_visit3_YES_response

description: Gene expression of Patient 113, visit3, response: YES, HC

source_name: SLE, Patient 113, visit3, response: YES, HC

value: B


title: AB6419

description: MARSseq


title: Pat_113_visit2_YES_response

description: Gene expression of Patient 113, visit2, response: YES, HC

source_name: SLE, Patient 113, visit2, response: YES, HC

value: Whole Blood


title: PGC1b_WT_DMSO_KLA rep1

description:
mouse_C57Bl6_BMDM_ChIP_PGC1b_KLA_rep1_YA_l20210719_ATGAGC
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt


title: AB6418

description: MARSseq


title: CHC_rep20

city: Tokyo

first: Y-H.

last: Taguchi

state: Non-US/Canada

address: 1-13-27 Kasuga,Bukyo-ku

department: Physics

institute: Chuo University

description: Gene expression in liver of CHC patient

hyb_protocol: 0.6 ug of Cy3-labelled cRNA (specific activity >6.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 25 ul containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 25 ul of 2x Agilent hybridization buffer HI-RPM was added to the fragmentation mixture and hybridized to Agilent SurePrint G3 Hmn GE 8x60K Microarray (G4851A) for 17 hours at 65°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37°C GE Wash buffer 2 (Agilent), then dried immediately.

scan_protocol: Slides were scanned immediately after washing on the Agilent DNA Microarray Scanner using one color scan setting for 8x60k array slides (Scan Area 61x21.6 mm, Scan resolution 3 um, Dye channel is set to Green and Green PMT is set to 100%).

data_processing: The scanned images were analyzed with Feature Extraction Software 10.7 (Agilent) using default parameters (protocol GE1_107_Sep09 and Grid: 028004_D_F_20120411) to obtain background subtracted and spatially to detrend Processed Signal intensities.  Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: CHC,liver,replicate 20

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.075 ug RNA using the Low Input Quick Amp Labeling Kit, One-color (Agilent) according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-2000 Spectrophotometer.

extract_protocol: Total RNA was prepared using the mirVana miRNA isolation kit (Ambion) following the manufacturer's recommendations. RNA was quantified using a NanoDrop-2000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: Twenty-four samples were surgically resected from hepatocallular carcinoma and twenty-four samples of chronic hepatitis type C were obtained by fine needle biopsy

value: chronic hepatitis type C

tag: gender

value: male

tag: age(yrs)


title: PGC1b_WT_DMSO_Veh rep2

description:
mouse_C57Bl6_BMDM_ChIP_PGC1b_Veh_rep2_YA_l20210719_ACTGAT
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt


title: AB6421

description: MARSseq

source_name: GL261 tumor

tag: tissue


title: CHC_rep21

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 21

value: female


title: PGC1b_WT_ERKi_KLA rep1

description:
mouse_C57Bl6_ERKi_BMDM_ChIP_PGC1b_KLA_rep1_YA_l20210719_CAACTA
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt

value: Wild type


title: CHC_rep23

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 23


title: Pat_81_visit1_YES_response

description: Gene expression of Patient 81, visit1, response: YES, MMF

source_name: SLE, Patient 81, visit1, response: YES, MMF

tag: diagnosis

value: SLE

tag: Sex

value: Male

value: MMF

value: YES


title: AB6417

description: MARSseq


title: PGC1b_WT_DMSO_KLA rep2

description:
mouse_C57Bl6_BMDM_ChIP_PGC1b_KLA_rep2_YA_l20210719_ATTCCT
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt


title: CHC_rep24

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 24


title: CHC_rep18

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 18


title: Pat_81_visit2_YES_response

description: Gene expression of Patient 81, visit2, response: YES, MMF

source_name: SLE, Patient 81, visit2, response: YES, MMF

tag: race

value: W

tag: sledai


title: Pat_113_visit1_YES_response

description: Gene expression of Patient 113, visit1, response: YES, HC

source_name: SLE, Patient 113, visit1, response: YES, HC

value: Female

value: HC


title: CHC_rep17

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 17

value: liver


title: PGC1b_WT_DMSO_Veh rep1

description:
mouse_C57Bl6_BMDM_ChIP_PGC1b_Veh_rep1_YA_l20210719_GGTAGC
PGC1b_WT_DMSO_ERKi_KLA_merged_allRawTags.txt

