title: 18.565_Tumor

description:
tumor tissue
18-565_L7_G821


title: 1-Baseline

status: Public on Sep 06 2022

type: SRA

city: San Diego

first: Peter

last: Olson

state: California

address: 3545 Cray Court

country: USA

institute: Mirati Therapeutics

description:
HTG EdgeSeq Precision ImmunoOncology panel
S1

library_source: transcriptomic

data_processing:
The data were analysed using HTG parser and HTG EdgeSeq Reveal software, to generate raw and normalised counts
Assembly: 1392 human gene panel
Supplementary files format and content: tab-delimited text file include raw read counts for each Sample

molecule: total RNA

organism: Homo sapiens

source_name: Kidney, NOS

extract_protocol:
formalin-fixed paraffin embedded (FFPE) samples with two 5 μm core needle biopsy sections
All samples were processed according to the manufacturer's protocol. The tissue was removed from the slides with a scalpel, lysed using proteinase K and HTG’s denaturation oil, and underwent target protection and clean up on the HTG EdgeSeq processor. Following this process, sequencing adaptors and barcodes were added and the library amplified. Amplified libraries were quantified with the Kapa library quantification kit, pooled, and sequenced on Illumina’s Miseq platform.
1392 gene HTG EdgeSeq Precision ImmunoOncology

tag: patient id

tag: tissue

value: Kidney, NOS

tag: source

value: Fixed - FFPE

tag: disease

value: Clear Cell Renal cell carcinoma

tag: treatment

value: Baseline

tag: time


title: 19.062_Normal

city: Hershey

first: Gregory

last: Yochum

state: PA

address: 700 HMC Crescent Road

institute: Penn State College of Medicine

description:
full thickness tumor adjacent tissue
19-062_L0_G821

data_processing:
Base calling with Illumina MiSeq.
Alignment with STAR version 2.7.3.
HTSeq counting of aligned reads.
DESeq2 rlog function for normalization.
Genome_build: hg38
Supplementary_files_format_and_content: *_htseq.out.txt: Count files contain raw counts for sequences aligning to each transcript.
Supplementary_files_format_and_content: raw_counts.csv: Comma-separated text file includes raw counts.

source_name: Sigmoid Colon

extract_protocol:
Tumors and adjacent colonic segments were surgically resected and aliquots were stored in RNAlater (Thermo Fisher) preservative. Samples were homogenized with a pestle and chloroform was added. The samples were centrifuged at 12,000 x g for 15 minutes. The aqueous layer was purified with RNeasy Mini Kit (Qiagen). Samples were selected for poly-adenylation, and cDNA libraries were made and sequenced on MiSeq (Illumina).
RNA libraries were prepared for sequencing using standard Illumina protocols.

tag: diagnosis

value: Early onset colorectal cancer

value: Adjacent normal tissue

tag: tumor stage

tag: age at surgery


title: 18.565_Normal

description:
full thickness tumor adjacent tissue
18-565_L0_G821


title: Sample_238_RORg_MHCII

city: New York

first: Chrysothemis

last: Brown

state: NY

department: Immunology Program, Sloan Kettering Institute

institute: Memorial Sloan Kettering Cancer Center

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol

data_processing:
base-calling was performed using HiSeq Control Software HD v3.4.0.38
samples were demultiplexed using bcl2FASTQ v2.20.0.422
FASTQ files from demultiplexed samples were aligned to GRCm38 (mm10) using STAR v2.7.7a with ‘--twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM’
The alignments of each sample were name-sorted using Samtools v1.11
The count matrix for all cells was created by counting alignments using featureCounts (subread v2.0.1)
Low-quality cells/genes were filtered and downstream analyses (normalization, PCA, etc.) was performed using Seurat v3.2.3.
Cells were clustered using PhenoGraph and UMAP embedding was computed using Seurat v3.2.3.
Genome_build: mm10
Supplementary_files_format_and_content: the count matrix (tab-delimited table) includes raw counts for all cells (smart-seq2 samples).
Supplementary_files_format_and_content: the cell metadata (csv table) includes clusters, annotations, etc. for all cells (corresponding to rows in the count matrix).

organism: Mus musculus

source_name: Mouse MLN RORgt+ MHCII+

extract_protocol:
RORgt+MHCII+ cells were enriched from a pool of MLN from 3-week-old RorcVenus-CreERT2 mice. Cells were depleted of Lineage (TCRb, TCRgd, CD19, B220, NK1.1)+ cells via staining with biotinylated antibodies followed by magnetic bead negative selection. Live, Lin(CD3, TCRb, TCRgd CD19, B220, NK1.1)–CD64–Ly6C–MHCII+RORgt(Venus)+ cells were then sorted into single wells. Cells were also stained for CD90, CD11c and CD11b for acquiring index sorting information on cell surface expression. Aire+ mTECs were enriched from a pool of thymi from 3-week old mice via staining with biotinylated antibodies against CD45 followed by magnetic bead negative selection. CD45–Epcam+MHCII+Aire(GFP)+ cells were sorted into single wells. Aire+ DCs were enriched from a pool of MLN from the same 3-week old mice. Cells were depleted of Lin+ cells as described above and live, Lin(CD3, TCRb, TCRgd CD19, B220, NK1.1)–CD90–CD64–Ly6C–CD11c+MHCII+Aire(GFP)+ cells were then sorted into single wells.
Single cells were sorted into Buffer RLT (Qiagen). Cell lysates were immediately sealed and spun down before transferring to dry ice and storing at -80 ºC. RNA was purified using the Agencourt RNAClean XP beads (Beckman Coulter) at a 2.2X ratio. First-strand cDNA synthesis was achieved using Maxima H Minus Reverse Transcriptase (ThermoFisher) according to the manufacturer’s protocol using oligo dT primers, with the addition of a custom template-switch oligo in a 1mM final concentration. cDNA was amplified for 24 cycles using KAPA HiFi HotStart ReadyMix (Kapa Biosystems KK2601). After PicoGreen quantification, 0.1-0.2ng of cDNA was used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina) in a total volume of 6.25µL with 12 cycles of PCR. Indexed libraries were pooled by volume and cleaned by aMPure XP beads (Beckman Coulter) at a 1X ratio. Pools were sequenced on a HiSeq 4000 in a PE50 or PE100 run using the HiSeq 3000/4000 SBS Kit (Illumina).

value: mesenteric lymph nodes (MLN)

