title: L. major promastigote parasite infected 04

city: Little Rock

first: Ravi

middle: W.

last: Sun

state: Arkansas

address: 4301 W Markham St

department: Department of Otolaryngology - Head and Neck Surgery

institute: University of Arkansas for Medical Sciences

data_processing:
read quality was assessed using FastQC (version 0.11.7) and multiQC (version 1.6)
Adaptors, polyA tails, and low-quality bases (Q < 20), and the first 12bp were trimmed using BBTools BBDuk (version 38.52) (minimum read length: 20 base pairs). Parameters: ref=polyA.fa.gz, truseq_rna.fa.gz ktrim=r k=13 useshortkmers=t mink=5 forcetrimleft=12 qtrim=lr trimq=20 minavgquality=20 minlength=20
Trimmed reads were aligned to the mouse reference genome (GRCm38 / mm10) using STAR (version 2.6.1a) allowing up to 2 mismatches depending on the alignment length. Reads mapping to more than 20 locations were discarded. Parameters: --sjdbGTFfile Mus_musculus.GRCm38.84.gtf --outFilterType BySJout --sjdbOverhang 74 --outFilterMultimapNmax 20 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.03
Gene level expression counts based on known gene annotation were quantified using HTSeq (htseq-counts) (version 0.9.1) in intersection-nonempty mode. Parameters: --mode intersection-nonempty --stranded yes  --type exon <gff_file> Mus_musculus.GRCm38.84.gtf
A counts-per-million (CPM) filter was applied to remove low abundant genes. Criteria for Retention: Genes with unique Entrez IDs and a minimum of 2 CPM in 4 or more samples.
The filtered counts were TMM normalized and observation-level and sample-specific quality weights calculated using edgeR's (version 3.28.1) calcNormFactors() and limma's (version 3.42.2) voomWithQualityWeights() functions (R version 3.6.3), respectively.
Genome_build: GRCm38 / mm10
Supplementary_files_format_and_content: tab-delimited text file of gene level counts for each sample

source_name: Ears

growth_protocol: Leishmania major (WHO/MHOM/IL/80/Friedlin) was used. Parasites were maintained in vitro in Schneider's Drosophilia medium supplemented with 20% heat-inactivated FBS, 2mM L-glutamine, 100U/mL penicillin, and 100 mg/ml streptomycin. Metacyclic stationary phase promastigotes were isolated from 4-5 days cultures by Ficoll density gradient seperation.

extract_protocol:
At 4 week, with or without infection, mice ears were excised and enzymatically digested using 0.25 mg/ml Liberase and 10 mg/ml Dnase-I in incomplete RPMI 1640 for 90 minutes at 370 C. After digesting, ears were minced manually to obtain cellular content in single cell suspensions. The total RNA was isolated from the cell lysate of naive and infected ears by using RNeasy plus mini kit according to the manufacturer's instruction.
cDNA libraries were prepared from total RNA using Lexogen's QuantSeq 3‘ (FWD) mRNA-Seq Library Prep Kit for Illumina following the manufacturer’s protocol. Library fragment sizes were validated using a Fragment Analyzer and quantified by a Qubit fluorometer. Equal amounts of each library were pooled for sequencing on the NextSeq 500 platform using a high output flow cell to generate approximately 25 million 75bp SE reads per sample.

treatment_protocol: For ear dermal infections, 2x10^6 L. major promastigote parasites in 10 µl PBS were injected intradermally into the ear.

value: Ears

tag: infection status

value: L. major promastigote parasite infected


title: L. major promastigote parasite infected 02

status: Public on Oct 08 2021

type: SRA

country: USA

library_source: transcriptomic

molecule: total RNA

organism: Mus musculus

tag: strain

tag: tissue


title: L. major promastigote parasite infected 05


title: naïve uninfected control 04

value: naïve uninfected control


title: L. major promastigote parasite infected 06


title: Whole blood, SLE patient 45 Dose 1 on Week 0, placebo

type: RNA

city: Brussels

first: Frédéric

middle: A

last: HOUSSIAU

address: Avenue Hippocrate 10

department: Institut de recherche expérimentale et clinique (IREC)

country: Belgium

institute: Université catholique de Louvain

description:
S5461120-29
A2786_2097

hyb_protocol: Following fragmentation and biotin labeling, 4.4 µg of cDNA were hybridized for 16 hours at 45C on GeneChip Human Genome U133 Plus 2.0 array. GeneChips were washed and stained in the Affymetrix GeneChip Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix Gene Chip Scanner 3000.

data_processing: The data were analyzed and RMA normalized using the Affymetrix Expression Console software v.1.4.1.

label: biotin

organism: Homo sapiens

source_name: SLE Patient 45 Dose 1 on Week 0

label_protocol: 100 ng total RNA was labeled using the NuGen WB Solution kit according to the manufacturer's instructions.

extract_protocol: Total RNA was extracted from PAXgene blood RNA tubes using the QIASymphony SP extraction robot from QIAGEN. The QIASymphony PAXgene blood RNA Extraction kit and PAXgene_RNA protocol were used.

treatment_protocol: Patients with SLE (185) with moderate to severe disease activity and positive interferon (IFN) gene signature were randomised to receive IFN-K or PBO intramuscular injections (on W0, W1, W4 and W12 and W24). At randomisation (D0) and W12, W24 and W36, the IFN gene signature, including the 21 IFN-regulated genes, was evaluated by Affymetrix.

tag: diagnosis

value: SLE

tag: treatment

value: PBO

tag: time point

value: Dose 1 on Week 0

value: Blood

tag: patient

value: Patient 45


title: Whole blood, SLE Patient 147 Follow-up on Week 36 ; IFN-K

description:
EP044982A30
A2786_2095

source_name: SLE Patient 147 Follow-up on Week 36

value: IFN-K

value: Follow-up on Week 36

value: Patient 147


title: L. major promastigote parasite infected 01


title: Whole blood, SLE Patient 146 Dose 1 on Week 0; IFN-K

description:
EE559962-7
A2786_2096

source_name: SLE Patient 146 Dose 1 on Week 0

value: Patient 146


title: naïve uninfected control 03


title: Mdm2Ex5/6Δ HOM; AAV-Control 3 [CKR9180805_S27_CK27_RMG29_2c_L]

city: Glasgow

first: Holly

last: Hall

address: Garscube Estate, Switchback Road, Bearsden

country: United Kingdom

institute: Cancer Research UK Scotland Institute

data_processing:
Base calling -bcl2fastq (version 2.15.0.4)
Alignment - HiSat2 version 2.1.0
Counts obtained - featureCounts
Expression levels were determined by a workflow combining HTSeq (version 2.2.4.0), the R environment (version 3.4.2), and packages from the Bioconductor data analysis suite.
Differential gene expression analysis: negative binomial distribution using the DESeq2 package
Genome_build: GRCh38.92
Supplementary_files_format_and_content: RPKM

molecule: polyA RNA

source_name: Mdm2Ex5/6Δ HOM; AAV-Control

growth_protocol: Mice homozygous for the Mdm2Ex5/6Δ (Mdm2tm2.1Glo) allele were bred on a mixed background and housed on a 12-hour light/12-hour dark cycle and provided with normal chow diet and water ad libitum until treatment at 8-12 weeks old.

extract_protocol:
Liver samples were isolated and snap frozen on dry ice and stored at -80°C until RNA extraction. To isolate RNA, tissue was homogenised using a Precellys tissue homogeniser and RNA was extracted using the RNeasy Plus Universal mini kit (Qiagen).
Libraries were prepared using an Illumina TruSeq Stranded mRNA HT Kit according to manufacturer's instructions.

treatment_protocol: 8-12 week old male mice were injected with either AAV8.TBG.PI.Cre.rBG (Addgene, 107787-AAV8) or AAV8.TBG.PI.Null.bGH (Addgene, 105536-AAV8) at a dose of 2x10^11 genetic copies (GC) / mouse and sampled 48 hrs after treatment.

tag: genotype/group

value: Mdm2Ex5/6{delta} HOM; AAV-Control

value: liver

value: 48 hours post AAV treatment


title: Mdm2Ex5/6Δ HOM; AAV-Control 2 [CKR9180804_S06_CK6_RMG29_2b_L]


title: naïve uninfected control 02


title: Whole blood, SLE Patient 138 Follow-up on Week 36 ; IFN-K

description:
EP054867A08
A2786_2094

source_name: SLE Patient 138 Follow-up on Week 36

value: Patient 138


title: L. major promastigote parasite infected 03


title: Mdm2Ex5/6Δ HOM; AAV-Control 1 [CKR9180804_S05_CK5_RMG29_2a_L]


title: Whole blood, SLE patient 55 Follow-up on Week 36, placebo

description:
EF173560-8
A2786_2086

source_name: SLE Patient 55 Follow-up on Week 36

value: Patient 55


title: Whole blood, SLE patient 18 Follow-up on Week 36, placebo

description:
EP051167A30
A2786_2088

source_name: SLE Patient 18 Follow-up on Week 36

value: Patient 18


title: Whole blood, SLE patient 58 Follow-up on Week 36, placebo

description:
EF256024-8
A2786_2090

source_name: SLE Patient 58 Follow-up on Week 36

value: Patient 58


title: naïve uninfected control 01

value: Ears

value: naïve uninfected control


title: Whole blood, SLE Patient 145 Follow-up on Week 36 ; IFN-K

description:
EF085403-30
A2786_2093

source_name: SLE Patient 145 Follow-up on Week 36

value: SLE

value: Patient 145


title: Whole blood, SLE patient 55 Dose 5 on Week 24, placebo

description:
EE806991-8
A2786_2084

source_name: SLE Patient 55 Dose 5 on Week 24

value: PBO

value: Dose 5 on Week 24

value: Blood


title: Whole blood, SLE Patient 103 Dose 5 on Week 24 ; IFN-K

description:
EF157126-8
A2786_2087

source_name: SLE Patient 103 Dose 5 on Week 24

value: IFN-K

value: Patient 103


title: Mdm2Ex5/6Δ HOM; AAV-Control 4 [CKR9180805_S28_CK28_RMG29_2d_L]


title: GRN KO 112

city: Munich

first: Anika

last: Reifschneider

address: Feodor-Lynen-Straße

country: Germany

institute: LMU

description: nCounter® Neuropathology panel

data_processing: NanoString data were normalized and analyzed using nSolver™ software version 4.0 (NanoString Technologies, Inc.).  The geometric mean of the 10 on-chip housekeeping genes was used for normalization of reads.

source_name: GRN KO_male_total brain

growth_protocol: Housing conditions included standard pellet food and water provided ad libitum, 12-hour light-dark cycle at temperature of 22 °C with maximal 5 mice per cage and cage replacement once per week and regular health monitoring.

extract_protocol: Total RNA was isolated using Qiagen RNeasy Mini Kit according to the manufacturer's protocol

tag: Sex

value: male

tag: genotype/variation

value: GRN KO

value: total brain


title: Whole blood, SLE Patient 99 Follow-up on Week 36 ; IFN-K

description:
EP082074A08
A2786_2085

source_name: SLE Patient 99 Follow-up on Week 36

value: Follow-up on Week 36

value: Patient 99


title: Mdm2Ex5/6Δ HOM; AAV-Cre 4 [CKR9180804_S32_CK32_RMG33_1d_L]

source_name: Mdm2Ex5/6Δ HOM; AAV-Cre

value: Mdm2Ex5/6{delta} HOM; AAV-Cre

value: liver

value: 48 hours post AAV treatment


title: GRN KO 102

description: nCounter® Neuropathology panel


title: GRN/TREM2 KO 122

description: nCounter® Neuropathology panel

source_name: GRN/TREM2 KO_male_total brain

value: GRN/TREM2 KO


title: Whole blood, SLE patient 57 Follow-up on Week 36, placebo

description:
EF256023-8
A2786_2091

source_name: SLE Patient 57 Follow-up on Week 36

value: Patient 57


title: GRN KO 111

description: nCounter® Neuropathology panel


title: GRN/TREM2 KO 110

description: nCounter® Neuropathology panel


title: GRN/TREM2 KO 119

description: nCounter® Neuropathology panel


title: CM23 CC2

city: Porto Alegre

first: Andriele

last: Wairich

state: Rio Grande do Sul

address: Av. Bento Gonçalves, 9500

department: Center for Biotechnology

country: Brazil

institute: Universidade Federal do Rio Grande do Sul

description:
shoot tissues of CM23 plants at the three week old satage, cultivated under control conditions
CM23_processedData

data_processing:
After sequencing, read quality was checked and all low-quality reads (PHRED value < 20) were removed.
Adapter sequences were trimmed using Trim Galore and the first twelve nucleotides were removed from the 5’ end.
Alignments were done using STAR on default settings and feature counting was performed with the SummarizeOverlaps function on Union mode from the GenomicAlignments package for R.
Differential expression analysis were performed (+Fe vs. control) through the standard protocol from DESeq2 package for R. Genes for which q-value < 0.05 were considered differentially expressed
Genome_build: O. sativa IRGSP-1.0, Oryza meridionalis v1.3
Supplementary_files_format_and_content: Differential Expression and Raw Counts

organism: Oryza sativa Japonica Group x Oryza meridionalis

source_name: shoot

growth_protocol: Seeds were submitted to 55 ºC for three days to break dormancy. Seeds were germinated and seedlings were grown in a mesh floating on solutions containing 0.5 mM CaCl2 and 10 µM FeCl3 for two weeks at 28 ºC. The solutions were replaced twice a week. Eight seedlings per genotype per treatment (n = 4) were transplanted into 60 L containers, each one containing 40 seedlings, filled with quarter-strength nutrient solution (Yoshida et al., 1976). After one week, nutrient solutions were changed to half-strength, and thereafter one time per week, the nutrient solution was replaced with a full-strength solution as described (Wu et al., 2019). The pH was adjusted to 5.5 every two days.