tag: genotype

value: Bone marrow-derived macrophages

tag: chip antibody


title: AB6416

description: MARSseq

value: GL261 tumor

value: 10-12 weeks


title: CHC_rep22

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 22


title: CHC_rep19

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 19


title: CHC_rep15

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 15


title: Pat_46_visit4_YES_response

description: Gene expression of Patient 46, visit4, response: YES, MMF

source_name: SLE, Patient 46, visit4, response: YES, MMF

tag: pga

tag: plaquenil


title: CHC_rep16

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 16

tag: cell type


title: Pat_46_visit3_YES_response

description: Gene expression of Patient 46, visit3, response: YES, MMF

source_name: SLE, Patient 46, visit3, response: YES, MMF


title: Input_NCoR_PGC1b_WT_ERKi_KLA rep2

description:
mouse_C57Bl6_ERKi_BMDM_ChIP_input_KLA_rep2_YA_l20210719_TCGAAG
NCoR_WT_ERKi_KLA_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages

tag: treatment


title: AB6415

description: MARSseq

tag: strain

tag: age

value: Mouse 5


title: Input_p300_WT_Day4 rep2

description:
mouse_C57Bl6_Osteoclast_ChIP_input_Day4_rep2_YA_l20190916_TAATCG
p300_WT_Day0_Day4_merged_allRawTags.txt

source_name: Bone marrow cell

value: Bone marrow cell


title: Input_NCoR_PGC1b_WT_ERKi_KLA rep1

description:
mouse_C57Bl6_ERKi_BMDM_ChIP_input_KLA_rep1_YA_l20210719_TACAGC
NCoR_WT_ERKi_KLA_merged_allRawTags.txt


title: AB6414

description: MARSseq

source_name: GL261 tumor

tag: day of_tumor_harvest

tag: biological replicate


title: Input_ERK1_WT_Day4 rep2

description:
mouse_C57Bl6_Day4_Osteoclast_ChIP_input_rep3_YA_l20210719_CACCGG
ERK1_WT_Day0_Day4_merged_allRawTags.txt


title: AB6410

description: MARSseq

value: Mouse 3


title: NCoR_WT_ERKi_KLA rep1

description:
mouse_C57Bl6_ERKi_BMDM_ChIP_NCoR1_KLA_rep1_YA_l20210719_CTTGTA
NCoR_WT_ERKi_KLA_merged_allRawTags.txt

value: NCoR


title: AB6408

description: MARSseq


title: AB6409

description: MARSseq


title: Pat_46_visit2_YES_response

description: Gene expression of Patient 46, visit2, response: YES, MMF

source_name: SLE, Patient 46, visit2, response: YES, MMF

value: Whole Blood


title: Input_ERK1_WT_Day4 rep1

description:
mouse_C57Bl6_Day4_Osteoclast_ChIP_input_NCoRWT_rep1_YA_l20210619_CAACTA
ERK1_WT_Day0_Day4_merged_allRawTags.txt

value: Wild type


title: NCoR_WT_ERKi_KLA rep2

description:
mouse_C57Bl6_ERKi_BMDM_ChIP_NCoR1_KLA_rep2_YA_l20210719_GATCAG
NCoR_WT_ERKi_KLA_merged_allRawTags.txt