tag: age

value: three weeks

tag: cell type

value: RORgt+ MHCII+


title: 18.466_Tumor

description:
tumor tissue
18-466_L7_G821

value: Tumor tissue


title: 18.466_Normal

description:
full thickness tumor adjacent tissue
18-466_L0_G821


title: 18.269_Normal

description:
full thickness tumor adjacent tissue
18-269_D0_G821

source_name: Descending Colon


title: 18.269_Tumor

description:
tumor tissue
18-269_D7_G821


title: Sample_236_RORg_MHCII


title: 18.177_Tumor

description:
tumor tissue
18-177_H7_G821

source_name: Cecum


title: Sample_243_RORg_MHCII


title: Sample_235_RORg_MHCII


title: 18.177_Normal

description:
full thickness tumor adjacent tissue
18-177_H0_G821


title: Sample_234_RORg_MHCII


title: 18.152_Tumor

description:
tumor tissue
18-152_L7_G821


title: 18.152_Normal

description:
full thickness tumor adjacent tissue
18-152_L0_G821


title: 17.477_Tumor

description:
tumor tissue
17-477_L7_G821


title: 17.477_Normal

description:
full thickness tumor adjacent tissue
17-477_L0_G821


title: 17.150_Tumor

description:
tumor tissue
17-150_E7_G821

source_name: Rectum


title: Sample_233_RORg_MHCII


title: 17.150_Normal

description:
full thickness tumor adjacent tissue
17-150_E0_G821


title: 15.288_Tumor

description:
tumor tissue
15-288_B7_G821

source_name: Ascending Colon


title: Sample_232_RORg_MHCII


title: 15.171_Tumor

description:
tumor tissue
15-171_L7_G821


title: 15.248_Normal

description:
full thickness tumor adjacent tissue
15-248_A0_G821


title: Sample_231_RORg_MHCII


title: 15.248_Tumor

description:
tumor tissue
15-248_A7_G821


title: Sample_229_RORg_MHCII


title: Sample_237_RORg_MHCII


title: Sample_230_RORg_MHCII


title: 15.164_Normal

description:
full thickness tumor adjacent tissue
15-164_E0_G821


title: 15.288_Normal

description:
full thickness tumor adjacent tissue
15-288_B0_G821


title: Sample_228_RORg_MHCII


title: 15.171_Normal

description:
full thickness tumor adjacent tissue
15-171_L0_G821


title: Sample_227_RORg_MHCII


title: 15.160_Normal

description:
full thickness tumor adjacent tissue
15-160_E0_G821


title: 15.018_Tumor

description:
tumor tissue
15-018_L7_G821


title: 15.130_Normal

description:
full thickness tumor adjacent tissue
15-130_B0_G821


title: Sample_226_RORg_MHCII


title: Sample_225_RORg_MHCII


title: Sample_224_RORg_MHCII


title: 15.018_Normal

description:
full thickness tumor adjacent tissue
15-018_L0_G821


title: Sample_223_RORg_MHCII


title: 15.164_Tumor

description:
tumor tissue
15-164_E7_G821


title: Sample_222_RORg_MHCII


title: Stimulated, biological rep3

type: RNA

city: Saint Louis

first: Kenneth

last: Murphy

state: MO

address: Clinical Science Research Building, 7th Floor, Room 7701A, Campus Box 8118

department: Pathology & Immunology

institute: Washington University School of Medicine

hyb_protocol: Following fragmentation and labeling, 2.5 ug of cDNA were hybridized onto the Gene 1.0 ST arrays and placed in GeneChip Hybridization Oven 640 for 18 hr at 45C. Gene Chip’s were washed and stained in the Affymetrix Fluidics Station 450.

scan_protocol: GeneChips were scanned using the Affymetrix GeneChip 7G 3000 Scanner.

data_processing: The data was analyzed with the Affymetrix GeneChip Command Console. Microarray expression data was processed using Command Console (Affymetrix, Inc) and the raw (.CEL) files generated were analyzed using Expression Console software with Affymetrix default RMA Gene analysis settings.(Affymetrix, Inc).  Probe summarization (Robust Multichip Analysis, RMA), quality control analysis, and probe annotation were performed according to recommended guidelines (Expression Console Software, Affymetrix, Inc.).

label: biotin

source_name: anti-CD40 stimulated migratory sdLN WT cDC1

label_protocol: Biotinylated cDNA were prepared according to the Affymetrix WT Pico reagent kit from 100pg-2ng total RNA.

growth_protocol: Migratory CD40+ cDC1 were isolated from skin draining lymph nodes of WT mice.

extract_protocol: Column extraction of total RNA was performed acording to the manufacturer's instructions.

treatment_protocol: B220- CD326- MHC IIhigh CD11cint XCR1+ Sirpa- CD40+ migratory cDC1 (SDLN) were sort-purified to extract RNA for microarray analysis.

value: skin draining lymph node

tag: strain

tag: genotype

value: WT


title: Sample_221_RORg_MHCII


title: 15.160_Tumor

description:
tumor tissue
15-160_E7_G821


title: 15.130_Tumor

description:
tumor tissue
15-130_B7_G821


title: Sample_220_RORg_MHCII


title: Sample_219_RORg_MHCII


title: Sample_218_RORg_MHCII


city: Hong Kong

first: Jian

last: Yan

state: Hong Kong Special Administrative Region

address: 83 Tat Chee Avenue, Kowloon

department: Department of Biomedical Sciences

country: China

institute: City University of Hong Kong

description: PCR products from SARS-CoV-2_variant_omicron_N_RNA-SELEX_cycle3_rep2

library_source: other

data_processing:
Illumina Casava v1.7 software used for basecalling.
Quality control of the raw sequencing data using FastQC version v0.11.7 with default parameters.
Sequences from the 40-nt random region without bases annotated as N were extracted using custom script.
Autoseed software was used for motif analysis.
The R ggseqlogog package was used to construct motif logos.
Assembly: NA
Supplementary files format and content: xls file was a tab-delimited file include the summary of position weight matrix(PWM) for all motifs.

molecule: protein

organism: Escherichia coli

source_name: Rosetta (DE3)

growth_protocol: The E. coli strains for protein purification were grown at 37 ℃ in LB (Luria-Bertani) broth with shaking at 220 rpm or on LB agar plates until OD600=0.6.

extract_protocol:
The pellet was suspended in 10 ml buffer A (0.5 mg/ml Lysozyme, 50 mM tris-HCl pH 7.5, 300 mM NaCl, 10 mM Imidazole, 1 mM DTT, 1 mM PMSF) and lysed by sonication at ten seconds interval for 10 minutes and then centrifuged at 4 °C (12000 rpm, 30 min) to collect protein supernatant. The supernatant was filtered with a 0.45 μm filter and the filtrate was added into a Ni-NTA column (Bio-Rad) which had been equilibrated with buffer A before using. The Ni-NTA beads was set at 4 ℃ for 30min before being eluted with Buffer A containing 300 mM imidazole
HT-SELEX was performed by using selection ligands containing  a 10 bp barcode after the 40 bp randomized region. The ligand libraries were produced by PCR amplification using the primers in Supplementary Table1 and 40 bp randomized oligo as template. The libraries were sequenced using BGI MGISEQ-2000 sequencer to analyze the uniformity of each base (A, T, C, G). RNA input was synthesized from the DNA-templates using T7 in vitro transcription and the remaining DNA template was digest by DNaseⅠ. To enable the RNA to form secondary structures, the RNA input libraries were then heated to 70°C followed by slow cooling. Then, 600 ng protein and 5 ul RNA input selection ligands were added into  binding buffer (50 mM NaCl, 1 mM MgCl2, 0.5 mM Na2EDTA , 1U/μL RNase inhibitor and 4% glycerol in 50 mM Tris-Cl, pH 7.5) until the total volume reached 25 ul. After incubated for 15 minutes at 37°C, the mixture was followed by additional 15 minutes at room temperature. Subsequently, 150- µL binding buffer, containing 10 µL pre-equilibrated Ni Sepharose 6 Fast Flow resin (GE Healthcare, 17-5318-01) was added into the mixture. After incubated for further 2 hours with gentle shaking at room temperature, the beads were then washed with gentle shaking 12 times with 200 μL of binding buffer to remove the unbound RNA ligands. Subsequently, the residual moisture on beads was carefully cleared by a soft centrifuging at 500 g for 30 s, and then the bound RNA was resuspended in 20 μL elution buffer (0.5 µM RT-primer, 1 mM EDTA and 0.1% Tween 20 in 10 mM Tris-Cl buffer, pH 7.0) and heated for 5 minutes at 70°C followed by 4°C to anneal the reverse transcription primer to the remaining RNA. Finally, the eluted RNA was used for reverse transcription and PCR amplification using the the primers in Supplementary Table 1, and the obtained PCR products were used as DNA template for the next cycle after containing a T7 promoter. This process was repeated four times. Each PCR products were purified and sequence using  BGI MGISEQ 2000 sequencer.

treatment_protocol: 1 mM IPTG (Isopropyl β-D-1-Thiogalactopyranoside) was added into the bacterial culture to induce protein expression at 16 °C for 16 h.