extract_protocol:
Total RNA was extracted with peqGOLD RNA kit (Peqlab; Erlangen, Germany) following the manufacturers’ instructions. The genomic DNA was removed with one column RNAase-free with DNAase. The integrity of RNA was tested on a bleach agarose gel (Aranda et al., 2012) and for purity using NanoDrop OneC (Thermo Fisher Scientific, Braunschweig, Germany).
For transcriptomic analysis, approximately 10 µg of total RNA was used for high-throughput cDNA sequencing by Illumina HiSeqTM 4000 technology (BGI Genomics Co.). RNAs derived from three biological replicates were used to generate the libraries. A total of eighteen libraries were constructed, from samples harvested seven days after the onset of treatments (control and +Fe). The cDNA libraries were prepared according to Illumina’s protocols. The libraries were sequenced using filter.

treatment_protocol: After three weeks of growth, plants were exposed to control condition or 250 mg L-1 of FeSO4.7H2O for fifteen days. Nitrogen gas was percolated into the culture solutions for 15 minutes every 4 hours.

tag: age

value: three weeks-old

value: Control

tag: replicate


title: TREM2 KO 484

description: nCounter® Neuropathology panel

source_name: TREM2 KO_male_total brain

value: TREM2 KO


title: Mdm2Ex5/6Δ HOM; AAV-Cre 2 [CKR9180804_S10_CK10_RMG33_1b_L]


title: CM23 Fe2

description:
shoot tissues of CM23 plants at the three week old satage, cultivated under Fe toxicity conditions
CM23_processedData

value: Fe toxicity


title: CM23 CC3


title: Mdm2Ex5/6Δ HOM; AAV-Cre 3 [CKR9180804_S31_CK31_RMG33_1c_L]


title: Whole blood, SLE Patient 144 Follow-up on Week 36 ; IFN-K

description:
EF085404-30
A2786_2092

source_name: SLE Patient 144 Follow-up on Week 36

value: SLE

value: Blood

value: Patient 144


title: Whole blood, SLE patient 61 Follow-up on Week 36, placebo

description:
EP050840A30
A2786_2089

source_name: SLE Patient 61 Follow-up on Week 36

value: PBO

value: Patient 61


title: TREM2 KO 461

description: nCounter® Neuropathology panel

value: male

value: total brain


title: THR15171122_S06_L001

description: Albumin-Cre; p53 WT liver 3

data_processing:
Base calling -bcl2fastq (version 2.15.0.4)
Alignment - Tophat (version 2.0.13) with Bowtie (version 2.2.6.0)
Counts obtained - featureCounts
Expression levels were determined by a workflow combining HTSeq (version 2.2.4.0), the R environment (version 3.4.2), and packages from the Bioconductor data analysis suite.
Differential gene expression analysis: negative binomial distribution using the DESeq2 package
Genome_build: GRCh38.75
Supplementary_files_format_and_content: RPKM

growth_protocol: C57BL/6J (N10) Albumin-Cre; p53WT/WT and Albumin-Cre; p53FL/FL male mice were housed on a 12-hour light/12-hour dark cycle and provided with normal chow diet and water ad libitum until treatment at ~70 days old.

extract_protocol:
Liver samples were isolated and preserved in Allprotect tissue reagent (Qiagen cat# 76405) until RNA extraction. To isolate RNA, tissue was homogenised using a Precellys tissue homogeniser and RNA was extracted using the RNeasy Plus Universal mini kit.
Libraries were prepared using an Illumina TruSeq Stranded mRNA LT Kit according to manufacturer's instructions.

treatment_protocol: Mice were given CCl4 (1mL/kg from stock solution of 20% CCl4 v/v in corn oil) via a single intraperitoneal (IP) injection administered in the morning. They were euthanised and sampled at 8 hours post-treatment.

value: 8 hours post CCl4

tag: genotype

value: p53 wild-type (Albumin-Cre; p53 WT)


title: Whole blood, SLE patient 56 Dose 1 on Week 0, placebo

description:
EE488072-7
A2786_2083

source_name: SLE Patient 56 Dose 1 on Week 0

value: Dose 1 on Week 0

value: Patient 56


title: Whole blood, SLE patient 54 Dose 1 on Week 0, placebo

description:
EE682380-7
A2786_2082

source_name: SLE Patient 54 Dose 1 on Week 0

value: Patient 54


title: Mer Fe3

description:
shoot tissues of Oryza meridionalis plants at the three week old satage, cultivated under Fe toxicity conditions
OMER_processedData

organism: Oryza meridionalis

value: O. meridionalis Wg2112


title: THR15171122_S02_L001

description: Albumin-Cre; p53 WT liver 1

value: liver


title: THR15171122_S04_L001

description: Albumin-Cre; p53 WT liver 2


title: Whole blood, SLE Patient 147 Dose 1 on Week 0; IFN-K

description:
EE760198-7
A2786_2080

source_name: SLE Patient 147 Dose 1 on Week 0

value: IFN-K

value: Patient 147


title: CM23 Fe1

value: three weeks-old

value: Fe toxicity


title: Mdm2Ex5/6Δ HOM; AAV-Cre 1 [CKR9180804_S09_CK9_RMG33_1a_L]

value: Mdm2Ex5/6{delta} HOM; AAV-Cre

value: 48 hours post AAV treatment


title: GRN KO 725

description: nCounter® Neuropathology panel

source_name: GRN KO_female _total brain

value: female

value: GRN KO


title: CM23 CC1

value: Control


title: WT 354

description: nCounter® Neuropathology panel

source_name: WT_male_total brain

value: male

value: WT

value: total brain


title: Mer CC3

description:
shoot tissues of Oryza meridionalis plants at the three week old satage, cultivated under control conditions
OMER_processedData


title: WT 3559

description: nCounter® Neuropathology panel


title: TREM2 KO 460

description: nCounter® Neuropathology panel

value: TREM2 KO


title: Whole blood, SLE Patient 140 Dose 1 on Week 0; IFN-K

description:
EE845603-7
A2786_2079

source_name: SLE Patient 140 Dose 1 on Week 0

value: SLE

value: Dose 1 on Week 0

value: Blood

value: Patient 140


title: THR15171122_S05_L001

description: Albumin-Cre; p53FL/FL liver 3

value: liver

value: 8 hours post CCl4

value: p53-deficient (Albumin-Cre; p53FL/FL)


title: Whole blood, SLE patient 55 Dose 4 on Week 12, placebo

description:
EE806985-7
A2786_2078

source_name: SLE Patient 55 Dose 4 on Week 12

value: PBO

value: Dose 4 on Week 12

value: Patient 55


title: Whole blood, SLE patient 52 Dose 1 on Week 0, placebo

description:
EE845604-7
A2786_2081

source_name: SLE Patient 52 Dose 1 on Week 0

value: Patient 52


title: Whole blood, SLE Patient 139 Dose 4 on Week 12 ; IFN-K

description:
EF086408-8
A2786_2074

source_name: SLE Patient 139 Dose 4 on Week 12

value: IFN-K

value: Patient 139


title: Whole blood, SLE patient 58 Dose 4 on Week 12, placebo

description:
EE871406-8
A2786_2077

source_name: SLE Patient 58 Dose 4 on Week 12

value: Patient 58


title: Whole blood, SLE Patient 102 Dose 4 on Week 12; IFN-K

description:
EE722491-7
A2786_2076

source_name: SLE Patient 102 Dose 4 on Week 12

value: Patient 102


title: THR15171122_S07_L001

description: Albumin-Cre; p53FL/FL liver 4


title: GRN KO 638

description: nCounter® Neuropathology panel

value: female

value: GRN KO

value: total brain


title: GRN KO 639

description: nCounter® Neuropathology panel


title: WT 352

description: nCounter® Neuropathology panel

value: male

value: WT


title: GRN/TREM2 KO 76

description: nCounter® Neuropathology panel

source_name: GRN/TREM2 KO_female _total brain

value: GRN/TREM2 KO


title: LbCRKO4-RNA.LbNOX.CR.6

city: San Francisco

first: Louis

last: Ptacek

state: CA

institute: University of California San Francisco

data_processing:
Using standard parameters, sequences were aligned to the mm10 genome with STAR (v2.5.2) and assigned to Ensembl features (GRCm38.vM12) with subread:featureCounts (v1.5.1). Analysis of differential expression was performed with standard parameters in DESeq2 (v1.24.0) after removal of genes with 0 read counts. FDR-adjusted p-value cutoff for significance was set to 0.05.
genome_build: mm10
supplementary_files_format_and_content: tab delimited text files contain non-normalized counts per gene. Generated with subread:featurecounts

source_name: Liver

extract_protocol:
RNA was isolated from 10-20mg of liver tissue using trizol reagent and purified on the Zymo Direct-Zol RNA miniprep kit. RNA quality was assessed by Bioanalyzer (Agilent). RNAs with a RNA Integrity Number (RIN) greater than 8 were used for library prep.
Libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit from NEB. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

value: 6 months

value: CR 1 month

tag: collection timepoint


title: GRN/TREM2 KO 75

description: nCounter® Neuropathology panel


title: MER Fe4

source_name: shoot

value: O. meridionalis Wg2112

value: three weeks-old

value: Fe toxicity


title: Whole blood, SLE Patient 139 Dose 1 on Week 0; IFN-K

description:
EE845605-7
A2786_2072

source_name: SLE Patient 139 Dose 1 on Week 0

value: SLE

value: Dose 1 on Week 0

value: Blood


title: THR15171122_S03_L001

description: Albumin-Cre; p53FL/FL liver 2

value: liver

value: 8 hours post CCl4

value: p53-deficient (Albumin-Cre; p53FL/FL)


title: Whole blood, SLE patient 61 Dose 1 on Week 0, placebo

description:
EE488466-7
A2786_2075

source_name: SLE Patient 61 Dose 1 on Week 0

value: PBO

value: Patient 61


title: Whole blood, SLE patient 58 Dose 1 on Week 0, placebo

description:
EE488314-7
A2786_2069

source_name: SLE Patient 58 Dose 1 on Week 0

value: Patient 58


title: LbCRKO4-RNA.LbNOX.CR.4


title: LbCRKO4-RNA.LbNOX.CR.3


title: PDGF Tumor Line 2

city: Cincinnati

first: Qing

middle: Richard

last: Lu

email: raorr@mail.uc.edu, richard.lu@cchmc.org

state: OH

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
Ras_PDGFRA_PDGFBCellLines_ProcessedData_Counts
PDN3

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2  and cutadapt v1.9.1.
The trimmed reads were aligned to the reference human genome version GRCm38/mm10 with the program STAR v2.6.1e
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package
For single cell RNA-seq datasets, gene barcode matrix files were generated from fastq files using the cellranger count method.
Genome_build: mm10
Supplementary_files_format_and_content: Single cell RNA-seq datasets have counts from CellRanger
Supplementary_files_format_and_content: RNA-seq datasets have count matrices combining samples from the same experiments

source_name: Mouse Brain Tumor

growth_protocol: TSM media was comprised of a Neurobasal/DMEM-F12 mixture with 2 mM Glutamax, sodium pyruvate and HEPES added. Complete media was made from base media by adding B27 and N2 supplements, heparin, rhEGF, rhFGF, rhPDGFBB, and rhPDGFAA to a final concentration of 20 ng/mL.