title: AB6407

description: MARSseq


title: Pat_326_visit2_YES_response

description: Gene expression of Patient 326, visit2, response: YES, HC

source_name: SLE, Patient 326, visit2, response: YES, HC

value: SLE


title: AB6406

description: MARSseq


title: Input_ERK1_WT_Day0 rep2

description:
mouse_C57Bl6_Day0_Osteoclast_ChIP_input_NCoRWT_rep2_YA_l20210619_ATTCCT
ERK1_WT_Day0_Day4_merged_allRawTags.txt


title: CHC_rep12

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 12

value: chronic hepatitis type C

tag: gender

value: male


title: Pat_35_visit2_NO_response

description: Gene expression of Patient 35, visit2, response: NO, PHC

source_name: SLE, Patient 35, visit2, response: NO, PHC

value: B

value: PHC

value: NO


title: CHC_rep13

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 13

value: female

tag: age(yrs)


title: CHC_rep14

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 14

tag: tissue

value: liver


title: Pat_24_visit5_NO_response

description: Gene expression of Patient 24, visit5, response: NO, MMF

source_name: SLE, Patient 24, visit5, response: NO, MMF

tag: diagnosis

value: Female

value: MMF


title: Input_ERK1_WT_Day0 rep1

description:
mouse_C57Bl6_Day0_Osteoclast_ChIP_input_NCoRWT_rep1_YA_l20210619_ATGAGC
ERK1_WT_Day0_Day4_merged_allRawTags.txt


title: Pat_35_visit1_NO_response

description: Gene expression of Patient 35, visit1, response: NO, PHC

source_name: SLE, Patient 35, visit1, response: NO, PHC

tag: Sex


title: Pat_46_visit1_YES_response

description: Gene expression of Patient 46, visit1, response: YES, MMF

source_name: SLE, Patient 46, visit1, response: YES, MMF

tag: race

value: W

value: YES


title: AB6405

description: MARSseq

value: GL261 tumor

value: 10-12 weeks


title: CHC_rep10

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 10


title: CHC_rep11

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 11


title: AB6404

description: MARSseq

value: Mouse 3


title: ERK1_WT_Day4 rep2

description:
mouse_C57Bl6_Day4_Osteoclast_ChIP_ERK1_rep3_YA_l20210719_CCGTCC
ERK1_WT_Day0_Day4_merged_allRawTags.txt

value: Bone marrow cell


title: Pat_32_visit2_NO_response

description: Gene expression of Patient 32, visit2, response: NO, PHC

source_name: SLE, Patient 32, visit2, response: NO, PHC

value: Whole Blood

value: Male

tag: sledai


title: Pat_32_visit1_NO_response

description: Gene expression of Patient 32, visit1, response: NO, PHC

source_name: SLE, Patient 32, visit1, response: NO, PHC

value: SLE


title: AB6403

description: MARSseq


title: ERK1_WT_Day4 rep1

description:
mouse_C57Bl6_Day4_Osteoclast_ChIP_ERK1_NCoRWT_rep1_YA_l20210619_CCGTCC
ERK1_WT_Day0_Day4_merged_allRawTags.txt

tag: genotype

value: Wild type


title: CHC_rep9

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 9

value: chronic hepatitis type C


title: CHC_rep7

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 7


title: AB5295

description: MARSseq

value: no treatment

value: Mouse 2


title: Pat_24_visit3_NO_response

description: Gene expression of Patient 24, visit3, response: NO, MMF

source_name: SLE, Patient 24, visit3, response: NO, MMF

value: B

value: NO


title: ERK1_WT_Day0 rep2

description:
mouse_C57Bl6_Day0_Osteoclast_ChIP_ERK1_NCoRWT_rep2_YA_l20210619_GGCTAC
ERK1_WT_Day0_Day4_merged_allRawTags.txt

source_name: Bone marrow cell

tag: chip antibody


title: CHC_rep8

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 8

value: liver

value: male


title: ERK1_WT_Day0 rep1

description:
mouse_C57Bl6_Day0_Osteoclast_ChIP_ERK1_NCoRWT_rep1_YA_l20210619_TAGCTT
ERK1_WT_Day0_Day4_merged_allRawTags.txt