value: Rosetta (DE3)


description: PCR products from SARS-CoV-2_variant_omicron_N_RNA-SELEX_cycle3_rep1


description: PCR products from SARS-CoV-2_variant_gamma_N_RNA-SELEX_cycle3_rep2


title: Sample_217_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: Stimulated, biological rep1

value: anti-CD40 stimulated migratory sdLN WT cDC1


description: PCR products from SARS-CoV-2_variant_delta_N_RNA-SELEX_cycle3_rep3


description: PCR products from SARS-CoV-2_variant_delta_N_RNA-SELEX_cycle3_rep1


description: PCR products from SARS-CoV-2_variant_delta_N_RNA-SELEX_cycle3_rep2


description: PCR products from SARS-CoV-2_variant_gamma_N_RNA-SELEX_cycle3_rep1


title: Unstimulated, biological rep2

source_name: Unstimulated migratory sdLN WT cDC1

value: Unstimulated migratory sdLN WT cDC1


title: Unstimulated, biological rep1


title: Stimulated, biological rep2


title: Unstimulated, biological rep3


title: Sample_216_RORg_MHCII


title: Sample_215_RORg_MHCII


title: E14.5 ureters , Fgfr1/2cDKO vs control, rep4

city: Hannover

first: Mark-Oliver

last: Trowe

address: Carl-Neuberg-Str. 1

department: Molekularbiologie

country: Germany

institute: Medizinische Hochschule Hannover

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2000 ng for M6392-M6393 und 2500ng for M6687-M6688 of each labelled cRNA population were used for hybridization.

scan_protocol: Slides were scanned on the Agilent Micro Array Scanner G2565CA (pixel resolution 3 µm, bit depth 20).

data_processing: Data extraction and processing of raw fluorescence intensity values were performed with the ‘Feature Extraction Software V10.7.3.1’ by using the recommended default extraction protocol file: GE2_107_Sep09.xml.  Measurements of on-chip replicates (quadruplicates) were averaged using the geometric mean of ‘ProcessedSignal’ (PS) values to retrieve one resulting value per unique non-control probe. Single Features were excluded from averaging, if they i) were manually flagged, ii) were identified as Outliers by the Feature Extraction Software, iii) lay outside the interval of ‘1.42 x interquartile range‘ regarding the PS distribution of the respective on-chip replicate population, or, iv) showed a coefficient of variation of pixel intensities per Feature that exceeded 0.5.  For inter-array normalization, averaged processed intensity values, ‘gProcessedSignal’ (gPS) and ‘rProcessedSignal’ (rPS), were further transformed as follows: All PS values (gPS and rPS) of one particular microarray (‘Array i’ in the formula shown below) were multiplied with a microarray-specific scaling factor. This factor was calculated by dividing a ‘reference 75th Percentile value’ (set as 1500 for the whole series) by the 75th Percentile value of the gPS values calculated by the Feature Extraction software for that microarray. Accordingly, normalized PS values for all samples (microarray data sets) were calculated by the following formula:   normalized PSArray i = PSArray i  x (1500 / 75th Percentile gPSArray i)  Finally, a lower intensity threshold (surrogate value) was defined based on intensity distribution of negative control features. This value was fixed to 15. All of those normalized PS values that fell below this intensity border were substituted by the respective surrogate value of 15.

source_name: control 4

label_protocol: 150 ng of total RNA were used as input. Synthesis of Cy3- or Cy5-labeled cRNA was performed in ¾ reaction volumes with the ‘Low Input Quick Amp Labeling Kit, Two Color’ (#5190-2944, Agilent Technologies) according to the manufacturer’s recommendations.

extract_protocol: Extraction of total RNA was performed using peqGOLD RNAPure (VWR Peqlab) according to the manufacturer’s recommendations.

treatment_protocol: Ureters were mechanically dissected from E14.5 embryos.

value: NMRI

tag: Sex

value: female

tag: developmental stage

value: ureter

source_name: Fgfr1/2cDKO 4


description: PCR products from SARS-CoV-2_variant_omicron_N_RNA-SELEX_cycle3_rep3


title: E14.5 ureters , Fgfr1/2cDKO vs control, rep2

source_name: control 2

value: male

source_name: Fgfr1/2cDKO 2


title: E14.5 ureters , Fgfr1/2cDKO vs control, rep1

source_name: control 1

source_name: Fgfr1/2cDKO 1


title: E14.5 ureters , Fgfr1/2cDKO vs control, rep3

source_name: control 3

source_name: Fgfr1/2cDKO 3


title: Sample_214_RORg_MHCII


description: PCR products from SARS-CoV-2_variant_gamma_N_RNA-SELEX_cycle3_rep3


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep12


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep13


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep11


title: Sample_213_RORg_MHCII


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep10


title: Sample_212_RORg_MHCII


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep6


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep7


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep9


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep8


title: Sample_211_RORg_MHCII


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep3


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep2


title: Sample_210_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: Sample_209_RORg_MHCII


title: Sample_208_RORg_MHCII


description: PCR products from SARS-CoV-2_origin_N_RBD2_RNA-SELEX_cycle3_rep3


description: PCR products from SARS-CoV-2_origin_N_RBD2_RNA-SELEX_cycle3_rep1


description: PCR products from SARS-CoV-2_origin_N_RBD1_RNA-SELEX_cycle3_rep2


description: PCR products from SARS-CoV-2_origin_N_RBD2_RNA-SELEX_cycle3_rep2


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep1


title: Sample_207_RORg_MHCII


description: PCR products from SARS-CoV-2_origin_N_RBD1_RNA-SELEX_cycle3_rep3


title: Sample_205_RORg_MHCII


title: SARS-CoV_N_RNA-SELEX_cycle3_rep4

description: PCR products from SARS-CoV_N_RNA-SELEX_cycle3_rep4

value: pET28+SARS-CoV_N vector transfected


description: PCR products from SARS-CoV-2_origin_N_RBD1_RNA-SELEX_cycle3_rep1


title: Sample_206_RORg_MHCII


title: Sample_204_RORg_MHCII


title: SARS-CoV_N_RNA-SELEX_cycle3_rep2

description: PCR products from SARS-CoV_N_RNA-SELEX_cycle3_rep2


title: Sample_203_RORg_MHCII


title: SARS-CoV_N_RNA-SELEX_cycle3_rep3

description: PCR products from SARS-CoV_N_RNA-SELEX_cycle3_rep3


title: SARS-CoV_N_RNA-SELEX_cycle3_rep1

description: PCR products from SARS-CoV_N_RNA-SELEX_cycle3_rep1


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep5


title: MERS-CoV_N_RNA-SELEX_cycle3_rep3

description: PCR products from MERS-CoV_N_RNA-SELEX_cycle3_rep3

value: pET28+MERS-CoV_N vector transfected


title: MERS-CoV_N_RNA-SELEX_cycle3_rep4

description: PCR products from MERS-CoV_N_RNA-SELEX_cycle3_rep4


title: MERS-CoV_N_RNA-SELEX_cycle3_rep1

description: PCR products from MERS-CoV_N_RNA-SELEX_cycle3_rep1


title: MERS-CoV_N_RNA-SELEX_cycle3_rep2

description: PCR products from MERS-CoV_N_RNA-SELEX_cycle3_rep2


title: Sample_202_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


description: PCR products from SARS-CoV-2_origin_N_RNA-SELEX_cycle3_rep4


title: BAT-CoV_N_RNA-SELEX_cycle3_rep4

description: PCR products from BAT-CoV_N_RNA-SELEX_cycle3_rep4

value: pET28+BAT-CoV_N vector transfected


title: Sample_200_RORg_MHCII


title: BAT-CoV_N_RNA-SELEX_cycle3_rep2

description: PCR products from BAT-CoV_N_RNA-SELEX_cycle3_rep2


title: BAT-CoV_N_RNA-SELEX_cycle3_rep1

description: PCR products from BAT-CoV_N_RNA-SELEX_cycle3_rep1


title: NA_PET28_RNA-SELEX_cycle3_rep7

description: PCR products from NA_PET28_RNA-SELEX_cycle3_rep7

value: pET28 empty vector transfected


title: Sample_199_RORg_MHCII

value: mesenteric lymph nodes (MLN)