extract_protocol:
Samples were homogenized in Trizol and nucleic acid fraction was separated using phenol-chloroform extraction and Phase-Lock-Gel Heavy Tubes. RNA was precipitated by ethanol extraction and incubation on ice and pelleted through centrifugation. RNA was then resuspended in DEPC-Water and treated with DNAse I for 10 min. Sample was then purified using a RNeasy column (Qiagen, 74104). The RNA concentration was measured using a Nanodrop spectrophotometer.
Libraries prepared by BGI for DNB-seq

tag: cell type

value: Brain Tumor Cells

value: Boy/J

value: untreated


title: PDGF Tumor Line 1

description:
Ras_PDGFRA_PDGFBCellLines_ProcessedData_Counts
PDN2


title: LbCRKO4-RNA.LbNOX.CR.5

value: 6 months


title: TREM2 KO 434

description: nCounter® Neuropathology panel

source_name: TREM2 KO_female _total brain

value: female

value: TREM2 KO

value: total brain


title: THR15171122_S01_L001

description: Albumin-Cre; p53FL/FL liver 1


title: PDGF Tumor Line 3

description:
Ras_PDGFRA_PDGFBCellLines_ProcessedData_Counts
PDN9


title: Whole blood, SLE Patient 103 Dose 1 on Week 0; IFN-K

description:
EE613345-7
A2786_2073

source_name: SLE Patient 103 Dose 1 on Week 0

value: IFN-K

value: Patient 103


title: Whole blood, SLE patient 51 Dose 1 on Week 0, placebo

description:
EE577732-29
A2786_2071

source_name: SLE Patient 51 Dose 1 on Week 0

value: SLE

value: Dose 1 on Week 0

value: Patient 51


title: TREM2 KO 433

description: nCounter® Neuropathology panel


title: LbCRKO4-RNA.LbNOX.CR.2

value: CR 1 month


title: Mer CC2

value: O. meridionalis Wg2112

value: three weeks-old

value: Control


title: Whole blood, SLE Patient 152 Dose 1 on Week 0; IFN-K

description:
EE488576-7
A2786_2068

source_name: SLE Patient 152 Dose 1 on Week 0

value: Blood

value: Patient 152


title: Whole blood, SLE Patient 99 Dose 1 on Week 0; IFN-K

description:
EE845292-7
A2786_2070

source_name: SLE Patient 99 Dose 1 on Week 0

value: Patient 99


title: MER Fe2

value: Fe toxicity


title: TREM2 KO 432

description: nCounter® Neuropathology panel


title: LbCRKO4-RNA.NULL.CR.6

value: 6 months


title: WT 426

description: nCounter® Neuropathology panel

source_name: WT_female _total brain

value: female

value: WT


title: LbCRKO4-RNA.NULL.CR.5


title: WT 424

description: nCounter® Neuropathology panel

value: total brain


title: MER CC1


title: LbCRKO4-RNA.LbNOX.CR.1


title: Whole blood, SLE Patient 147 Dose 4 on Week 12 ; IFN-K

description:
EF085371-8
A2786_2065

source_name: SLE Patient 147 Dose 4 on Week 12

value: IFN-K

value: Dose 4 on Week 12

value: Patient 147


title: Whole blood, SLE Patient 146 Dose 4 on Week 12 ; IFN-K

description:
EF085367-8
A2786_2064

source_name: SLE Patient 146 Dose 4 on Week 12

value: SLE

value: Patient 146


title: Whole blood, SLE Patient 143 Dose 5 on Week 24 ; IFN-K

description:
EF085365-8
A2786_2063

source_name: SLE Patient 143 Dose 5 on Week 24

value: Dose 5 on Week 24

value: Patient 143


title: Whole blood, SLE Patient 144 Dose 4 on Week 12; IFN-K

description:
EE559961-7
A2786_2067

source_name: SLE Patient 144 Dose 4 on Week 12

value: Patient 144


title: Ras Tumor Line 1

description:
Ras_PDGFRA_PDGFBCellLines_ProcessedData_Counts
HDN2

growth_protocol: Serum free DMEM/F12 media supplemented with putrescine, heparin, progesterone, BSA, 1X ITS supplement, glucose and1% penicillin/streptomycin . To base media, EGF and FGF were added to final concentrations of 20 ng/mL.

value: Brain Tumor Cells

value: Boy/J

value: untreated


title: Whole blood, SLE patient 53 Dose 5 on Week 24, placebo

description:
EF085366-8
A2786_2066

source_name: SLE Patient 53 Dose 5 on Week 24

value: PBO

value: Blood

value: Patient 53


title: Ras Tumor Line 2

description:
Ras_PDGFRA_PDGFBCellLines_ProcessedData_Counts
HDN3


title: Ras PLX3397 Ms 4

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasPLX7

treatment_protocol: Mice with treated via oral gavage daily with 100 mg/kg vehicle or PLX3397  starting 7 days after tumor implantation until they reached moribundity

value: Brain Tumor


title: GRN/TREM2 KO 73

description: nCounter® Neuropathology panel

source_name: GRN/TREM2 KO_female _total brain

value: female

value: GRN/TREM2 KO


title: WT 423

description: nCounter® Neuropathology panel

value: WT

value: total brain


title: Ras PLX3397 Ms 3

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasPLX62


title: Ras PLX3397 Ms 2

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasPLX61


title: Ras Veh Ms 3

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasVeh4


title: LbCRKO4-RNA.NULL.CR.4

source_name: Liver

value: 6 months

value: CR 1 month


title: LbCRKO4-RNA.NULL.CR.3


title: CM23 Fe3

source_name: shoot

value: three weeks-old

value: Fe toxicity


title: Ras Veh Ms 4

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasVeh5


title: untreated HUVEC rep1

city: Bochum

first: Daniela

last: Wenzel

address: Universitätsstr. 150

department: Department of Systems Physiology

institute: University of Bochum

description:
replicate 1
CTRLrep1

hyb_protocol: Standard Illumina hybridization protocol

scan_protocol: Standard Illumina scanning protocol

data_processing: Background correction, log2 transformation and quantile normalization were performed.

source_name: human umbilical vein endothelial cell

label_protocol: The Illumina® Total Prep™ RNA Amplification Kit was used for conversion in cRNA

growth_protocol: HUVEC were seeded in a 6-well cell culture plate (200,000 cells/well)

extract_protocol: RNA was extracted with  RLT lysis buffer per well (Qiagen, Hilden, Germany)  and Zymo Spin II columns (Zymo Research, Irvine, USA).

treatment_protocol: HUVEC were treated with URB (20 μM), AEA (10 μM) or ethanol one day after seeding

tag: agent


title: LbCRKO4-RNA.NULL.CR.2


title: untreated HUVEC rep3

description:
replicate 3
CTRLrep3


title: Ras Veh Ms 2

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasVeh3


title: Whole blood, SLE Patient 152 Dose 5 on Week 24 ; IFN-K

description:
EF077712-8
A2786_2058

source_name: SLE Patient 152 Dose 5 on Week 24

value: SLE

value: IFN-K

value: Dose 5 on Week 24

value: Patient 152


title: Ras Veh Ms 1

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasVeh1

source_name: Mouse Brain Tumor

value: Boy/J

value: untreated


title: Whole blood, SLE Patient 144 Dose 5 on Week 24 ; IFN-K

description:
EF085369-29
A2786_2062

source_name: SLE Patient 144 Dose 5 on Week 24

value: Blood

value: Patient 144


title: Whole blood, SLE Patient 145 Dose 5 on Week 24 ; IFN-K

description:
EF085368-8
A2786_2061

source_name: SLE Patient 145 Dose 5 on Week 24

value: Patient 145


title: LbCRKO4-RNA.NULL.CR.1


title: Ras PLX3397 Ms 1

description:
RasBulkTumor_VehvsPLX3397_Processed.txt
RasPLX4

value: Brain Tumor


title: LSECs_day7_2

first: Stefaan

last: Verhulst

address: Laarbeeklaan 103, D022

department: BMWE

institute: Vrije Universiteit Brussel

data_processing:
Trimming FastQ files (polyA, rRNA, barcodes)
Mapping using STAR
Assembly using StringTie
Genome_build: Mus_musculus.GRCm38.94
Supplementary_files_format_and_content: Matrix table with raw gene counts for every ensemble gene ID and every sample

source_name: LSECs

extract_protocol:
Isolated LSECs were immediately collected for RNA analysis without culturing. Total RNA was extracted from cells using the ReliaPrep RNA Cell Miniprep System (Promega, Madison, USA) according to supplier protocol.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Male Balb/c mice were subjected to either acute or chronic hepatotoxic liver injury. For acute liver injury, mice aged 10-12 weeks were injected once with carbon tetrachloride (CCl4) and livers collected for further analysis after 1, 3 and 7 days. All mice were injected intraperitoneally with CCl4 diluted in mineral oil at a dosage of 0.5µL per gram body weight. As control, non-treated (i.e. healthy) mice aging 10-12 weeks were used. LSEC isolation was performed through liver perfusion followed by antibody staining with CD32 and F480. LSECs were sorted based on CD32+ F480- UV- and PI-.

value: Balb/c

value: LSECs

value: single CCl4 injection

tag: disease state

value: single + 7days


title: LSECs_day7_1


title: Whole blood, SLE patient 61 Dose 5 on Week 24, placebo

description:
EE899207-8
A2786_2059

source_name: SLE Patient 61 Dose 5 on Week 24

value: PBO

value: Patient 61


title: LSECs_day3_3

value: single + 3 days


title: LSECs_day7_3


title: LSECs_day7_4


title: LSECs_day3_2


title: Whole blood, SLE patient 16 Dose 5 on Week 24, placebo

description:
EE703702-8
A2786_2060

source_name: SLE Patient 16 Dose 5 on Week 24

value: SLE

value: Patient 16


title: LSECs_day3_4


title: Whole blood, SLE patient 56 Dose 5 on Week 24, placebo

description:
EF173551-8
A2786_2055

source_name: SLE Patient 56 Dose 5 on Week 24

value: Dose 5 on Week 24

value: Patient 56


title: EtOH-ctrl HUVEC rep3

description:
replicate 3
ETOHrep3

value: EtOH control


title: Whole blood, SLE patient 58 Dose 5 on Week 24, placebo

description:
EE871405-8
A2786_2054

source_name: SLE Patient 58 Dose 5 on Week 24

value: Patient 58


title: untreated HUVEC rep2

description:
replicate 2
CTRLrep2

value: untreated


title: Whole blood, SLE patient 18 Dose 5 on Week 24, placebo

description:
EE908781-7
A2786_2057

source_name: SLE Patient 18 Dose 5 on Week 24

value: Blood

value: Patient 18


title: Whole blood, SLE Patient 156 Dose 5 on Week 24 ; IFN-K

description:
EE899204-8
A2786_2053

source_name: SLE Patient 156 Dose 5 on Week 24

value: IFN-K

value: Patient 156


title: EtOH-ctrl HUVEC rep1

description:
replicate 1
ETOHrep1


title: ER+, biological rep31

city: Shanghai

first: Enuo

last: Liu

address: 2140 Xietu Road

country: China

institute: Shanghai Institute for Biomedical and Pharmaceutical Technologies

description: gene expression data from ER+ breast cancer tissue

hyb_protocol: Labeled cDNA samples were used to hybridize to microarrays.

scan_protocol: After washing and staining, the microarrays were scanned by the Affymetrix Scanner 3000 (Affymetrix).

data_processing:
For microarray analysis, Affymetrix GeneChip Command Console (version 4.0, Affymetrix) software was used to extract raw data. Next, Expression Console (version1.3.1, Affymetrix) software offered RMA normalization for gene analysis.
Differentially expressed genes were then identified through Genesrping software (version 13.1; Agilent Technologies).

source_name: FFPE of breast tissue

label_protocol: Briefly, total RNAs were transcribed to double strand cDNAs and purification. Next, 2nd cycle cDNAs were uesd to followed fragmentation and biotin labeling.

growth_protocol: Fifty-five FFPE samples of ductual breast cancer patients with ER positive cancer and 15 FFPE samples of ductal breast cancer patients with ER negative cancer were selected to analyze the microbiota and its association with gene expression.

extract_protocol: The RecoverAll™ Total Nucleic Acid Isolation Kit (AMBION, AM1975) was used to extract total RNA from paraffin-embedded (FFPE) tissues according to the manufacturer’s protocol.

treatment_protocol: Sections of formalin-fixed paraffin embedded (FFPE) were prepared from breast tumors of patients.

value: ER+ tumor tissue


title: LSECs_day1_2

value: Balb/c

value: LSECs

value: single CCl4 injection

value: single + 1 day


title: ER+, biological rep33


title: AEA-treated HUVEC rep3

description:
replicate 3
AEArep3

value: Anandamide treated


title: URB597-treated HUVEC rep1

description:
replicate 1
URBrep1

value: URB597 treated


title: LSECs_day1_1


title: AEA-treated HUVEC rep1

description:
replicate 1
AEArep1


title: ER+, biological rep29


title: ER+, biological rep30


title: EyeBank_cultured_hCECs_from_hTECs_interval_post-mortem_19days_010_rep1

city: Québec

first: Gaëtan

last: Le-Bel

state: Quebec

address: Local H2-00, Hôpital du Saint-Sacrement,1050 Chemin Sainte-Foy

country: Canada

institute: CUO-Recherche

description: Gene expression of passage 2 hCECs from hTECs with post-mortem interval of 19days

hyb_protocol: 600 ng of Cy3-labelled cRNA (specific activity >8.0 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 was added to the fragmentation mixture and hybridized to Agilent Whole SurePrint G3 Human GE 8x60K (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 SureScanner (G4900DA) using one color scan setting for 1x60k array slides (Scan resolution 3um, 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 to obtain background subtracted and spatially detrended Processed Signal intensities. Features flagged in Feature Extraction as Feature Non-uniform outliers were excluded.