title: AB5294

description: MARSseq

source_name: GL261 tumor


title: Pat_24_visit1_NO_response

description: Gene expression of Patient 24, visit1, response: NO, MMF

source_name: SLE, Patient 24, visit1, response: NO, MMF

value: Female

value: MMF

tag: pga


title: Pat_24_visit4_NO_response

description: Gene expression of Patient 24, visit4, response: NO, MMF

source_name: SLE, Patient 24, visit4, response: NO, MMF

tag: plaquenil


title: AB5293

description: MARSseq

tag: cell type

value: GL261 tumor


title: H3K27ac_Pgc1b_flox_Cre_KLA rep1

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_H3K27ac_PGC1bfloxLysMCre_rep1_YA_l20210619_CATGGC
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages

value: PGC1b flox/flox, LysMCre

tag: treatment

value: KLA

value: Bone marrow-derived macrophages


title: AB5292

description: MARSseq

tag: strain

value: 10-12 weeks


title: H3K27ac_Pgc1b_flox_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_H3K27ac_PGC1bflox_rep2_YA_l20210619_CAACTA
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt

value: PGC1b flox/flox


title: AB5291

description: MARSseq

tag: age


title: Healthy20

description: Gene expression of Healthy 20

source_name: Healthy 20

value: Whole Blood

value: Healthy


title: CHC_rep5

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 5

value: chronic hepatitis type C


title: Healthy19

description: Gene expression of Healthy 19

source_name: Healthy 19


title: Pat_24_visit2_NO_response

description: Gene expression of Patient 24, visit2, response: NO, MMF

source_name: SLE, Patient 24, visit2, response: NO, MMF

value: SLE


title: CHC_rep6

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 6


title: H3K27ac_Pgc1b_flox_KLA rep1

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_H3K27ac_PGC1bflox_rep1_YA_l20210619_ATTCCT
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt


title: AB5290

description: MARSseq

value: no treatment

tag: day of_tumor_harvest

value: Mouse 2


title: Healthy18

description: Gene expression of Healthy 18

source_name: Healthy 18


title: CHC_rep2

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 2

value: female


title: CHC_rep3

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 3

value: liver


title: CHC_rep1

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 1

value: male


title: HCC_rep23

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 23

value: hepatocallular carcinoma


title: HCC_rep24

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 24


title: H3K27ac_Pgc1b_flox_Cre_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_PGC1bfloxLysMCre_rep2_YA_l20210619_CACTCA
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt

value: Veh


title: Healthy17

description: Gene expression of Healthy 17

source_name: Healthy 17


title: Healthy15

description: Gene expression of Healthy 15

source_name: Healthy 15


title: H3K27ac_Pgc1b_flox_Cre_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_PGC1bfloxLysMCre_rep1_YA_l20210619_CACCGG
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt


title: AB5289

description: MARSseq

source_name: GL261 tumor

value: GL261 tumor

tag: biological replicate


title: AB5284

description: MARSseq

value: Mouse 8


title: H3K27ac_Pgc1b_flox_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_PGC1bflox_rep2_YA_l20210619_ATGAGC
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt


title: Healthy14

description: Gene expression of Healthy 14

source_name: Healthy 14


title: AB5283

description: MARSseq


title: H3K27ac_Pgc1b_flox_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_PGC1bflox_rep1_YA_l20210619_ACTGAT
H3K27ac_Pgc1b_flox_Cre_Veh_KLA_merged_allRawTags.txt


title: H3K27ac_WT_RGFP966_KLA rep2

description:
mouse_C57Bl6_RGFP966_BMDM_ChIP_H3K27ac_KLA6h_rep2_YA_l20201026_CAACTA
H3K27ac_WT_DMSO_RGFP966_KLA_merged_allRawTags.txt

value: Wild type


title: AB5282

description: MARSseq


title: HCC_rep20

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 20

tag: gender


title: AB5281

description: MARSseq


title: HCC_rep22

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 22

tag: age(yrs)