title: Sample_197_RORg_MHCII

value: three weeks


title: NA_pET28_RNA-SELEX_cycle3_rep5

description: PCR products from NA_pET28_RNA-SELEX_cycle3_rep5


title: Sample_198_RORg_MHCII

value: RORgt+ MHCII+


title: NA_pET28_RNA-SELEX_cycle3_rep4

description: PCR products from NA_pET28_RNA-SELEX_cycle3_rep4


title: NA_pET28_RNA-SELEX_cycle3_rep3

description: PCR products from NA_pET28_RNA-SELEX_cycle3_rep3


title: Sample_196_RORg_MHCII


title: NA_pET28_RNA-SELEX_cycle3_rep1

description: PCR products from NA_pET28_RNA-SELEX_cycle3_rep1


title: RNA-SELEX_cycle0_FSR-2968

description: PCR products from RNA-SELEX_cycle0_FSR-2968

value: no treatment


title: Sample_195_RORg_MHCII


title: Sample_201_RORg_MHCII


title: RNA-SELEX_cycle0_FSR-2967

description: PCR products from RNA-SELEX_cycle0_FSR-2967


title: Sample_194_RORg_MHCII


title: RNA-SELEX_cycle0_FSR-2966

description: PCR products from RNA-SELEX_cycle0_FSR-2966


title: RNA-SELEX_cycle0_FSR-2965

description: PCR products from RNA-SELEX_cycle0_FSR-2965


title: RNA-SELEX_cycle0_FSR-2964

description: PCR products from RNA-SELEX_cycle0_FSR-2964


title: RNA-SELEX_cycle0_FSR-2963

description: PCR products from RNA-SELEX_cycle0_FSR-2963


title: RNA-SELEX_cycle0_FSR-2961

description: PCR products from RNA-SELEX_cycle0_FSR-2961


title: RNA-SELEX_cycle0_FSR-2962

description: PCR products from RNA-SELEX_cycle0_FSR-2962


title: Sample_193_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: RNA-SELEX_cycle0_FSR-2960

description: PCR products from RNA-SELEX_cycle0_FSR-2960


title: BAT-CoV_N_RNA-SELEX_cycle3_rep3

description: PCR products from BAT-CoV_N_RNA-SELEX_cycle3_rep3


title: NA_PET28_RNA-SELEX_cycle3_rep6

description: PCR products from NA_PET28_RNA-SELEX_cycle3_rep6


title: NA_pET28_RNA-SELEX_cycle3_rep2

description: PCR products from NA_pET28_RNA-SELEX_cycle3_rep2


title: RNA-SELEX_cycle0_FSR-2958

description: PCR products from RNA-SELEX_cycle0_FSR-2958


title: Sample_190_RORg_MHCII


title: RNA-SELEX_cycle0_FSR-2957

description: PCR products from RNA-SELEX_cycle0_FSR-2957


title: RNA-SELEX_cycle0_FSR-2956

description: PCR products from RNA-SELEX_cycle0_FSR-2956


title: RNA-SELEX_cycle0_FSR-2955

description: PCR products from RNA-SELEX_cycle0_FSR-2955


title: Sample_189_RORg_MHCII


title: RNA-SELEX_cycle0_FSR-2954

description: PCR products from RNA-SELEX_cycle0_FSR-2954


title: Sample_188_RORg_MHCII


title: RNA-SELEX_cycle0_FSR-2951

description: PCR products from RNA-SELEX_cycle0_FSR-2951


title: RNA-SELEX_cycle0_FSR-2952

description: PCR products from RNA-SELEX_cycle0_FSR-2952


title: Sample_187_RORg_MHCII


title: Sample_192_RORg_MHCII


title: RNA-SELEX_cycle0_FSR-2953

description: PCR products from RNA-SELEX_cycle0_FSR-2953


title: RNA-SELEX_cycle0_FSR-2949

description: PCR products from RNA-SELEX_cycle0_FSR-2949


title: RNA-SELEX_cycle0_FSR-2947

description: PCR products from RNA-SELEX_cycle0_FSR-2947


title: RNA-SELEX_cycle0_FSR-2948

description: PCR products from RNA-SELEX_cycle0_FSR-2948


title: RNA-SELEX_cycle0_FSR-2950

description: PCR products from RNA-SELEX_cycle0_FSR-2950


title: Sample_186_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: RNA-SELEX_cycle0_FSR-2946

description: PCR products from RNA-SELEX_cycle0_FSR-2946


title: RNA-SELEX_cycle0_FSR-2945

description: PCR products from RNA-SELEX_cycle0_FSR-2945


title: Sample_185_RORg_MHCII


title: Sample_184_RORg_MHCII


title: RNA-SELEX_cycle0_FSR-2959

description: PCR products from RNA-SELEX_cycle0_FSR-2959


title: RNA-SELEX_cycle0_FSR-2944

description: PCR products from RNA-SELEX_cycle0_FSR-2944


title: Sample_183_RORg_MHCII


title: Sample_191_RORg_MHCII


title: Sample_182_RORg_MHCII


title: Total_tRNAqPCR_P0_2

city: Berlin

first: Matthew

middle: Lee

last: Kraushar

state: Berlin

address: Ihnestrasse 63-73

department: Department of Computational Molecular Biology

institute: Max Planck Institute for Molecular Genetics

description:
tRNA qRT-PCR
mature tRNA

data_processing: Ct Values for each decoder/gene taken from provided excel sheets. dCt values calculated as the difference between decoder Ct values and the mean of 5S and 18S RNA Ct values.

label: Arraystar SYBR Green

source_name: neocortex

growth_protocol: Neocortex tissue was sub-dissected from embryos and pups from timed pregnant mice, as described in Kraushar et al. Molecular Cell. 81; 2021.

extract_protocol:
Frozen neocortex tissue was lysed in buffer containing detergent by crogenic pulverization (as described, Kraushar et al. Molecular Cell. 81; 2021), followed by lysate clarification with centrifugation, then RNA extraction with TriZOL LS according to the manufacturer's protocol
RT-PCR data was collected performed as per: 10.1038/nmeth.3478

value: neocortex tissue

tag: activation agent

value: Embryonic Day P0


title: Total_tRNAqPCR_P0_1

description:
tRNA qRT-PCR
mature tRNA


title: Sample_181_RORg_MHCII

source_name: Mouse MLN RORgt+ MHCII+


title: Total_tRNAqPCR_E17_2

description:
tRNA qRT-PCR
mature tRNA

value: Embryonic Day E17


title: Total_tRNAqPCR_E15.5_2

description:
tRNA qRT-PCR
mature tRNA

value: Embryonic Day E15.5


title: Sample_180_RORg_MHCII


title: Total_tRNAqPCR_E15.5_1

description:
tRNA qRT-PCR
mature tRNA


title: Total_tRNAqPCR_E14_2

description:
tRNA qRT-PCR
mature tRNA

value: Embryonic Day E14


title: Sample_178_RORg_MHCII


title: Total_tRNAqPCR_E14_1

description:
tRNA qRT-PCR
mature tRNA


title: hemB_wo_Fe_4

city: London

first: David

last: Heinrichs

state: ON

address: Microbiology and Immunology, 3014 Dental Sciences Building, 1151 Richmond Street

country: Canada

institute: University of Western Ontario

data_processing:
Sequencing reads were mapped to the reference S. aureus USA300 FPR3757 genome in Geneious Prime 2020.1.2 (https://www.geneious.com). Expression analysis and comparisons were performed using DESeq2 (Love MI et al Genome Biol 2014).
Genome_build: Staphylococcus aureus USA300_FPR3757
Supplementary_files_format_and_content: xlsx file format, contains RPKM values and calculated differential expression, fold change and p-values for every transcript.
Supplementary_files_format_and_content: The processed data file contains all replicates combined and the calculations of differential expression/fold changes are based on the comparison with the appropriate control group. Each sheet is named after the corresponding comparison.