source_name: Primary human corneal epithelial cells

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 200 ng RNA (hCECs monoculture) or 100 ng RNA (hCECs from hTECs) using the One-Color LowInput QuickAmp Labeling Kit One-Color (Agilent) according to the manufacturer's instructions

growth_protocol: hCECs were isolated from the limbal area of the post-mortem corneas either directly upon reception of the corneal tissue (PMI 0) or at different post-mortem intervals (PMI), ranging from 1 to 19 . For both transportation and storage, corneas were maintained in Optisol-GS in corneal viewing chambers at 4°C. Once isolated, the ten individual hCEC populations (PMI 0, 1, 2, 3, 4, 14, 15, 17, 18, and 19 ) were seeded in tissue culture flasks along with a lethally irradiated (6000 rad) human fibroblasts feeder layer and cultured in Dulbecco–Vogt modification of Eagle's medium with Ham's F12 in a 3:1 ratio (DME-HAM) supplemented with 5% Fetal Clone II serum, 5 μg/ml of insulin, 0.4 μg/ml of hydrocortisone, 10 ng/ml of epidermal growth factor, 0.212 mg/ml of isoproterenol hydrochloride, 100 IU/ml of penicillin and 25 μg/ml of gentamycin. Cells were maintained in 37°C and 8% CO2 incubators until they reached near-confluence and culture medium was changed after 2 days.

extract_protocol: Total RNA was isolated using the RNeasy Mini Kit (QIAGEN, Cat#74104)

treatment_protocol: The two-layers hTECs were produced following the self-assembly approach. Briefly, corneal fibroblasts were cultured in the presence of ascorbic acid (50 μg/ml) for 35 days to promote the production of their own extracellular matrix (ECM). Two fibroblasts sheets were then superimposed to form a reconstructed stroma, on which hCECs were seeded. Reconstructed tissues were cultured for 7 days under submerged conditions in complete DHc supplemented with ascorbate and then transferred to the air-liquid interface for 7 days in EGF-free DHc to induce epithelial differentiation.

tag: post-mortem interval

value: 19 days

value: F

value: Primary human corneal epithelial cells


title: Whole blood, SLE Patient 147 Dose 5 on Week 24 ; IFN-K

description:
EF085376-29
A2786_2051rr

source_name: SLE Patient 147 Dose 5 on Week 24

value: SLE

value: Dose 5 on Week 24

value: Patient 147


title: EyeBank_cultured_hCECs_from_hTECs_interval_post-mortem_18days_009_rep1

description: Gene expression of passage 2 hCECs from hTECs with post-mortem interval of 18days

value: 18 days

value: M


title: EtOH-ctrl HUVEC rep2

description:
replicate 2
ETOHrep2

value: EtOH control


title: LSECs_day3_1

tag: strain

value: single + 3 days


title: URB597-treated HUVEC rep2

description:
replicate 2
URBrep2


title: Whole blood, SLE patient 54 Dose 5 on Week 24, placebo

description:
EF200133-29
A2786_2049

source_name: SLE Patient 54 Dose 5 on Week 24

value: PBO

tag: tissue

value: Blood

value: Patient 54


title: AEA-treated HUVEC rep2

description:
replicate 2
AEArep2


title: ER+, biological rep32

value: ER+ tumor tissue


title: URB597-treated HUVEC rep3

description:
replicate 3
URBrep3


title: Whole blood, SLE patient 57 Dose 5 on Week 24, placebo

description:
EE871403-8
A2786_2056

source_name: SLE Patient 57 Dose 5 on Week 24

tag: diagnosis

value: Patient 57


title: ER+, biological rep28


title: healthy_4

value: Balb/c

value: LSECs

tag: treatment

value: Healthy


title: Whole blood, SLE patient 52 Dose 5 on Week 24, placebo

description:
EF347923-29
A2786_2050

source_name: SLE Patient 52 Dose 5 on Week 24

tag: time point

value: Patient 52


title: healthy_3


title: healthy_2


title: PPARa-RNA.KO.AdLib.4

data_processing:
Using standard parameters, sequences were aligned to the mm10 genome with STAR (v2.5.2) and assigned to Ensembl features (GRCm38.vM12) with subread:featureCounts (v1.5.1). Analysis of differential expression was performed with standard parameters in DESeq2 (v1.24.0) after removal of genes with 0 read counts. FDR-adjusted p-value cutoff for significance was set to 0.05.
genome_build: mm10
supplementary_files_format_and_content:tab delimited text files contain non-normalized counts per gene. Generated with subread:featurecounts

source_name: Liver

extract_protocol:
Total RNA was isolated from mouse liver tissue using RLT Buffer (Qiagen) and RNeasy columns (Qiagen). RNA quality was assessed using a Bioanalyzer (Agilent).
Stranded RNA-seq Kit with RiboErase (HMR) (Kapa)

value: 6 months

value: PPARa -/-

value: Ad Libitum feeding

value: morning -- time uncontrolled


title: PPARa-RNA.KO.AdLib.3


title: Whole blood, SLE Patient 146 Dose 5 on Week 24 ; IFN-K

description:
EF085375-8
A2786_2046

source_name: SLE Patient 146 Dose 5 on Week 24

value: SLE

value: IFN-K

value: Dose 5 on Week 24

tag: patient

value: Patient 146


title: Whole blood, SLE Patient 99 Dose 5 on Week 24; IFN-K

description:
EF035543-8
A2786_2047

source_name: SLE Patient 99 Dose 5 on Week 24

value: Patient 99


title: Whole blood, SLE Patient 140 Dose 5 on Week 24 ; IFN-K

description:
EF347918-34
A2786_2052

source_name: SLE Patient 140 Dose 5 on Week 24

value: Blood

value: Patient 140


title: healthy_1

source_name: LSECs


title: EyeBank_cultured_hCECs_from_hTECs_interval_post-mortem_17days_008_rep1

description: Gene expression of passage 2 hCECs from hTECs with post-mortem interval of 17days

value: 17 days

value: F

value: Primary human corneal epithelial cells


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_19days_010_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 19days

value: 19 days


title: ER+, biological rep27

value: ER+ tumor tissue


title: ER+, biological rep26


title: Whole blood, SLE patient 16 Follow-up on Week 36, placebo

description:
EF235247-8
A2786_2048

source_name: SLE Patient 16 Follow-up on Week 36

value: PBO

value: Follow-up on Week 36

value: Patient 16


title: ER+, biological rep25


title: PPARa-RNA.KO.AdLib.2

value: 6 months

value: PPARa -/-

value: Ad Libitum feeding


title: LbCR4-BMAL1-LbNOX.CR.2

library_source: genomic

data_processing:
Bowtie2 (v2.2.4) was used to align sequencing data to the mm10 genome with standard parameters. For each ChIP, peaks were called using the HOMER findPeaks command with settings -style factor, -size 275, -fragLength 250. For scatter plots, peaks identified in any replicate in the control condition were combined with HOMER mergePeaks and tag-density for each individual replicate was quantified by HOMER annotatePeaks with setting -size given, and averaged.
genome_build: mm10
supplementary_files_format_and_content:bigWig files were created using MACS2(2.1.0) with options -B --SPMR --nomodel --extsize 300 -q 0.1 -g mm --broad

molecule: genomic DNA

extract_protocol:
Liver was collected at the indicated time points and processed for ChIP-seq as previously published. Briefly, liver was fixed in disuccinimidyl glutarate (2mM in PBS + 1% DMSO, 30 min) and formaldehyde (1% in PBS, 10 min) prior to aliquoting and freezing at -80˚C. For FOXO1 (abcam ab39670) or BMAL1 (Bass Lab, Millipore ABE2599) ChIP-Seq, nucleii from a quarter of a liver were isolated in buffer (150 mM NaCl, 5 mM EDTA pH8, 50 mM Tris-HCl pH8, 0.35% NP-40) in the presence of protease inhibitors by needle, then sheared in 1% SDS buffer in a sonicator (diagenode) for 6 cycles 30on/30off at 4˚C. An aliquot for input samples was taken after shearing. Chromatin was diluted 1:10 in dilution buffer (.01% SDS, 1.1% Triton X-100, 167 mM NaCl, 1.2 mM EDTA pH8, 1.67 mM Tris-HCl pH8), and immunoprecipitations with 15 µg of antibody were performed overnight at 4˚C, rotating. Secondary-conjugated, BSA-blocked paramagnetic beads were used to pull down protein/DNA complexes. Chromatin was de-crosslinked and purified by Qiagen MinElute column. Inputs were quantified by Qubit Fluorometer (Invitrogen) for each liver, and 2 ng of equimolar pools of the replicates per condition were processed into libraries.
library prep with NEBNext Ultra II library prep kit. Libraries were size-selected to 200-600 bp on the Sage Pippin Prep prior to PCR amplification. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

value: CR 1 month

tag: chip antibody

value: BMAL1 (Bass Lab, Millipore ABE2599)


title: PPARa-RNA.KO.AdLib.1

value: morning -- time uncontrolled


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_17days_008_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 17days

tag: Sex


title: LbCR4-BMAL1-LbNOX.CR.1


title: Whole blood, SLE patient 53 Follow-up on Week 36, placebo

description:
EF085401-8
A2786_2044

source_name: SLE Patient 53 Follow-up on Week 36

value: SLE

value: Patient 53


title: Whole blood, SLE Patient 143 Follow-up on Week 36 ; IFN-K

description:
EP044980A30
A2786_2045

source_name: SLE Patient 143 Follow-up on Week 36

value: IFN-K

value: Blood

value: Patient 143


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_18days_009_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 18days

value: 18 days

value: M

value: Primary human corneal epithelial cells


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_15days_007_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 15days

value: 15 days


title: EyeBank_cultured_hCECs_from_hTECs_interval_post-mortem_1day_002_rep1

description: Gene expression of passage 2 hCECs from hTECs with post-mortem interval of 1day

value: 1 day

value: F


title: EyeBank_cultured_hCECs_from_hTECs_interval_post-mortem_2days_003_rep1

description: Gene expression of passage 2 hCECs from hTECs with post-mortem interval of 2days

value: 2 days


title: EyeBank_cultured_hCECs_from_hTECs_interval_post-mortem_0day_001_rep1

description: Gene expression of passage 2 hCECs from hTECs with post-mortem interval of 0day

value: 0 day


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_14days_006_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 14days

value: 14 days


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_4days_005_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 4days

value: 4 days


title: Whole blood, SLE patient 55 Dose 1 on Week 0, placebo

description:
EE488071-7
A2786_2039

source_name: SLE Patient 55 Dose 1 on Week 0

value: PBO

value: Dose 1 on Week 0

value: Patient 55


title: Whole blood, SLE Patient 103 Follow-up on Week 36 ; IFN-K

description:
EP163224A08
A2786_2043

source_name: SLE Patient 103 Follow-up on Week 36

value: SLE

value: Follow-up on Week 36

value: Patient 103


title: ER+, biological rep23

value: ER+ tumor tissue


title: ER+, biological rep19


title: Whole blood, SLE patient 57 Dose 1 on Week 0, placebo

description:
EE488315-7
A2786_2038

source_name: SLE Patient 57 Dose 1 on Week 0

value: Blood

value: Patient 57


title: ER+, biological rep21

source_name: FFPE of breast tissue


title: Whole blood, SLE Patient 102 Dose 1 on Week 0; IFN-K

description:
EE305743-29
A2786_2042

source_name: SLE Patient 102 Dose 1 on Week 0

value: IFN-K

value: Patient 102


title: ER+, biological rep22


title: Whole blood, SLE patient 16 Dose 1 on Week 0, placebo

description:
EE305758-29
A2786_2041

source_name: SLE Patient 16 Dose 1 on Week 0

value: Patient 16


title: ER+, biological rep18


title: Whole blood, SLE Patient 156 Dose 1 on Week 0; IFN-K

description:
EE488467-7
A2786_2040

source_name: SLE Patient 156 Dose 1 on Week 0

value: Patient 156


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_3days_004_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 3days

source_name: Primary human corneal epithelial cells

value: 3 days

value: M

value: Primary human corneal epithelial cells


title: LbCR4-BMAL1-NULL.CR.3

value: 6 months

value: CR 1 month

value: BMAL1 (Bass Lab, Millipore ABE2599)


title: ER+, biological rep17


title: ER+, biological rep20


title: ER+, biological rep16


title: LbCR4-BMAL1-LbNOX.Reg.3

value: Reg 1 month


title: LbCR4-BMAL1-NULL.CR.2


title: ER+, biological rep15


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_2days_003_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 2days

value: 2 days

value: F


title: LbCR4-BMAL1-LbNOX.Reg.2


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_0day_001_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 0day

value: 0 day


title: Whole blood, SLE Patient 144 Dose 1 on Week 0; IFN-K

description:
EE694156-7
A2786_2036

source_name: SLE Patient 144 Dose 1 on Week 0

value: SLE

value: Dose 1 on Week 0

value: Patient 144


title: NR2F1-NR2F2 DKO H9 Cardiomyocytes day 19 rep1

city: New Haven

first: Fabio

middle: R

last: Santori

state: CT

address: 300 Cedar Street

department: Immunobiology

institute: Yale University

data_processing:
Standard 10x Genomics Cell Ranger Pipeline, cellranger-3.1.0, and bcl2fastq (v2.20.0.422)
Genome_build: GRCh38-3.0.0
Supplementary_files_format_and_content: output files from the Cell Ranger pipeline, including filtered count matrices in tsv

source_name: Cardiomyocyte

growth_protocol: Cardiomyocyte differentiation was performed as described in (Burridge et al., 2014; Lian et al., 2013). Single cell suspensions of human ESC were prepared and plated for 24 hours onto Matrigel-coated 12-well tissue culture plates. Differentiation was initiated by culturing ESCs in RPMI-1640 medium supplemented with Insulin-free B-27 and CHIR99021 inhibitor for 48 hours followed by 24-hour culture in Insulin-free RPMI/B27 medium without inhibitor. 72 hours after addition of CHIR99021, cells were switched into the Insulin-free RPMI/B27 supplemented with IWP2 inhibitor. The media was replaced for the Insulin-free RPMI/B27 medium without inhibitor at day 5. On day 7 of differentiation media was replaced for fresh Insulin-containing RPMI/B27 medium and changed every two days.