title: HCC_rep21

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 21

tag: tissue


title: Healthy13

description: Gene expression of Healthy 13

source_name: Healthy 13

tag: diagnosis


title: HCC_rep19

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 19


title: AB5279

description: MARSseq


title: H3K27ac_WT_RGFP966_KLA rep1

description:
mouse_C57Bl6_RGFP966_BMDM_ChIP_H3K27ac_KLA6h_rep1_YA_l20201026_ATTCCT
H3K27ac_WT_DMSO_RGFP966_KLA_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages

value: Bone marrow-derived macrophages


title: Healthy16

description: Gene expression of Healthy 16

source_name: Healthy 16

tag: Sex


title: H3K27ac_WT_DMSO_KLA rep2

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_KLA6h_rep2_YA_l20201026_ATGAGC
H3K27ac_WT_DMSO_RGFP966_KLA_merged_allRawTags.txt


title: Healthy12

description: Gene expression of Healthy 12

source_name: Healthy 12

tag: race


title: Healthy10

description: Gene expression of Healthy 10

source_name: Healthy 10

tag: sledai


title: AB5278

description: MARSseq

value: 10-12 weeks


title: HCC_rep18

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 18


title: Healthy11

description: Gene expression of Healthy 11

source_name: Healthy 11


title: AB5277

description: MARSseq


title: H3K27ac_WT_DMSO_KLA rep1

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_KLA6h_rep1_YA_l20201026_ACTGAT
H3K27ac_WT_DMSO_RGFP966_KLA_merged_allRawTags.txt

tag: genotype


title: HCC_rep17

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 17


title: H3K27ac_WT_DMSO_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_Veh6h_rep2_YA_l20201026_GGTAGC
H3K27ac_WT_DMSO_RGFP966_KLA_merged_allRawTags.txt

tag: chip antibody


title: AB5276

description: MARSseq


title: Healthy9

description: Gene expression of Healthy 9

source_name: Healthy 9

tag: pga


title: H3K27ac_WT_DMSO_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_ChIP_H3K27ac_Veh6h_rep1_YA_l20201026_GAGTGG
H3K27ac_WT_DMSO_RGFP966_KLA_merged_allRawTags.txt


title: Healthy8

description: Gene expression of Healthy 8

source_name: Healthy 8

tag: plaquenil


title: HCC_rep15

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 15

tag: cell type


title: AB5274

description: MARSseq

source_name: GL261 tumor

tag: treatment


title: ERK1_WT_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_ERK1_rep2_YA_l20210517_CATGGC
ERK1_WT_Veh_KLA_merged_allRawTags.txt

value: KLA


title: CHC_rep4

description: Gene expression in liver of CHC patient

source_name: CHC,liver,replicate 4


title: HCC_rep16

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 16


title: HCC_rep14

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 14


title: ERK1_WT_KLA rep1

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_ERK1_rep1_YA_l20210517_CACTCA
ERK1_WT_Veh_KLA_merged_allRawTags.txt


title: AB5273

description: MARSseq

tag: strain


title: Healthy5

description: Gene expression of Healthy 5

source_name: Healthy 5

value: Whole Blood


title: AB5272

description: MARSseq

tag: age


title: ERK1_WT_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_ChIP_ERK1_rep2_YA_l20210517_CACCGG
ERK1_WT_Veh_KLA_merged_allRawTags.txt


title: Healthy4

description: Gene expression of Healthy 4

source_name: Healthy 4

value: Healthy


title: HCC_rep12

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 12


title: Healthy7

description: Gene expression of Healthy 7

source_name: Healthy 7


title: ERK1_WT_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_ChIP_ERK1_rep1_YA_l20210517_CAACTA
ERK1_WT_Veh_KLA_merged_allRawTags.txt