organism: Staphylococcus aureus subsp. aureus USA300

source_name: Bacteria

growth_protocol: An individual bacterial colony was picked off a plate and grown overnight in tris minimal succinate (TMS) supplemented with 0.4 µM hemin. Cells were sub-cultured to a starting OD600 of 0.01 in iron restricted TMS supplemented with hemin and 1.5 µM transferrin. Cells were grown until mid-log phase at which point cells were treated with 10 µM ferric ammonium sulfate or left untreated for 1 hour before cells were harvested.

extract_protocol:
To extract RNA from frozen S. aureus and hemB S. aureus, cell pellets were washed with TE buffer (pH 8.0) and re-suspended in a Tris-HCl mixture with 1 mg/mL lysostaphin (pH 7.5) to lyse for 1 hour at 37°C. RNA was extracted using an AurumTM Total RNA Mini Kit (BioRAD #7326820).
RNA samples were processed by the Microbial Genome Sequencing Center in Pittsburgh, PA. Ribosomal RNA (rRNA) was depleted (Qiagen FastSelect5S/16S/23S) and cDNA libraries were generated (Qiagen Total Stranded RNA). cDNA libraries were sequenced using NextSeq 550 using a 75bp x 8bp x 8bp setup.

treatment_protocol: Cells were treated with 10 µM ferric ammonium sulfate or left untreated.

tag: bacterial strain

tag: mutation in strain

value: hemB


title: hemB_wo_Fe_6


title: hemB_wo_Fe_2


title: Sample_177_RORg_MHCII

tag: tissue


title: hemB_wo_Fe_3


title: Total_tRNAqPCR_E12.5_1

description:
tRNA qRT-PCR
mature tRNA

value: Embryonic Day E12.5


title: hemB_Fe_6

value: 10 uM ferric ammonium sulfate


title: hemB_wo_Fe_1


title: hemB_Fe_2


title: Sample_175_RORg_MHCII


title: Total_tRNAqPCR_E12.5_2

description:
tRNA qRT-PCR
mature tRNA


title: hemB_Fe_1


title: Sample_176_RORg_MHCII


title: WT_wo_Fe_5


title: Sample_174_RORg_MHCII


title: WT_wo_Fe_1


title: WT_wo_Fe_3


title: Sample_173_RORg_MHCII


title: Sample_172_RORg_MHCII


title: WT_Fe_5


title: WT_Fe_2


title: Total_tRNAqPCR_E17_1

description:
tRNA qRT-PCR
mature tRNA


title: WT_Fe_4


title: Sample_179_RORg_MHCII


title: WT_Fe_1


title: Sample_171_RORg_MHCII


title: Sample_170_RORg_MHCII


title: MDA1_T05_IP

city: Houston

first: Anil

middle: K

last: Sood

state: TX

address: 6767 Bertner Ave

department: genetics

institute: MDACC

description:
10x Genomics
IP = infusion product

library_source: transcriptomic single cell

data_processing: The 10x Genomics Cell Ranger pipeline (v. 3.1.0) was used to demultiplex and generate unique molecular identifier (UMI) matrices for all samples in the MDA1 cohort. UMI matrices for the MDA2 and PUMCH cohorts were also generated from the provided FASTQ files using this version of the CellRanger pipeline. The UMI data were then processed in R (v.3.5.3) using the Seurat package (V.3). Cells with more than 6000 genes, fewer than 200 genes, greater than 20% UMI in mitochondrial genes, or a UMI:gene ratiogreater than 10 or less than 1.3 were filtered. To filter out non   T cells from the data sets, all samples were combined, the top 5000 variable genes were reduced to 50 top principal components and clustered using Seurat's SNN clustering function. Clusters with significant average expression (Wilcoxon test) of CD3 genes (i.e., T cells) were then extracted for further analysis. This gene selection, principal component analysis, and clustering step was performed once more to further remove clusters not expressing CD3 genes.

source_name: surgical sample

growth_protocol: Single cell suspensions are made from fresh normals

extract_protocol:
RNAs are extracted from single cell suspensions
Single cell capture, barcoding and library preparation was performed by following the 10X Genomics Single Cell Chromium 5’ protocol (PN-1000075)

treatment_protocol: samples are collected before treatment

value: fresh tumor

value: surgical sample

value: Not Provided


title: Sample_169_RORg_MHCII


title: Sample_168_RORg_MHCII


title: MDA1_T07_IP

description:
10x Genomics
IP = infusion product


title: MDA1_T03_IP

description:
10x Genomics
IP = infusion product


title: UM-UC3 cells, 1 mM

city: Wuhan

first: Yu

last: Xiao

address: Donghu Road 169

department: Department of Urology

institute: Zhongnan Hospital of Wuhan University

data_processing:
Basecalls performed using CASAVA version 1.8
Adapters and low-quality read ends were removed using Trimmomatic, based on quality control statistics generated by FastQC.
Quality filtered reads were then mapped to GRCh38 using Hisat2
The expression level of each transcript was calculated according to the fragments per kilobase of exon per million mapped reads (FPKM) . StringTie was used to quantify gene and isoform abundances.
R statistical package software EdgeR (Empirical analysis of Digital Gene Expression in R) was utilized for differential expression analysis.
Assembly: GRCh38
Supplementary files format and content: Excel file reports FPKMs for each sample. The "Gene" sheet is the expression profile of all genes. If the average expression of each group is lower than 0.01, it will be filtered out in the "Expression" sheet.

source_name: bladder

growth_protocol: 5637 cells were cultured and maintained in RPMI 1640 medium supplemented with 10% fetal bovine serum, UM-UC3 cells were cultured and maintained in MEM medium supplemented with 10% fetal bovine serum.

extract_protocol:
The RNA was isolated from 5637 and UM-UC3 cells using RNeasy Mini Kit (cat. #74101; Qiagen, Duesseldorf, Germany) followed the manufacturer’s protocol. In each RNA sample, contamination of genomic DNA is removed through DNase I digestion (cat. #79254; Qiagen). The NanoPhotometer (cat. #N60; Implen, Munich, Germany) was used to measure the quantity of each RNA sample.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: Treated with melatonin of annotated concentration or DMSO.

value: bladder

tag: cell line

value: bladder cancer cells

value: WT

value: melatonin, 1 mM


title: MDA1_T04_IP

description:
10x Genomics
IP = infusion product


title: UM-UC3 cells, 2 mM

value: melatonin, 2 mM


title: MDA1_T01_IP

description:
10x Genomics
IP = infusion product


title: Sample_165_RORg_MHCII

value: mesenteric lymph nodes (MLN)

value: three weeks

value: RORgt+ MHCII+


title: 5637 cells, 4 mM

value: melatonin, 4 mM


title: MDA1_T02_IP

description:
10x Genomics
IP = infusion product


title: UM-UC3 cells, 0 mM

value: DMSO


title: E15.5+6d ureter cultures, Fgfr1/2cDKO vs control, rep2

hyb_protocol: cRNA fragmentation, hybridization and washing steps were carried out as recommended in the ‘Two-Color Microarray-Based Gene Expression Analysis Low Input Quick Amp Labeling Protocol V6.7’, except that 2000 ng of labeled cRNA were used for hybridization.

treatment_protocol: Ureters were mechanically dissected from E15.5 embryos and cultured on transwell membranes for 6d.