extract_protocol:
Live cells from WT, NR2F2-KO and NR2F1/2-DKO cultures were sorted and analyzed in duplicates on day 6 and 19 of cardiomyocyte differentiation. Single cell separation, library preparation and sequencing were performed by the Yale Center for Genome Analysis according to standard 10x Genomics protocols. Minimum sequencing depth was 20,000 read pairs per cell. Cell Ranger™ analysis pipeline was used for initial analysis and visualization.
Silane magnetic beads were used to remove leftover biochemical reagents and primers from the post GEM reaction mixture. Full-length, barcoded cDNA was then amplified by PCR to generate sufficient mass for library construction. Enzymatic Fragmentation and Size Selection were used to optimize the cDNA amplicon size prior to library construction. R1 (read 1 primer sequence) were added to the molecules during GEM incubation. P5, P7, a sample index, and R2 (read 2 primer sequence) were added during library construction via End Repair, A-tailing, Adaptor Ligation, and PCR. The final libraries contain the P5 and P7 primers used in Illumina bridge amplification.
The Single Cell 3’ Protocol was used to produce Illumina-ready sequencing libraries.

treatment_protocol: No treatment was applied to cells

value: ES-derived cardiomyocytes

tag: cell line

value: H9 human embryonic stem cells NIHhESC-10-0062


title: NR2F1-NR2F2 DKO H9 Cardiomyocytes day 19 rep2


title: Whole blood, SLE patient 53 Dose 1 on Week 0, placebo

description:
EE760194-7
A2786_2034

source_name: SLE Patient 53 Dose 1 on Week 0

value: PBO

value: Blood

value: Patient 53


title: NR2F2-KO H9 derived Cardiomyocytes day 19 rep2


title: Whole blood, SLE Patient 143 Dose 1 on Week 0; IFN-K

description:
EE694157-7
A2786_2037

source_name: SLE Patient 143 Dose 1 on Week 0

value: IFN-K

value: Patient 143


title: LbCR4-BMAL1-NULL.Reg.3

source_name: Liver

tag: age

value: 6 months


title: Whole blood, SLE patient 18 Dose 1 on Week 0, placebo

description:
EE765429-7
A2786_2035

source_name: SLE Patient 18 Dose 1 on Week 0

value: Patient 18


title: LbCR4-BMAL1-LbNOX.Reg.1

value: BMAL1 (Bass Lab, Millipore ABE2599)


title: ER+, biological rep13

value: ER+ tumor tissue


title: LbCR4-BMAL1-NULL.Reg.2

value: Reg 1 month


title: ER+, biological rep12


title: ER+, biological rep24


title: Whole blood, SLE Patient 138 Dose 1 on Week 0; IFN-K

description:
EE577733-7
A2786_2033

source_name: SLE Patient 138 Dose 1 on Week 0

value: Patient 138


title: NR2F2-KO H9 derived Cardiomyocytes day 19 rep1


title: ER+, biological rep14


title: ER+, biological rep11


title: ER+, biological rep10


title: WT H9 derived Cardiomyocytes day 19 rep2

value: WT


title: S1CR4-BMAL1-LSKO.CR.3

value: Alb-Cre; Sirt1fx/fx

value: CR 1 month


title: WT H9 derived Cardiomyocytes day 19 rep1


title: LbCR4-BMAL1-NULL.Reg.1


title: NR2F1-NR2F2 DKO H9 Cardiomyocytes day 6 rep2


title: NR2F1-NR2F2 DKO H9 Cardiomyocytes day 6 rep1


title: S1CR4-BMAL1-LSKO.CR.1


title: S1CR4-BMAL1-LSKO.CR.2


title: Whole blood, SLE Patient 145 Dose 1 on Week 0; IFN-K

description:
EE760196-7
A2786_2032

source_name: SLE Patient 145 Dose 1 on Week 0

value: SLE

value: Dose 1 on Week 0

value: Patient 145


title: Whole blood, SLE patient 52 Follow-up on Week 36, placebo

description:
EP129878A08
A2786_2031

source_name: SLE Patient 52 Follow-up on Week 36

value: PBO

value: Follow-up on Week 36

value: Patient 52


title: NR2F2-KO H9 derived Cardiomyocytes day 6 rep2

value: ES-derived cardiomyocytes

value: H9 human embryonic stem cells NIHhESC-10-0062


title: Whole blood, SLE Patient 146 Follow-up on Week 36 ; IFN-K

description:
EP044981A08
A2786_2030

source_name: SLE Patient 146 Follow-up on Week 36

value: IFN-K

value: Blood

value: Patient 146


title: S1CR4-BMAL1-CTRL.CR.3

value: 6 months

value: BMAL1 (Bass Lab, Millipore ABE2599)


title: Whole blood, SLE Patient 152 Follow-up on Week 36 ; IFN-K

description:
EF077717-8
A2786_2027

source_name: SLE Patient 152 Follow-up on Week 36

value: Patient 152


title: Whole blood, SLE Patient 139 Follow-up on Week 36 ; IFN-K

description:
EP129876A08
A2786_2029

source_name: SLE Patient 139 Follow-up on Week 36

value: Patient 139


title: Whole blood, SLE Patient 140 Follow-up on Week 36 ; IFN-K

description:
EF198309-8
A2786_2026

source_name: SLE Patient 140 Follow-up on Week 36

value: Patient 140


title: ER+, biological rep08

source_name: FFPE of breast tissue

value: ER+ tumor tissue


title: ER+, biological rep09


title: ER+, biological rep05


title: S1CR4-BMAL1-CTRL.CR.2

value: CR 1 month


title: LbCR4-BMAL1-NULL.CR.1


title: ER+, biological rep07


title: Whole blood, SLE patient 54 Follow-up on Week 36, placebo

description:
EF200149-8
A2786_2028

source_name: SLE Patient 54 Follow-up on Week 36

value: SLE

value: Patient 54


title: WT H9 derived Cardiomyocytes day 6 rep2

value: WT


title: S1CR4-BMAL1-CTRL.CR.1


title: S1CR4-BMAL1-LSKO.Reg.3

value: Alb-Cre; Sirt1fx/fx

value: Reg 1 month


title: ER+, biological rep06


title: NR2F2-KO H9 derived Cardiomyocytes day 6 rep1

value: ES-derived cardiomyocytes


title: HEK293T_GFP_RNA_Rep3

city: Erlangen

first: Michaela

last: Petter

address: Wassertrumstr. 3-5

department: Mirkobiologisches Institut

institute: Univeritätsklinikum Erlangen

data_processing:
Alignment of reads using
Samtools version 1.12 to generate bam files
Expression analysis using Cufflinks version 2.2.1
Differential expression analysis using Cuffdiff (Cufflinks version 2.2.1)
Genome_build: hg38 / GRC38, UCSC
Supplementary_files_format_and_content: Output generated by cuffdiff showing the rpkm value per gene per different condition and the fold change and pvalue for differential expression analysis

source_name: HEK293T cell line

growth_protocol: HEK293T cells (human embryonic kidney cells), were cultured at 37°C and 5% CO2 in Dulbecco’s modified Eagle’s medium (Invitrogen) containing 10% heat-inactivated fetal bovine serum (Biochrom).

extract_protocol:
RNA was isolated with TriFast reagent (VWR) according to manufacturer’s instructions. Isolated RNA was treated with DNase I (Qiagen) for 30 min at 37 °C and again purified using TriFast reagent.
libraries were generated by GATC / Eurofins as strand specific c-DNA libraries

treatment_protocol: For RNA-sequencing HEK293T cells were transfected with GFP or GFP-NLS-AnkG, GFP-sorted in cooperation with the FACS-CORE unit Erlangen. RNA was isolated with TriFast reagent (VWR). For RIP-Seq HEK293T cells were transfected with plasmids for GFP-NLS-AnkG. After 24 h RNA-IP was performed using an anti-GFP antibody and a RIP-assay (EZ-Magna Nuclear RIP (Cross-Linked) Nuclear RNA-Binding Protein Immunoprecipitation Kit (Millipore)).

tag: transfected with

value: GFP


title: WT H9 derived Cardiomyocytes day 6 rep1

value: H9 human embryonic stem cells NIHhESC-10-0062

tag: genotype


title: ER+, biological rep04


title: S1CR4-BMAL1-LSKO.Reg.2

tag: collection timepoint


title: Whole blood, SLE patient 51 Follow-up on Week 36, placebo

description:
EF347927-8
A2786_2025

source_name: SLE Patient 51 Follow-up on Week 36

value: PBO

value: Follow-up on Week 36

value: Blood

value: Patient 51


title: ER+, biological rep03


title: ER+, biological rep02


title: Fresh tissue from sample 3413 (Normal adjacent material)

city: Sao Paulo

first: Alexis Germán

last: Murillo Carrasco

email: agmurilloc@gmail.com, agmurilloc@usp.br

state: Sao Paulo

address: Av. Dr. Arnaldo 251, Sao Paulo

institute: ICESP

description: miRNA expression data from fresh tissue

hyb_protocol: Each sample was hybridized on the array, washed and stained with the Affymetrix Fluidics Station 450 and scanned using Affymetrix GeneChip Scanner 3000 7G.

scan_protocol: Expression Console software (Thermo Scientific, USA) was used for quality assessment.

data_processing: Transcriptome Analysis Console (TAC) software version 4.0.2 (Thermo Fisher Scientific, USA) was used for background correction, normalization, summarization of raw data (CEL files) by Robust Multichip Average plus Detection Above Background (RMA+DABG), considering only the probesets for mature miRNAs or pre-miRNAs from Homo sapiens specie (N=4603).

label: Biotin

source_name: sample of normal-adjacent tissue from a patient

label_protocol: miRNAs expression profiling was performed using GeneChip miRNA 4.0 Array (Thermo Fisher Scientific, USA) following manufacturer’s protocol.

extract_protocol: Total RNA was extracted from 30 mg of penile tissues using miRVana® (Thermo Fisher Scientific, USA), according to manufacturer´s instructions. RNA concentration and purity were determined by NanoDrop ND1000 (Thermo Fisher Scientific, USA) and 4200 TapeStation Instrument (Agilent Technologies, USA) was used to evaluate RNA integrity. Only samples with A260/A280 ratio between 1.8 and 2.1 and RNA Integrity Number (RIN) above 7 were considered for microarray analysis.

value: Normal-adjacent tissue

tag: lymph node metastasis

value: Not available


title: S1CR4-BMAL1-CTRL.Reg.2

value: 6 months

value: BMAL1 (Bass Lab, Millipore ABE2599)


title: S1CR4-BMAL1-LSKO.Reg.1


title: S1CR4-BMAL1-CTRL.Reg.3


title: Whole blood, SLE Patient 139 Dose 5 on Week 24 ; IFN-K

description:
EF347920-8
A2786_2023

source_name: SLE Patient 139 Dose 5 on Week 24

value: IFN-K

value: Dose 5 on Week 24

value: Patient 139


title: Fresh tissue from sample 3412 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: ER+, biological rep01

value: ER+ tumor tissue


title: HEK293T_GFP_RNA_Rep2


title: EyeBank_cultured_hCECs_monoculture_interval_post-mortem_1day_002_rep1

description: Gene expression of passage 1 hCECs cultivated in monoculture until they reached near-confluence with post-mortem interval of 1day

source_name: Primary human corneal epithelial cells

value: 1 day

value: F

tag: cell type

value: Primary human corneal epithelial cells


title: Sample 1 Antibody Tags

city: Leiden

first: Indu

last: Khatri

address: Albinusdreef 2

department: Immunology

country: Netherlands

institute: LUMC

description: Antibody tags

data_processing:
The raw sequencing data from different visits were processed using Cell Ranger (v3.1.0) against the GRCh38 human reference genome with default parameters.
Single-cell RNA-seq data were processed in R with Seurat (v3.2.3).
Cells were discarded if they met any of the following criteria: percentage of mitochondrial counts > 25; the number of unique features < 100 or >5000.
Immunoglobulin V genes were removed from the counts for clustering analysis.
MULTIseqDemux was used with default parameters to demultiplex the data to independent visits (corresponding to HTO1-HTO5 tags) and eliminated doublets and negatives among the cells
Genome_build: GRCh38
Supplementary_files_format_and_content: BCR processed information
Supplementary_files_format_and_content: MetaData information for cells
Supplementary_files_format_and_content: Filtered Count data for GEX
Supplementary_files_format_and_content: HTO Counts

source_name: PBMC

growth_protocol: EDTA-blood samples for single-cell sequencing were collected at baseline and days 5 (d5), d7, d10 and d14 post-vaccination, PBMCs were isolated via density gradient and stored in liquid nitrogen until use.