source_name: Bone marrow-derived macrophages


title: tumor, day 24,  replicate 2, scRNAseq, animal ID 634-5

city: Stockholm

first: Jean

last: Hausser

address: Solnavägen 9

department: CMB

country: Sweden

institute: Karolinska Institutet

description: 10x Genomics

data_processing:
Three sequencing runs (NXT0438, NXT0444, NXT0446) on cDNA libraries containing our 8 samples (629-1, 629-5, 632-2, 632-3, 634-1, 634-5, 636-1, 636-4) were performed by the the Gene Expression Core Facility (GECF) of  EPFL, Lausanne . The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: custom mm10-3.0.0 with Luciferase and GFP
Supplementary files format and content: Tab-separated values files and matrix files

source_name: breast cancer

growth_protocol: 86R2.2 cell cultures were initially derived from a MMTV-PyMT GEMM in a C57BL/6J background5 and cultured in DMEM supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin. Cells were transfected with GFP and Luciferase by a lentiviral vector encoded in a pFUGWPol2-ffLuc2-eGFP plasmid. Following transfection, cells were passaged 5 times to remove lentiviral particles. GFP-positive cells were selected by FAC-sorting. Mice were injected in the fourth left mammary fat pad with 500 86R2.2 cells in a solution 1:1 with Matrigel (Corning).

extract_protocol:
Tumor samples were collected on days 11, 14, 18, and 24 post-tumor initiation (Figure 1A). Animals were sacrificed by lethal anesthesia with an intraperitoneal injection of pen- tobarbital (150 mg/kg). Tumors were localized in the fourth mammary fat pad by palpation and visual inspection.  Using a scalpel, 10-250 mg of tumor tissue was cut for single-cell RNA sequencing. The tissue was further cut into 1-2 mm-sided cubes. The cubes were positioned on a 40 μm filter and washed with 15 mL Hanks’ Balanced Salt Solution (HBSS). Tumor fragments were collected into C-tubes (Miltenyi, Switzerland) using a pipette tip, and 4.7 mL of DMEM Glutamax w/o FBS were poured over the reversed filter to detach any small remaining fragments into the C-tube. Enzymes H (200 μL), A (25 μL), and R (100 μL) from the GentleMACS tumor dissociation kit (Miltenyi, Switzerland) were added to the C-tube. C- tubes were processed using the human tissue dissociation kit program 1 for soft tissues on a GentleMACS OctoDissociator instrument (Miltenyi, Switzerland) for 65 minutes. The dissociated tumor tissue was filtered through a 40 μm filter into a 50 mL falcon by pre-washing with 10 mL of HBSS, pouring the dissociated tumor tissue on the filter, using a syringe plunger on the filter to gently squeeze tissue through the filter, and washing the filter with 5 mL HBSS to yield 20 mL volume of dissociated tissue. Dissociated cells were pelleted at 300xG for 10 min at 4 degrees Celsius. The supernatant was discarded, and pellets were re-suspended in 10 mL 1x red blood cell lysis buffer and incubated at room temperature for 10 min. Cells were pelleted again at 400xG for 10min at 4 degrees Celsius, re-suspended in 5 mL of filtered DMEM w/FBS, and counted twice on a Countess automatic cell counter (ThermoFisher Scientific). Viability was quantified by Tryptan Blue staining. Cell counts and viability were estimated by averaging the two measurements.
Cells were checked for the absence of significant doublets or aggregates and loaded into a Chromium Single Cell Controller (10x Genomics, Pleasanton, CA) in a chip together with beads, master mix reagents (containing RT enzyme and poly-dt RT primers), and oil to generate single-cell-containing droplets. Single-cell Gene Expression libraries were then prepared using Chromium Single Cell 3’ Library & Gel Bead Kit v3.0 (PN-1000075) following the manufacturer's instruction (protocol CG000183 Rev C). Quality control of the libraries was performed with a TapeStation 4200 (Agilent) and QuBit dsDNA high-sensitivity assay (Thermo Fisher Scientific) following manufacturer instructions. With this procedure, the cDNAs from distinct droplets harbor a distinct and unique 10x cell barcode.