value: NMRI

value: female

value: ureter


title: Sample_164_RORg_MHCII


title: 5637 cells, 2 mM


title: 5637 cells, 1 mM


title: Sample_162_RORg_MHCII


title: Sample_163_RORg_MHCII


title: HBL1_24h_NGI-1_Replicate 2

city: Bethesda

last: Huang

state: Maryland

address: 9000 Rockville Pike

institute: National Cancer Institute

description: TREATMENT

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped to hg19 human genome using STAR2
Raw read counts per gene were called with Htseq-Count
Assembly: hg19
Supplementary files format and content: Tab-delimited text files of raw count of each gene and each sample

growth_protocol: TMD8 and HBL1 cells were grown in advanced RPMI supplemented with 5% FBS with pen/strep and glutamine.

extract_protocol:
RNA wass extracted using the Qiagen AllPrep Kit.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: The DLBCL cell lines TMD8 and HBL1 were grown at 0.5 x 10^6 cells/ml and either treated in duplicates with vehicle (DMSO), 5 µM NGI-1, 50 nM acalabrutinib or 20 nM copanlisib for 3, 6 and 24 hours. 2 x 10^6 cells were collected for each sample.

value: human DLBCL cell line

value: Cas9 engineered

value: 5 uM NGI-1_24h


title: 5637 cells, 0 mM


title: HBL1_24h_ACAL_Replicate 2

description: TREATMENT

value: 50 nM acalabrutinib_24h


title: HBL1_24h_Copa_Replicate 2

description: TREATMENT

value: 20 nM copanlisib_24h


title: Sample_167_RORg_MHCII


title: UM-UC3 cells, 4 mM

value: bladder

value: bladder cancer cells


title: Sample_166_RORg_MHCII


title: HBL1_24h_DMSO_Replicate 2

description: CTRL


title: Sample_161_RORg_MHCII


title: HBL1_6h_NGI-1_Replicate 2

description: TREATMENT

value: 5 uM NGI-1_6h


title: Sample_160_RORg_MHCII


title: HBL1_6h_ACAL_Replicate 2

description: TREATMENT

value: 50 nM acalabrutinib_6h


title: HBL1_6h_DMSO_Replicate 2

description: CTRL


title: Sample_159_RORg_MHCII

value: mesenteric lymph nodes (MLN)


title: HBL1_3h_ACAL_Replicate 2

description: TREATMENT

value: 50 nM acalabrutinib_3h


title: HBL1_6h_Copa_Replicate 2

description: TREATMENT

value: 20 nM copanlisib_6h


title: E15.5+6d ureter cultures, Fgfr1/2cDKO vs control, rep1

value: male


title: Sample_158_RORg_MHCII

value: three weeks

value: RORgt+ MHCII+


title: Sample_157_RORg_MHCII


title: TMD8_24h_NGI-1_Replicate 2

description: TREATMENT


title: TMD8_24h_Copa_Replicate 2

description: TREATMENT


title: TMD8_24h_DMSO_Replicate 2

description: CTRL


title: HBL1_3h_DMSO_Replicate 2

description: CTRL


title: Sample_156_RORg_MHCII


title: TMD8_24h_ACAL_Replicate 2

description: TREATMENT


title: TMD8_6h_Copa_Replicate 2

description: TREATMENT


title: TMD8_6h_NGI-1_Replicate 2

description: TREATMENT


title: TMD8_6h_ACAL_Replicate 2

description: TREATMENT


title: TMD8_6h_DMSO_Replicate 2

description: CTRL


title: Sample_154_RORg_MHCII


title: Sample_155_RORg_MHCII


title: Sample_153_RORg_MHCII


title: TMD8_3h_Copa_Replicate 2

description: TREATMENT

value: 20 nM copanlisib_3h


title: TMD8_3h_NGI-1_Replicate 2

description: TREATMENT

value: 5 uM NGI-1_3h


title: Sample_152_RORg_MHCII


title: TMD8_3h_ACAL_Replicate 2

description: TREATMENT

value: human DLBCL cell line


title: TMD8_3h_DMSO_Replicate 2

description: CTRL

value: Cas9 engineered


title: HBL1_3h_Copa_Replicate 2

description: TREATMENT


title: HBL1_3h_NGI-1_Replicate 2

description: TREATMENT


title: Sample_150_RORg_MHCII


title: Sample_151_RORg_MHCII


title: HBL1_24h_Copa_Replicate 1

description: TREATMENT


title: HBL1_24h_ACAL_Replicate 1

description: TREATMENT


title: HBL1_6h_NGI-1_Replicate 1

description: TREATMENT


title: HBL1_24h_DMSO_Replicate 1

description: CTRL


title: HBL1_6h_Copa_Replicate 1

description: TREATMENT


title: Sample_148_RORg_MHCII


title: Sample_149_RORg_MHCII


title: HBL1_6h_ACAL_Replicate 1

description: TREATMENT


title: HBL1_6h_DMSO_Replicate 1

description: CTRL


title: Sample_147_RORg_MHCII


title: Sample_146_RORg_MHCII


title: Sample_145_RORg_MHCII


title: HBL1_3h_Copa_Replicate 1

description: TREATMENT


title: HBL1_3h_DMSO_Replicate 1

description: CTRL


title: HBL1_3h_ACAL_Replicate 1

description: TREATMENT


title: Rh30_QC6350-Pax3FOXO1-Rep3_CaR090121_hg19

city: Memphis

first: Hongjian

last: Jin

state: TN

address: 262 Danny Thomas Place

department: Center for Applied Bioinformatics

institute: St Jude Children's Research Hospital

library_source: genomic

data_processing:
Library strategy: CUT&RUN
Fastq files were demultiplexed using illumine local run manager, then trimmed 3’ raw reads with cutadapt (v1.2.1) using Trim_Galore (v0.6.6). Quality trimmed reads were mapped to both hg19 and E. coli K12, MG1655 for normalization purpose by bwa (v0.7.17) and converted to bam file by samtools (v1.9). Uniquely mapped paired reads were extracted by samtools and sorted by biobambam2 (v2.0.87), then bedtools (v 2.17.0) were used to convert bam to bedpe file. Fragments size shorter than 2kb were extracted and center 80bp of each fragment were used to generate bigwig track file by UCSC tools(v4). For pairwise comparisons, E. coli normalization is included to generate bigwig file. Calculated the ratio using E. coli spike-in reads to unique aligned reads for each sample, then count scale factor due to after normalization the E. coli spike-in signal is equal across all samples. MACS2 (v2.1.1) is used to call narrow peaks across all samples.
Assembly: hg19
Supplementary files format and content: bigwig,narrowPeak

molecule: genomic DNA

growth_protocol: RH30 cells were cultured with RPMI 1640 media supplemented with 100 U/mlpenicillin/streptomycin and 10% fetal bovine serum. Cells were maintained at 37 °C in an atmosphere of 5% CO2.