extract_protocol:
Cells were collected in a BSA-coated Eppendorf tube filled with an RPMI + 10% FCS solution to avoid excessive cell loss. At baseline, first 10,000 total CD19+ B cells were sorted, and after adjusting the sorting gate to exclusively sort PB/PCs, another 1,201 CD19+CD38++CD24+CD27+ PB/PCs were sorted. For subsequent visits, all available PB/PCs were sorted (11,051 cells). In total, we sorted 22,252 cells. Directly after the sort, samples were spun down and resuspended into the recommended volume (RPMI + 10% FCS).
Reverse transcription PCR and library preparation were carried out under the Chromium Single Cell 3’ v3 protocol (10X Genomics) per manufacturer’s recommendations. After amplification of the cDNA, a 5 ́gene expression library and paired heavy and light chain library were generated from cDNA of the same cell using Chromium Single Cell VDJ reagent kit (scBCR-rep library; v1.1chemistry, 10X Genomics). After library preparation, quality control was performed using a bioanalyzer (Agilent 2100 Bioanalyzer; Agilent Technologies). The libraries were sequenced in the NovaSeq6000 sequencer (Illumina) using the v1.0 sequencing reagent kit (read length: 2 x 150bp).

treatment_protocol: 78.2 million PBMCs from 5 different time-points were individually (per time-point) stained with an Ab cocktail for surface markers for 30min at RT in the dark (CD19 BV786, CD24 BV650, CD27 BV421, CD38 PerCP Cy5.5), followed by a life/dead staining (Zombie NIR Fixable Viability kit, Biolegend) according to the manufacturer’s protocol. Next, samples were prepared for multiplexing according to the protocols provided on the 10x Genomics website (www.10xgenomics.com). In short, Fc block was added and after a 10 min incubation at 4°C, unique cell hashing Abs (10x Genomics) were added to each sample separately (per time-point). After incubation for 20 min at 4°C, cells were washed three times and resuspended in PBS. Next, all post-vaccination samples were pooled and sorted on a high-speed cell sorter (BD FACSAria III, BD Biosciences at the flow cytometry core facility of LUMC) using a 85μm nozzle and a pressure of 45PSI, while the baseline sample was sorted separately, but in the same collection tube, to ensure an enrichment of plasmablasts/plasma cells (PB/PCs) in the sorted sample.

value: PBMC

tag: hto

value: HTO1:Day 0 B cells and PB/PCs, HTO2:Day 5 PB/PCs, HTO3:Day 7 PB/PCs, HTO4:Day 10 PB/PCs and HTO5:Day 14 PB/PCs

tag: library

value: single-cell HTO


title: HEK293T_AnkG-GFP_RNA_Rep1

value: GFP-NLS-AnkG


title: LbCR4-INPUT-LbNOX.CR.2

source_name: Liver

tag: strain

value: CR 1 month

value: Input (N/A)


title: HEK293T_AnkG-GFP_RNA_Rep2


title: S1CR4-BMAL1-CTRL.Reg.1

value: Reg 1 month


title: HEK293T_GFP_RNA_Rep1

value: GFP


title: HEK293T_AnkG-GFP_RNA_Rep3


title: Fresh tissue from sample 3411 (Normal adjacent material)

description: miRNA expression data from fresh tissue

tag: tissue

value: Normal-adjacent tissue

value: Not available


title: Fresh tissue from sample 3410 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: Whole blood, SLE patient 51 Dose 5 on Week 24, placebo

description:
EF198313-33
A2786_2020

data_processing: The data were analyzed and RMA normalized using the Affymetrix Expression Console software v.1.4.1.

source_name: SLE Patient 51 Dose 5 on Week 24

extract_protocol: Total RNA was extracted from PAXgene blood RNA tubes using the QIASymphony SP extraction robot from QIAGEN. The QIASymphony PAXgene blood RNA Extraction kit and PAXgene_RNA protocol were used.

tag: diagnosis

value: SLE

value: PBO

value: Blood

value: Patient 51


title: Whole blood, SLE Patient 102 Follow-up on Week 36 ; IFN-K

description:
EF249175-8
A2786_2018

source_name: SLE Patient 102 Follow-up on Week 36

tag: treatment

value: IFN-K

value: Follow-up on Week 36

value: Patient 102


title: Fresh tissue from sample 1863 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: Whole blood, SLE patient 56 Follow-up on Week 36, placebo

description:
EE806990-29
A2786_2021

source_name: SLE Patient 56 Follow-up on Week 36

tag: time point

value: Patient 56


title: Whole blood, SLE Patient 103 Dose 4 on Week 12 ; IFN-K

description:
EF157128-8
A2786_2019

source_name: SLE Patient 103 Dose 4 on Week 12

value: Dose 4 on Week 12

tag: patient

value: Patient 103


title: Whole blood, SLE Patient 138 Dose 5 on Week 24 ; IFN-K

description:
EF086404-8
A2786_2022

source_name: SLE Patient 138 Dose 5 on Week 24

value: Dose 5 on Week 24

value: Patient 138


title: Fresh tissue from sample 1866 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: Sample 1 B-cell receptor repertoire

description: B-cell receptor repertoire

value: PBMC

value: single-cell BCR


title: Sample 1 Gene Expression

description: Gene Expression

value: single-cell GEX


title: Whole blood, SLE Patient 99 Dose 4 on Week 12 ; IFN-K

description:
EF035541-8
A2786_2017

source_name: SLE Patient 99 Dose 4 on Week 12

value: Patient 99


title: S1CR4-INPUT.LSKO.CR.1

value: 6 months

value: Alb-Cre; Sirt1fx/fx

value: CR 1 month

tag: chip antibody

value: Input (N/A)


title: LbCR4-INPUT-NULL.Reg.1

value: Reg 1 month


title: LbCR4-INPUT-LbNOX.Reg.1


title: untreated PDAC 12 [D1756Q]

city: Rochester

first: Bradley

last: Mills

address: 601 Elmwood Avenue

institute: University of Rochester

data_processing:
Adapter trimming was performed using fastq-mcf program (v1.05) and cutadapt (v2.5).
Contamination removal was performed using Bowtie2 (v2.5.1).
Alignment was performed using STAR (v2.7.3a).
Raw read counts were estimated using HTSeq (v0.11.2) and normalized using DESeq2.
Aligned reads were used for estimating gene expression using cufflinks (v2.2.1).
Genome_build: GRCh37/hg19
Supplementary_files_format_and_content: Tab-delimited text file includes raw and normalized read counts for every gene across each sample.

source_name: pancreatic ductal adenocarcinoma

extract_protocol:
PDAC ws surgically resected (median of 7 days post-SBRT), FFPE, and tissue scrolls were generated from 5 um sections.
SMARTer Stranded Total RNA-Seq Pico Input Kit (Takara)

treatment_protocol: stereotactic body radiotherapy (25 Gy in 5 oligofractions)

tag: subject status

value: patients with resectable PDAC

value: resectable PDAC; whole tissue

value: untreated

tag: tissue type

value: FFPE tissue section from resection


title: untreated PDAC 13 [3393284]


title: untreated PDAC 11 [W90PJ9]


title: S1CR4-INPUT.LSKO.Reg.1

tag: age


title: Whole blood, SLE patient 52 Dose 4 on Week 12, placebo

description:
EF086402-8
A2786_2014

source_name: SLE Patient 52 Dose 4 on Week 12

value: SLE

value: PBO

value: Dose 4 on Week 12

value: Blood

value: Patient 52


title: Whole blood, SLE Patient 140 Dose 4 on Week 12 ; IFN-K

description:
EF086407-8
A2786_2015

source_name: SLE Patient 140 Dose 4 on Week 12

value: IFN-K

value: Patient 140


title: Fresh tissue from sample 1360 (Normal adjacent material)

description: miRNA expression data from fresh tissue

value: Normal-adjacent tissue

value: Not available


title: Whole blood, SLE Patient 152 Dose 4 on Week 12 ; IFN-K

description:
EE807608-8
A2786_2013

source_name: SLE Patient 152 Dose 4 on Week 12

value: Patient 152


title: Fresh tissue from sample 348 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: Fresh tissue from sample 127 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: LbCR4-INPUT-NULL.CR.1

value: 6 months

value: CR 1 month


title: Whole blood, SLE patient 56 Dose 4 on Week 12, placebo

description:
EE806984-7
A2786_2016

source_name: SLE Patient 56 Dose 4 on Week 12

value: Patient 56


title: Fresh tissue from sample 1358 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: Fresh tissue from sample 309 (Normal adjacent material)

description: miRNA expression data from fresh tissue


title: untreated PDAC 10 [209CNV]

value: patients with resectable PDAC


title: Whole blood, SLE patient 51 Dose 4 on Week 12, placebo

description:
EF086403-8
A2786_2010

source_name: SLE Patient 51 Dose 4 on Week 12

value: Patient 51


title: Fresh tissue from sample 3413 (Tumor material)

description: miRNA expression data from fresh tissue

source_name: sample of tumor tissue from a patient with lymph node metastasis

value: Tumor

value: Yes


title: Fresh tissue from sample 3410 (Tumor material)

description: miRNA expression data from fresh tissue


title: S1CR4-INPUT.CTRL.Reg.1

value: Reg 1 month

value: Input (N/A)


title: Fresh tissue from sample 3411 (Tumor material)

description: miRNA expression data from fresh tissue


title: Whole blood, SLE Patient 102 Dose 5 on Week 24; IFN-K

description:
EE722493-7
A2786_2012

source_name: SLE Patient 102 Dose 5 on Week 24

value: SLE

value: Dose 5 on Week 24

value: Patient 102


title: S1CR4-FOXO1.LSKO.CR.2

value: Alb-Cre; Sirt1fx/fx


title: Whole blood, SLE patient 18 Dose 4 on Week 12, placebo

description:
EE908780-7
A2786_2011

source_name: SLE Patient 18 Dose 4 on Week 12

value: PBO

value: Dose 4 on Week 12

value: Blood

value: Patient 18


title: S1CR4-FOXO1.LSKO.Reg.2

value: 6 months


title: untreated PDAC 9 [Z10-G2]

value: resectable PDAC; whole tissue

value: untreated

value: FFPE tissue section from resection


title: Fresh tissue from sample 3412 (Tumor material)

description: miRNA expression data from fresh tissue

source_name: sample of tumor tissue from a patient without lymph node metastasis

value: Not


title: Fresh tissue from sample 1866 (Tumor material)

description: miRNA expression data from fresh tissue

value: Tumor


title: S1CR4-FOXO1.LSKO.Reg.1

source_name: Liver


title: untreated PDAC 8 [D51FTA]

value: patients with resectable PDAC


title: S1CR4-FOXO1.CTRL.CR.2

value: CR 1 month


title: S1CR4-FOXO1.LSKO.CR.1


title: SBRT-treated PDAC 8 [14LLJ2]

value: SBRT


title: SBRT-treated PDAC 9 [2CAA70]


title: SBRT-treated PDAC 6 [4F1IYL]


title: S1CR4-FOXO1.CTRL.Reg.2

value: Reg 1 month


title: Fresh tissue from sample 1863 (Tumor material)

description: miRNA expression data from fresh tissue

value: Yes


title: Whole blood, SLE Patient 138 Dose 4 on Week 12 ; IFN-K

description:
EF086406-8
A2786_2008

source_name: SLE Patient 138 Dose 4 on Week 12

value: SLE

value: IFN-K

value: Patient 138


title: SBRT-treated PDAC 5 [VRV40D]


title: Whole blood, SLE patient 16 Dose 4 on Week 12, placebo

description:
EE703698-7
A2786_2006

source_name: SLE Patient 16 Dose 4 on Week 12

value: PBO

value: Dose 4 on Week 12

value: Patient 16


title: Whole blood, SLE Patient 156 Dose 4 on Week 12 ; IFN-K

description:
EE899206-8
A2786_2009

source_name: SLE Patient 156 Dose 4 on Week 12

value: Blood

value: Patient 156


title: Fresh tissue from sample 1358 (Tumor material)

description: miRNA expression data from fresh tissue


title: S1CR4-FOXO1.CTRL.CR.1

value: 6 months


title: Whole blood, SLE patient 54 Dose 4 on Week 12, placebo

description:
EE847830-8
A2786_2005

source_name: SLE Patient 54 Dose 4 on Week 12

value: Patient 54


title: SBRT-treated PDAC 7 [HC95QJ]

value: resectable PDAC; whole tissue

value: FFPE tissue section from resection


title: Whole blood, SLE patient 57 Dose 4 on Week 12, placebo

description:
EE871404-8
A2786_2007

source_name: SLE Patient 57 Dose 4 on Week 12

value: Patient 57


title: SBRT-treated PDAC 4 [QZ2T2C]

value: patients with resectable PDAC


title: S1CR4-FOXO1.CTRL.Reg.1


title: SBRT-treated PDAC 2 [9DSNWF]

value: SBRT


title: LbCR4-FOXO1.LbNOX.CR.1

value: CR 1 month


title: SBRT-treated PDAC 3 [C1A8AG]


title: 2m_P9_Negative_BioRep2

city: Beijing

first: liping

last: liu

state: Beijing

address: Yiheyuanlu 5#

institute: Peking University

data_processing:
Library strategy: CUT&TAG
Sequencing adapters and low quality reads were removed from the raw data with Trimmomatic (V0.39).
Reads aligned to mm10 with bowtie2 (V2.3.5.1).
MACS2 was used to call peaks, and DiffBind (V2.12.0) was used for filtration and feature count of peaks.
Genome_build: mm10
Supplementary_files_format_and_content: bedgraph

growth_protocol: Fresh isolated fibroblast from 2-month-old mice cultured with high-glucose DMEM supplemented with 10% fetal serum, 1% penicillin-streptomycin and 0.01% plasmocin. When cell attained 80-90% confluence, they were passaged at 1:3 ratio in 10cm dishes.