value: tumor-microenvironment cells

value: breast cancer

value: 6-10 weeks old


title: AB5271

description: MARSseq

value: no treatment

tag: day of_tumor_harvest


title: Healthy3

description: Gene expression of Healthy 3

source_name: Healthy 3


title: HCC_rep13

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 13


title: AB5275

description: MARSseq

tag: biological replicate


title: AB5270

description: MARSseq


title: Input_PGC1b_ERK1_WT_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_input_rep2_YA_l20210517_TCGAAG
PGC1b_WT_Veh_KLA_merged_allRawTags.txt


title: Input_PGC1b_ERK1_WT_KLA rep1

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_input_rep1_YA_l20210517_TAATCG
PGC1b_WT_Veh_KLA_merged_allRawTags.txt


title: Healthy2

description: Gene expression of Healthy 2

source_name: Healthy 2


title: HCC_rep11

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 11

tag: gender


title: Healthy6

description: Gene expression of Healthy 6

source_name: Healthy 6


title: Healthy1

description: Gene expression of Healthy 1

source_name: Healthy 1


title: HCC_rep10

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 10

tag: age(yrs)


title: HCC_rep8

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 8

tag: tissue

value: female


title: HCC_rep9

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 9

value: liver


title: AB5269

description: MARSseq

source_name: GL261 tumor


title: tumor, day 24,  replicate 1, scRNAseq, animal ID 634-1

description: 10x Genomics


title: tumor, day 14,  replicate 2, scRNAseq, animal ID 636-4

description: 10x Genomics


title: HCC_rep6

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 6

value: male


title: tumor, day 18,  replicate 2, scRNAseq, animal ID 629-5

description: 10x Genomics


title: AB5268

description: MARSseq


title: tumor, day 11,  replicate 2, scRNAseq, animal ID 632-3

description: 10x Genomics


title: tumor, day 14,  replicate 1, scRNAseq, animal ID 636-1

description: 10x Genomics


title: Input_PGC1b_ERK1_WT_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_ChIP_input_rep2_YA_l20210517_CTCAGA
PGC1b_WT_Veh_KLA_merged_allRawTags.txt


title: HCC_rep7

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 7

value: hepatocallular carcinoma


title: tumor, day 18,  replicate 1, scRNAseq, animal ID 629-1

description: 10x Genomics


title: AB5264

description: MARSseq


title: AB5267

description: MARSseq


title: PGC1b_WT_KLA rep2

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_PGC1b_rep2_YA_l20210517_ATTCCT
PGC1b_WT_Veh_KLA_merged_allRawTags.txt


title: Input_PGC1b_ERK1_WT_Veh rep1

description:
mouse_C57Bl6_Veh_BMDM_ChIP_input_rep1_YA_l20210517_CTATAC
PGC1b_WT_Veh_KLA_merged_allRawTags.txt

value: Veh


title: HCC_rep3

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 3


title: AB5266

description: MARSseq

value: GL261 tumor


title: PGC1b_WT_KLA rep1

description:
mouse_C57Bl6_KLA6h_BMDM_ChIP_PGC1b_rep1_YA_l20210517_ATGAGC
PGC1b_WT_Veh_KLA_merged_allRawTags.txt


title: AB5265

description: MARSseq

value: Mouse 8


title: HCC_rep5

description: Gene expression in liver of HCC patient

source_name: HCC,liver,replicate 5


title: PGC1b_WT_Veh rep2

description:
mouse_C57Bl6_Veh_BMDM_ChIP_PGC1b_rep2_YA_l20210517_ACTGAT
PGC1b_WT_Veh_KLA_merged_allRawTags.txt

value: Wild type


title: AB5262

description: MARSseq


title: tumor, day 11,  replicate 1, scRNAseq, animal ID 632-2

description: 10x Genomics