extract_protocol: The CUT&RUN library DNAs of Rh30 with and without QC6352 200 nM treatments were prepared by following the protocol as described previously 6 with minor modifications. Briefly, 200,000 Rh30 cells treated with or without QC6352 were washed 3 times with CUT&RUN washing buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM spermidine (S2501-5G, Sigma-Aldrich), 1× protease inhibitor cocktails (11836170001, Roche) and then transferred to a 1.5-ml tube containing 50 µL washing buffer. Cells were collected with concanavalin A-coated beads (BP531, Bangs laboratories) and incubated with antibodies (1:100), normal rabbit IgG (CS200581, Millipore),  rabbit anti-KDM4B (A301-478A, Bethyl Laboratories) and mouse anti-PAX3-FOXO1 (a gift from Dr. Taosheng Chen) overnight at 4 °C in the antibody incubation buffer (20 mM HEPES at pH 7.5, 150 mM NaCl, 0.5 mM Spermidine, 1× protease inhibitor cocktails, 2 mM EDTA and 0.02% digitonin). The samples with mouse anti-PAX3-FOXO1 antibody were washed 3 times with washing buffer and incubated with rabbit anti-mouse secondary antibody (ab6709, Abcam) overnight at 4 °C. After unbound antibodies were washed away, 140 μg/ml protein A-MNase (pA-MN; a gift from Dr. Steven Henikoff) was added at a 1:280 ratio and incubated for 1 hr at 4 °C. After washing, 3 μl of 100 mM CaCl2 was added to activate pA-MN for 30 min at 4 °C and the reaction was stopped by adding the same volume of 2× STOP buffer (340 mM NaCl, 20 mM EDTA, 4 mM EGTA, 0.05% digitonin, 100 µg/ml RNase A and 50 µg/ml glycogen). The protein–DNA complexes were released by 10-min incubation at 37°C followed by centrifugation at 16,000 g for 5 min at 4 °C. After transferring the supernatant to a new 1.5 ml Eppendorf tube, 2 μl of 10% (wt/vol) SDS and 1.5 μl of proteinase K (20 mg/ml) were added and incubated for 1 hr at 50 °C. DNA was then extracted with phenol/chloroform/isoamylalcohol followed by ethanol precipitation with glycogen and then dissolved in water. Sequencing libraries were prepared using an Accel-NGS 1S plus DNA library preparation kit (10096, Swift Biosciences) and Accel-NGS 1S plus combinatorial Dual Indexing Kit (18096, Swift Biosciences) for Illumina platforms following the manufacturer's instructions. The PCR products were cleaned with SPRIselect beads and quantified using Qubit dsDNA HS assay kit (Q32854, Thermo fisher). The libraries were sequenced on a HiSeq2500 with paired-end 50-bp reads (Illumina).

tag: chip antibody


title: Rh30_QC6350-Pax3FOXO1-Rep2_CaR090121_hg19

tag: treatment

value: PAX3-FOXO1 (a gift from Dr. Taosheng Chen)


title: TMD8_24h_NGI-1_Replicate 1

description: TREATMENT

value: 5 uM NGI-1_24h


title: Rh30_QC6350-Pax3FOXO1-Rep1_CaR090121_hg19


title: HBL1_24h_NGI-1_Replicate 1

description: TREATMENT


title: TMD8_24h_Copa_Replicate 1

description: TREATMENT

value: 20 nM copanlisib_24h


title: Sample_144_RORg_MHCII


title: Rh30_QC6350-KDM4B-Rep3_CaR090121_hg19

value: KDM4B (Invitrogen, 712791)


title: TMD8_6h_Copa_Replicate 1

description: TREATMENT


title: TMD8_24h_ACAL_Replicate 1

description: TREATMENT

value: 50 nM acalabrutinib_24h


title: Sample_142_RORg_MHCII


title: TMD8_24h_DMSO_Replicate 1

description: CTRL


title: HBL1_3h_NGI-1_Replicate 1

description: TREATMENT


title: Rh30_DMSO-Pax3FOXO1-Rep3_CaR090121_hg19

value: DMSO


title: Rh30_QC6350-KDM4B-Rep2_CaR090121_hg19


title: Rh30_QC6350-KDM4B-Rep1_CaR090121_hg19


title: Sample_143_RORg_MHCII


title: TMD8_6h_DMSO_Replicate 1

description: CTRL


title: TMD8_6h_ACAL_Replicate 1

description: TREATMENT

value: 50 nM acalabrutinib_6h


title: TMD8_3h_Copa_Replicate 1

description: TREATMENT


title: Sample_140_RORg_MHCII

value: mesenteric lymph nodes (MLN)


title: Rh30_DMSO-Pax3FOXO1-Rep2_CaR090121_hg19


title: TMD8_3h_ACAL_Replicate 1

description: TREATMENT

value: 50 nM acalabrutinib_3h


title: Sample_139_RORg_MHCII


title: Sample_138_RORg_MHCII


title: Rh30_DMSO-Pax3FOXO1-Rep1_CaR090121_hg19


title: TMD8_6h_NGI-1_Replicate 1

description: TREATMENT

value: 5 uM NGI-1_6h


title: Sample_137_RORg_MHCII


title: Rh30_DMSO-KDM4B-Rep2_CaR090121_hg19


title: MDA1_T04

description: 10x Genomics

source_name: fresh tumor

value: fresh tumor

tag: tissue source

value: surgical sample

value: Not Provided


title: Rh30_DMSO-KDM4B-Rep3_CaR090121_hg19


title: MDA1_T03

description: 10x Genomics


title: MDA1_T06

description: 10x Genomics


title: MDA1_T07

description: 10x Genomics


title: TMD8_3h_DMSO_Replicate 1

description: CTRL


title: Sample_141_RORg_MHCII

value: three weeks

value: RORgt+ MHCII+


title: TMD8_3h_NGI-1_Replicate 1

description: TREATMENT

value: human DLBCL cell line

value: 5 uM NGI-1_3h


title: MDA1_T02

description: 10x Genomics


title: MDA1_T05

description: 10x Genomics


title: Sample_135_RORg_MHCII


title: MDA1_U05

description: 10x Genomics


title: MDA2_U09

description: 10x Genomics


title: MDA1_T01

description: 10x Genomics


title: Sample_134_RORg_MHCII


title: MDA2_T10

description: 10x Genomics


title: Sample_133_RORg_MHCII


title: MDA2_T14

description: 10x Genomics


title: Sample_136_RORg_MHCII


title: MDA2_T15

description: 10x Genomics


title: MDA2_U02

description: 10x Genomics


title: Rh30_QC6350-IgG-Rep2_CaR090121_hg19

value: IgG (Epicypher 13-0042)


title: Rh30_DMSO-KDM4B-Rep1_CaR090121_hg19


title: Rh30_QC6350-IgG-Rep3_CaR090121_hg19


title: Rh30_QC6350-IgG-Rep1_CaR090121_hg19


title: Rh30_DMSO-IgG-Rep3_CaR090121_hg19


title: MDA2_T01

description: 10x Genomics


title: MDA2_T02

description: 10x Genomics


title: Sample_132_RORg_MHCII


title: MDA2_U08

description: 10x Genomics


title: Rh30_DMSO-IgG-Rep2_CaR090121_hg19


title: Sample_131_RORg_MHCII


title: MDA2_T09

description: 10x Genomics


title: Ataxia Telangiectasia sample-6

city: New Haven

first: Takehiro

last: Takahashi

state: Connecticut

address: 300 Cedar Street TAC S630

institute: Yale University

description:
AT_6
Human_Ataxia_normalized_counts.xlsx

data_processing:
Sequencing raw data were aligned using STAR (STAR/2.5.3a-foss-2016b) with hg38 for human samples (Dobin et al., 2013) with parameters: --runThreadN 20 --outSAMtype BAM SortedByCoordinate --limitBAMsortRAM 35129075129 --outFilterMultimapNmax 1 --outFilterMismatchNmax 999 --outFilterMismatchNoverLmax 0.02 --alignIntronMin 20 --alignIntronMax 1000000 --alignMatesGapMax 1000000 for mapping cellular genes.
For endogenous retroelements, ERVMAP (Tokuyama et al., 2018; Treger et al., 2019) and RepEnrich2 (Criscione et al., 2014) were used using modules, Python/2.7.13-foss-2016b, Bowtie2/2.2.9-foss-2016b, BEDTools/2.27.1-foss-2016b and SAMtools/1.9-foss-2016b using repeatmasker h38 assembly.
Counts were counted using BEDTools (BEDTools/2.27.1-foss-2016b) (Quinlan and Hall, 2010), coverageBed function, and normalized using DESeq2 (Love et al., 2014).
Genome_build: hg38 (GRCh38)
Supplementary_files_format_and_content: Human_Ataxia_normalized_counts.xlsx: Matrix table of normalized counts for cellular genes, uniquely mappable endogenous retrovirus (ERVs), and endogenous retroelements from Repenrich.