extract_protocol:
Libraries were prepared in situ
CUT&Tag was performed with Hyperactive In-Site ChIP Library Prep Kit (Vazyme Biotech, TD902). In brief, 60,000 cells were incubated with 10 μl pre-washed ConA beads for 10 min. Primary antibody (E2F4, Proteintech, 10923-1-AP, 1:50; ATF3, abcam, ab207434, 1:50) was added and cultured for 2 hours at room temperature.As a negative control, we just simply omitted the primary antibody according to the Nature protocols (Kaya-Okur, Wu et al. 2020). After washing twice with dig-wash buffer, Secondary antibody was added and incubated at room temperature for 45 min. After washing twice with dig-wash buffer, 0.58 μl pG-Tn5 was added with 100μl dig-300 buffer. Samples were incubated at room temperature for 1 hour and then washed twice with dig-wash buffer. 300μl tagmentation buffer was added and incubated at 37 °C for 1h. The reaction was stopped with 10μl 0.5M EDTA, 3μl 10% SDS and 2.5μl 20mg/ml Proteinase K. After extraction with phenol-chloroform and ethanol precipitation, PCR was performed to amplify the libraries using 16 cycles. All libraries were sequenced by Illumina Hiseq PE150.As a negative control, we just simply omitting the primary antibody according to the Nature protocol (Kaya-Okur, Wu et al. 2020).

treatment_protocol: serial passage

value: skin

value: fibroblast

tag: passage

value: no antibody


title: Fresh tissue from sample 348 (Tumor material)

description: miRNA expression data from fresh tissue

value: Tumor

value: Not


title: 2m_P9_Negative_BioRep1


title: Whole blood, SLE Patient 143 Dose 4 on Week 12 ; IFN-K

description:
EF085374-8
A2786_2003

source_name: SLE Patient 143 Dose 4 on Week 12

value: SLE

value: IFN-K

value: Dose 4 on Week 12

value: Patient 143


title: Whole blood, SLE Patient 145 Dose 4 on Week 12 ; IFN-K

description:
EE760195-7
A2786_2002

source_name: SLE Patient 145 Dose 4 on Week 12

value: Blood

value: Patient 145


title: untreated PDAC 7 [Y6YFCC]

source_name: pancreatic ductal adenocarcinoma

value: resectable PDAC; whole tissue

value: untreated


title: Fresh tissue from sample 309 (Tumor material)

description: miRNA expression data from fresh tissue


title: Fresh tissue from sample 127 (Tumor material)

description: miRNA expression data from fresh tissue


title: LbCR4-FOXO1.LbNOX.CR.2

value: 6 months

tag: genotype


title: SBRT-treated PDAC 1 [T6LSKY]

value: patients with resectable PDAC

value: FFPE tissue section from resection


title: 2m_P9_ATF3_BioRep1


title: LbCR4-FOXO1.NULL.CR.3

value: CR 1 month

tag: collection timepoint


title: 2m_P9_ATF3_BioRep2

value: skin


title: Whole blood, SLE patient 61 Dose 4 on Week 12, placebo

description:
EE899205-8
A2786_2004

source_name: SLE Patient 61 Dose 4 on Week 12

value: PBO

value: Patient 61


title: Whole blood, healthy individual, no treatment 9

description:
Baseline sample 9
A2786_19

source_name: Whole blood, no treatment

value: Healthy


title: untreated PDAC 6 [4HLVHH]


title: 2m_P9_E2F4_BioRep2

value: fibroblast


title: untreated PDAC 5 [U3ZUDM]


title: Whole blood, healthy individual, no treatment 10

description:
Baseline sample 10
A2786_20


title: Whole blood, SLE patient 53 Dose 4 on Week 12, placebo

description:
EE760197-7
A2786_2001

source_name: SLE Patient 53 Dose 4 on Week 12

value: SLE

value: Patient 53


title: LbCR4-FOXO1.NULL.CR.2


title: 2m_P9_E2F4_BioRep1


title: LbCR4-FOXO1.NULL.CR.1


title: Fresh tissue from sample 1360 (Tumor material)

description: miRNA expression data from fresh tissue

value: Tumor

tag: lymph node metastasis

value: Yes


title: untreated PDAC 3 [Z1UWYX]


title: 2m_P2_Negative_BioRep2

tag: cell type

value: no antibody


title: 2m_P2_Negative_BioRep1


title: LbCR4-FOXO1.LbNOX.Reg.3

value: Reg 1 month


title: LbCR4-FOXO1.NULL.Reg.2


title: LbCR4-FOXO1.LbNOX.Reg.1


title: Whole blood, healthy individual, no treatment 7

description:
Baseline sample 7
A2786_17

value: Blood


title: Whole blood, healthy individual, no treatment 8

description:
Baseline sample 8
A2786_18


title: S1CR4-INPUT.CTRL.CR.1

value: Input (N/A)


title: Whole blood, healthy individual, no treatment 6

description:
Baseline sample 6
A2786_16


title: untreated PDAC 4 [CWJEC3]

value: resectable PDAC; whole tissue

value: untreated


title: 2m_P2_ATF3_BioRep1


title: A549 cells - Interferon gamma (+) AX0085 (+) rep_1

city: Seoul

first: Jaesang

last: Kim

address: 52, Ewhayeodae-gil

country: South Korea

institute: Ewha Womans Universiyt

data_processing:
bcl2fastq2 (Version 2.20) was used for base calling.
TrimGalore (version 0.6.7) was used for trimming adapter sequences and discarding low quality reads.
The reads were mapped against the human reference genome (GRCh38/hg38) using STAR alignment program (version 2.7.9a)
Gene expression matrix was generated using FeatureCount function in Rsubread version 2.6.4
Differentially expressed genes (DEGs) were identified using DESeq2 with the adjusted P-value <0.05 and |fold change| > 2 threshold.
Gene set analyses of DEGs for pathways and gene ontology (GO) terms and Gene Set Enrichment Analysis (GSEA) were performed using clusterProfiler version 4.0.4, a R package for interpretation of omics data.
Genome_build: GRCh38/hg38
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: A549 cell-line

growth_protocol: Cells were typically cultured in RPMI-1640 supplemented with 10% fetal bovine serum and 1% penicillin/streptomycin in humidified incubators at 37°C with 5% CO2.

extract_protocol:
Total RNA for RNA-seq was isolated using RNeasy Mini Kit, and mRNA libraries were prepared using the TruSeq Stranded mRNA Preparation kit
mRNA libraries were prepared using the TruSeq Stranded mRNA Preparation kit (Illumina, San Diego, CA, USA) according to the manufacturer’s instructions.

treatment_protocol: 20ng of interferon gamma were added and cells were cultured for 24 hours prior to adding AX0085 to 0.5 uM. Cells were harvested after another 24 hours.

tag: cell-line

value: adenocarcinomic human alveolar basal epithelial cells

value: Interferon gamma (+) AX0085 (+)


title: LbCR4-RNA.LbNOX.CR.4

value: 6 months

value: CR 1 month


title: Whole blood, healthy individual, no treatment 2

first: Frédéric

last: HOUSSIAU

institute: Université catholique de Louvain

description:
Baseline sample 2
A2786_12


title: LbCR4-FOXO1.NULL.Reg.1


title: A549 cells - Interferon gamma (+) AX0085 (-) rep_2

value: Interferon gamma (+) AX0085 (-)


title: A549 cells - Interferon gamma (+) AX0085 (+) rep_2


title: A549 cells - Interferon gamma (+) AX0085 (-) rep_1


title: LbCR4-RNA.LbNOX.CR.3


title: LbCR4-RNA.LbNOX.CR.2


title: Cur CC4

description:
shoot tissues of Oryza sativa plants at the three week old satage, cultivated under control conditions
SAT_processedData

data_processing:
After sequencing, read quality was checked and all low-quality reads (PHRED value < 20) were removed.
Adapter sequences were trimmed using Trim Galore and the first twelve nucleotides were removed from the 5’ end.
Alignments were done using STAR on default settings and feature counting was performed with the SummarizeOverlaps function on Union mode from the GenomicAlignments package for R.
Differential expression analysis were performed (+Fe vs. control) through the standard protocol from DESeq2 package for R. Genes for which q-value < 0.05 were considered differentially expressed
Genome_build: O. sativa IRGSP-1.0, Oryza meridionalis v1.3
Supplementary_files_format_and_content: Differential Expression and Raw Counts

organism: Oryza sativa Japonica Group

source_name: shoot

extract_protocol:
Total RNA was extracted with peqGOLD RNA kit (Peqlab; Erlangen, Germany) following the manufacturers’ instructions. The genomic DNA was removed with one column RNAase-free with DNAase. The integrity of RNA was tested on a bleach agarose gel (Aranda et al., 2012) and for purity using NanoDrop OneC (Thermo Fisher Scientific, Braunschweig, Germany).
For transcriptomic analysis, approximately 10 µg of total RNA was used for high-throughput cDNA sequencing by Illumina HiSeqTM 4000 technology (BGI Genomics Co.). RNAs derived from three biological replicates were used to generate the libraries. A total of eighteen libraries were constructed, from samples harvested seven days after the onset of treatments (control and +Fe). The cDNA libraries were prepared according to Illumina’s protocols. The libraries were sequenced using filter.

value: O. sativa cv. Curinga

value: three weeks-old

value: Control

tag: replicate


title: A549 cells - Interferon gamma (-) AX0085 (+) rep_2

value: Interferon gamma (-) AX0085 (+)


title: Whole blood, healthy individual, no treatment 4

description:
Baseline sample 4
A2786_14

value: Healthy


title: Whole blood, healthy individual, no treatment 5

description:
Baseline sample 5
A2786_15


title: LbCR4-RNA.LbNOX.CR.5

extract_protocol:
RNA was isolated from 10-20mg of liver tissue using trizol reagent and purified on the Zymo Direct-Zol RNA miniprep kit. RNA quality was assessed by Bioanalyzer (Agilent). RNAs with a RNA Integrity Number (RIN) greater than 8 were used for library prep.
Libraries were constructed from 250 ng of RNA using the NEBNext RNA Ultra Directional library prep kit from NEB. Average library size and concentration were determined by Bioanalyzer and qPCR (NEBNext Library Quant kit), respectively, prior to pooling.

tag: strain


title: S_replicate2

type: genomic

city: Montpellier

first: Alexandre

last: Djiane

address: 208 rue des apothicaires

department: IRCM

country: France

institute: Inserm

description: Wing discs fully mutant for scrib

hyb_protocol: Both ChIP and input were co-hybridized to NimbleGen D. melanogaster ChIP-chip 2.1 M whole-genome tiling arrays in the NimbleGen hybridisation station at 42°C for 16 h and then washed according to the NimbleGen Wash Buffer kit instructions.

scan_protocol: Arrays are scanned at 5 µm resolution with a GenePix 4000B (Axon) dual laser scanner at 100% Power, with Lines to average = 1 and Focus position = 0 at their respective optimal PMT gains selected by the Auto-PMT function (0.005% saturation tolerance).

data_processing:
The data obtained were normalized using quantile normalization across the replicate arrays in R. Window smoothing and peak calling were performed using the Bioconductor package Ringo (Toedling et al., 2007) with a winHalfSize of 300 bp and min.probes = 5. Probe levels 555 were then assigned P-values based on the normalNull method, corrected for multiple testing using the Hochberg–Benjamini algorithm and then condensed into regions using distCutOff of 200 bp.
The sgr files represent quantile-normalized log2 ratio (IP/Input) ratios.

organism: Drosophila melanogaster

source_name: Su(H) ChIP DNA from S wing discs replicate 2

label_protocol: For whole-genome analysis, 1 μg double-stranded ChIP or input DNA (corresponding to 180 discs for each replicate) was labelled with either Cy3- or Cy5-random primers using the Nimblegen Dual Colour kit.

growth_protocol: 6 days after egg laying

extract_protocol: After dissection in PBS 1X, Protein/DNA complexes from 60 wing discs (80 for S condition) were cross-linked with 1% formaldehyde for 10 minutes. The reaction was then quenched by 0.125 M Glycine and washed 3x in PBS. Wing disc cells were resuspended in 50μL Nuclear Lysis Buffer (Tris-HCl pH 8.1 20mM, EDTA 10mM, SDS 1%). Lysates were sonicated on a Bioruptor (Diagenode), and diluted 10x in Immunoprecipitation Dilution Buffer (Tris-HCl pH 8.1 20mM, EDTA 2mM, SDS 0.01%, NaCl 150mM, Triton X-100 1%) and precleared with rabbit IgG (Sigma) and protein G Agarose (Santa Cruz Biotechnology). ChIP reactions were performed by incubating lysates overnight at 4°C with 1ng of Goat anti-Su(H) (Santa Cruz Biotechnology, sc15813), and immunocomplexes were then isolated with Protein G Agarose for 2h, washed 2x with Wash Buffer 1 (Tris-HCl pH 8.1 20mM, EDTA 2mM, SDS 0.1%, NaCl 50mM, Triton X-100 1%) and 2x with Wash Buffer 2 (Tris-HCl pH 8.1 10mM, EDTA 1mM, LiCl 250mM, NP-40 1%, Deoxycholic acid 0.4%), before a decross-linking step at 65°C in 0.25M NaCl. Samples were then treated with 0.2 mg/mL proteinase K and 50mg/mL RNase A. The DNA was then purified on columns (Qiagen, 28106)

value: w- / w-; + ; FRT82B scrib1 / Df(3R)BSC752

tag: developmental stage

value: 3rd instar larva

tag: tissue

value: Wing discs

value: Su(H), Santa Cruz Biotechnology, sc15813

tag: fraction

value: ChIP DNA

source_name: Total input DNA from S wing discs replicate 2

value: input DNA


title: Whole blood, SLE Patient 156 Follow-up on Week 36 ; IFN-K

city: Brussels

address: Avenue Hippocrate 10

description:
EP050839A08
A2786_2024

source_name: SLE Patient 156 Follow-up on Week 36

tag: diagnosis

value: SLE

tag: treatment

value: IFN-K

tag: time point

value: Follow-up on Week 36

value: Blood

value: Patient 156


title: Whole blood, healthy individual, no treatment 3

description:
Baseline sample 3
A2786_13


title: untreated PDAC 1 [QLSPMR]

tag: subject status

value: patients with resectable PDAC

value: resectable PDAC; whole tissue

value: untreated

value: FFPE tissue section from resection


title: LbCR4-FOXO1.LbNOX.Reg.2

source_name: Liver

value: 6 months

value: Reg 1 month

tag: chip antibody


title: untreated PDAC 2 [VNB-Q1]

tag: tissue type


title: LbCR4-RNA.LbNOX.CR.1

tag: age

value: CR 1 month


title: Cur Fe2

description:
shoot tissues of Oryza sativa plants at the three week old satage, cultivated under Fe toxicity conditions
SAT_processedData

value: O. sativa cv. Curinga

value: three weeks-old

value: Fe toxicity


title: LbCR4-RNA.NULL.CR.4

tag: genotype


title: 2m_P2_E2F4_BioRep1

value: skin

value: fibroblast

tag: passage


title: NS_replicate2

description: Overexpression of activated Notch (Nicd) and mutant for scribble (scrib1)

source_name: Su(H) ChIP DNA from NS wing discs replicate 2

value: y-, w-, abxUbx-Flp / w-; Act>y+>Gal4, UAS eGFP / UAS Nicd; FRT82B tubGal80 / FRT82B scrib1

value: 3rd instar larva

value: Wing discs

value: Su(H), Santa Cruz Biotechnology, sc15813

value: ChIP DNA

source_name: Total input DNA from NS wing discs replicate 2

value: input DNA


title: N_replicate1

description: Overexpression of activated Notch (Nicd)

source_name: Su(H) ChIP DNA from N wing discs replicate 1

value: y-, w-, abxUbx-Flp / w-; Act>y+>Gal4, UAS eGFP / UAS Nicd; FRT82B tubGal80 / FRT82B

source_name: Total input DNA from N wing discs replicate 1


title: SF3B1 H698R-mut strain2 rep3

first: Zhan

last: Ding

address: FengLin 300

institute: CAS Center for Excellence in Molecular Plant Science

data_processing:
Raw data (raw reads) of fastq format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality
Reads mapped to dm6 whole genome using hisat2(v2.1.0) with defeault parameters. Reference genome and gene model annotation files were downloaded from FlyBase r6.16.
FeatureCounts(v1.6.3) was used to count the reads numbers mapped to each gene.
The abundance of each gene was calculated by stringtie(v2.0).
Genome_build: dm6
Supplementary_files_format_and_content: tab-delimited text files include gene abundance values for each Sample .

extract_protocol:
Total RNAs from larvae were isolated by TRIzol (Ambion) and treated with RNase-free DNase I (Invitrogen). For RT-PCR, cDNAs were reverse transcribed using RevertAid Reverse Transcriptase (Thermo) and amplified by Ex-Taq (TaKaRa).A total amount of 1 µg RNA per sample was used as input material for the RNA sample preparations. Sequencing libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations and index codes were added to attribute sequences to each sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: strain background

value: Whole Body


title: NS_replicate1

source_name: Su(H) ChIP DNA from NS wing discs replicate 1

source_name: Total input DNA from NS wing discs replicate 1


title: Cur CC3

first: Andriele

last: Wairich

institute: Universidade Federal do Rio Grande do Sul

value: Control


title: HCMEC_siDDX24_rep2

city: Zhuhai

first: Fangbin

last: Chen

state: Guangdong

address: Meihua East Road No.52

institute: Sun Yat-sen University

data_processing:
Basecalls performed using CASAVA version 1.9.
Raw data  sequenced reads were trimmed for adaptor sequence by Trimmomatic-0.39.
Clean data RNA-seq reads were aligned to the GRCh38.p13 genome assembly by STRA version= 2.7.7a.
Counts of reads aligning to known genes were generated by featureCounts by RSEM.
Genome_build: GRCh38.p13
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: human cerebral microvascular endothelial cells

growth_protocol: Cells cultured in Endothelial Cell Medium (ScienCell) supplemented with 10% fetal bovine serum (FBS, ScienCell), 1% endothelial cell growth supplement (ECGS, ScienCell), and grown at 37 °C in a 5% CO2 humid atmosphere.

extract_protocol:
RNA was extracted using Trizol reagent
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: siNRA transfection with Lipofectamine 3000 following the manufacturer's instructions

tag: cell type

value: brain endothelial cell

tag: transfection

value: DDX24 siRNA


title: Cur Fe1

address: Av. Bento Gonçalves, 9500

tag: replicate


title: A549 cells - Interferon gamma (-) AX0085 (+) rep_1

tag: cell-line

value: adenocarcinomic human alveolar basal epithelial cells

value: Interferon gamma (-) AX0085 (+)


title: PDGFB Vehicle Cd11b+ TAMs Ms1

first: Qing

last: Lu

address: 3333 Burnet Ave

institute: Cincinnati Children's Hospital Medical Center

description:
PDGFB_PLX3397_TAM_3days_counts
PDGF_Veh_TAM

data_processing:
RNA-seq reads in FASTQ format were first subjected to quality control to assess the need for trimming of adapter sequences or bad quality segments. The programs used in these steps were FastQC v0.11.7, Trim Galore! v0.4.2  and cutadapt v1.9.1.
The trimmed reads were aligned to the reference human genome version GRCm38/mm10 with the program STAR v2.6.1e
Aligned reads were stripped of duplicate reads with the program sambamba v0.6.8
Gene-level expression was assessed by counting features for each gene, as defined in the NCBI's RefSeq database
Read counting was done with the program featureCounts v1.6.2 from the Rsubread package
For single cell RNA-seq datasets, gene barcode matrix files were generated from fastq files using the cellranger count method.
Genome_build: mm10
Supplementary_files_format_and_content: Single cell RNA-seq datasets have counts from CellRanger
Supplementary_files_format_and_content: RNA-seq datasets have count matrices combining samples from the same experiments

source_name: Mouse Brain Tumor

extract_protocol:
Mice were perfused with ice cold PBS and brain tumors were dissected out. Tumor tissue was then dissociated using Miltenyi Neural Tissue Dissociation Kit P using the 37 C NTDK program on the Miltenyi gentleMacs Octo Dissociator with heaters. Cell suspensions were filtered and treated with Red Blood Cell Lysing Buffer . They were then resuspended in 0.1% BSA and then incubated with CD11b Microbeads. CD11b+ cell populations were then isolated using MS columns , resuspended in Trizol with poly-acryl carrier, and then cleaned up using  a Qiagen RNEasy kit
Libraries prepared by CCHMC Gene Expression Core using Nextera kit for sequencing on Novo-Seq platform

treatment_protocol: Mice with treated via oral gavage daily with 100 mg/kg vehicle or PLX3397 for three days starting at 14 days after tumor implantation

value: Cd11b+ TAMs

tag: strain

value: Boy/J

value: Vehicle


title: Cur Fe4

value: O. sativa cv. Curinga

value: three weeks-old

value: Fe toxicity


title: Cur CC2


title: SF3B1 H698R-mut strain2 rep1

tag: developmental stage

tag: tissue


title: SF3B1 H698D-mut strain2 rep3


title: PDGFB PLX3397 Cd11b+ TAMs Ms2

description:
PDGFB_PLX3397_TAM_3days_counts
PDGF_PLX_TAM2


title: A549 cells - Interferon gamma (-) AX0085 (-) rep_1

value: Interferon gamma (-) AX0085 (-)


title: N_replicate2

source_name: Su(H) ChIP DNA from N wing discs replicate 2

value: 3rd instar larva

value: Wing discs

value: Su(H), Santa Cruz Biotechnology, sc15813

tag: fraction

source_name: Total input DNA from N wing discs replicate 2


title: S_replicate1

description: Wing discs fully mutant for scrib

source_name: Su(H) ChIP DNA from S wing discs replicate 1

value: w- / w-; + ; FRT82B scrib1 / Df(3R)BSC752

value: ChIP DNA

source_name: Total input DNA from S wing discs replicate 1

value: input DNA


title: LbCR4-RNA.NULL.CR.6

first: Louis

last: Ptacek

institute: University of California San Francisco

value: 6 months

tag: treatment

value: CR 1 month

tag: collection timepoint


title: 2m_P2_E2F4_BioRep2

value: skin

value: fibroblast


title: LbCR4-RNA.NULL.CR.3


title: PDGFB PLX3397 Cd11b+ TAMs Ms1

description:
PDGFB_PLX3397_TAM_3days_counts
PDGF_PLX_TAM1

value: Cd11b+ TAMs


title: HCMEC_siDDX24_rep1

value: brain endothelial cell

value: DDX24 siRNA


title: SF3B1 H698D-mut strain2 rep2

value: Whole Body


title: SF3B1 H698R-mut strain2 rep2


title: SF3B1 H698R-mut strain1 rep3


title: LbCR4-RNA.NULL.CR.1


title: HUVEC_siDDX24_rep2

source_name: human umbilical vein endothelial cells

value: non-brain endothelial cell


title: HCMEC_siNC_rep-1

value: control siRNA


title: A549 cells - Interferon gamma (-) AX0085 (-) rep_2

source_name: A549 cell-line

value: adenocarcinomic human alveolar basal epithelial cells

value: Interferon gamma (-) AX0085 (-)


title: LbCR4-RNA.LbNOX.Reg.6

value: Reg 1 month


title: LbCR4-RNA.NULL.CR.2


title: SF3B1 H698R-mut strain1 rep2


title: LbCR4-RNA.LbNOX.Reg.4


title: HBO treatment3

first: Xuehua

address: 8 Gongti South Road, Chaoyang District Beijing

department: Department of Hyperbaric Oxygen

institute: Beijing Chaoyang Hospital, Capital Medical University

data_processing:
illumina Hiseq 2500 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to GRCm38 whole genome using Hisat2（version:2.0.4）
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Mortazavi A et al., Nat Methods, 2008. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample ...
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every sample

source_name: spinal cord

extract_protocol:
Spinal cord tissues were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. TransZol Up Plus RNA Kit（Cat#ER501-01，Trans）was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

value: spinal cord

value: 7-9 weeks

value: wild type

value: HBO treatment


title: HUVEC_siNC_rep2


title: HCMEC_siNC_rep_2