source_name: Human cerebellar vermis

extract_protocol:
Total RNA was extracted from the frozen postmortem human cerebellar vermis using RNeasy Fibrous Tissue Kit (Qiagen).
Library was constructed using NEBNext rRNA Depletion Kit (NEB E6310).

value: Cerebellar vermis

value: Female

tag: diagnosis

value: Ataxia Telangiectasia


title: Sample_130_RORg_MHCII


title: Sample_129_RORg_MHCII


title: Rh30_DMSO-IgG-Rep1_CaR090121_hg19


title: MDA2_T08

description: 10x Genomics


title: MDA2_T06

description: 10x Genomics


title: MDA2_T07

description: 10x Genomics


title: Ataxia Telangiectasia sample-4

description:
AT_4
Human_Ataxia_normalized_counts.xlsx

value: Male


title: Sample_128_RORg_MHCII


title: Sample_127_RORg_MHCII


title: MDA2_T24

description: 10x Genomics


title: MDA2_T22

description: 10x Genomics


title: MDA2_T04

description: 10x Genomics


title: MDA2_T23

description: 10x Genomics


title: MDA2_T03

description: 10x Genomics


title: Ataxia Telangiectasia sample-5

description:
AT_5
Human_Ataxia_normalized_counts.xlsx


title: MDA2_T05

description: 10x Genomics


title: Sample_126_RORg_MHCII


title: MDA2_T25

description: 10x Genomics


title: Ataxia Telangiectasia sample-2

description:
AT_2
Human_Ataxia_normalized_counts.xlsx


title: Sample_124_RORg_MHCII


title: MDA2_T26

description: 10x Genomics


title: Sample_125_RORg_MHCII


title: MDA2_U11

description: 10x Genomics


title: MDA2_T11

description: 10x Genomics


title: MDA2_U05

description: 10x Genomics


title: Ataxia Telangiectasia sample-1

description:
AT_1
Human_Ataxia_normalized_counts.xlsx


title: Sample_123_RORg_MHCII


title: Control subject sample-5

description:
Ctrl_5
Human_Ataxia_normalized_counts.xlsx

value: Control


title: MDA2_T13

description: 10x Genomics


title: MDA2_U24

description: 10x Genomics


title: MDA2_U15

description: 10x Genomics


title: Control subject sample-4

description:
Ctrl_4
Human_Ataxia_normalized_counts.xlsx


title: Ataxia Telangiectasia sample-3

description:
AT_3
Human_Ataxia_normalized_counts.xlsx


title: MDA2_T17

description: 10x Genomics


title: MDA2_U17

description: 10x Genomics


title: Sample_121_RORg_MHCII


title: MDA2_T18A

description: 10x Genomics


title: Control subject sample-3

description:
Ctrl_3
Human_Ataxia_normalized_counts.xlsx


title: MDA2_T18B

description: 10x Genomics


title: Sample_120_RORg_MHCII


title: Control subject sample-6

description:
Ctrl_6
Human_Ataxia_normalized_counts.xlsx


title: Sample_119_RORg_MHCII


title: Sample_117_RORg_MHCII


title: MDA2_T20

description: 10x Genomics


title: Sample_118_RORg_MHCII


title: MDA2_U18

description: 10x Genomics


title: MDA2_U12

description: 10x Genomics


title: Control subject sample-1

description:
Ctrl_1
Human_Ataxia_normalized_counts.xlsx


title: MDA2_T19

description: 10x Genomics


title: Input_Runx2-FLAG_Ob_1

city: Bunkyo-ku

first: Hironori

last: Hojo

state: Tokyo

address: 7-3-1 Hongo

department: Center for Disease Biology and Integrative Medicine

country: Japan

institute: The University of Tokyo

data_processing:
DNA-sequence information was aligned to the unmasked mouse genome by bowtie
Peak calling was performed by two-sample analysis on CisGenome software (Ji et al., 2008) with a P-value cutoff of 10-5 comparing with the negative control
In the analysis with ATAC_Col2, ATAC_Col10 and ATAC_Sp7 data sets, to identify the cell-type specific and shared regions, we selected ATAC-seq peaks with the ATAC-seq normalized peak intensity based on the following criteria: raw fe > 30, fold change > 5, and p-value < 0.05, for cell-type specific regions. The differential accessible regions were called as below. C2: C2-Cho-distinct peaks; C10: C10-Cho-distinct peaks; S7: S7-Ob-distinct peaks; C2C10: peaks with high intensity in both C2-Cho and C10-Cho but not in S7-Ob; C10S7: peaks with high intensity in both C10-Cho and S7-Ob but not in C2-Cho; C2S7: peaks with high intensity in both C2-Cho and S7-Ob but not in C10-Cho. These peaks were listed in "ATAC_C2_C10_Sp7_peaks.xlsx”
In the analysis with ATAC_POB_Runx2_cHetKO and ATAC_POB_Runx2_cHomKO data sets, to identify the differential binding regions between the genotypes, DiffBind was applied with the following parameters "summits = 150" in the step of "dba.count" to resize peaks. To obtain statistically different chromatin-accessible regions, we selected the peaks based on FDR < 0.05. The differential accessible regions were listed in “ATAC_Runx2KO_peaks. xlsx”
In the analysis with ATAC_3T3cells data sets, to identify Runx2-responsive and osteoblast induction-responsive regions, DiffBind was applied with the following parameters "summits = 250" in the step of "dba.count" to resize peaks. Pairwise comparison was performed among ATAC-seq profiles of day 0 GFP expression samples, day 0 Runx2 expression samples, day 3 GFP expression samples, day 3 Runx2 expression samples, and no expression samples (None). The Runx2-responsive and the osteoblast induction-responsive regions were selected as ATAC-seq peaks whose intensity was statistically upregulated by both Runx2 expression and osteogenic induction on day 3, based on the following criteria: FDR < 0.05, fold change > 4. The Runx2-responsive regions were listed in “ATAC_3T3_Runx2_responsive_regions.xlsx”.
Genome_build: mm9
Supplementary_files_format_and_content: peak files

source_name: P1 calvaria osteoblasts

extract_protocol:
Rib chondrocytes were manually dissected from the neonatal mouse ribs. The ribs were initially digested in 2 mg/mL Pronase (53702, EMD Millipore Corporation) for 30 min at 37 °C, washed three times with phosphate buffered saline (PBS), and then digested in 0.2% collagenase D (1088858, Roche Applied Science) for 3 h at 37 °C. Calvarial osteoblasts were manually dissected from osteoblast-enriched partial calvarias consisting of the frontal bone and a rostral part of the parietal bone. The partial calvarias were digested in five changes of 0.1% collagenase D and 0.2% dispase for 10 min each at 37 °C.   Cultured 3T3 cells were digested in trypsin-EDTA solution 1X (Wako, 206-17291) for 5 to 15 min at  37 °C.
ChIP-seq libraries were constructed using a ThruPLEX®-FD Prep Kit (R40012, Rubicon Genomics) according to the manufacturer′s instructions. ATAC-seq libraries were constructed as previously described (Buenrostro et al., 2013).

treatment_protocol: For in vitro cell culture, osteogenic medium contains 10% FBS/DMEM supplemented with 50 μg/ml ascorbic acid phosphate, 10 mM β-glycerophosphate, and 100 ng/ml rhBMP‑2

value: Calvarial osteoblasts at P1

value: Runx2-BioFL/+ knock-in


title: MDA2_T21

description: 10x Genomics


title: Sample_122_RORg_MHCII

value: mesenteric lymph nodes (MLN)


title: 12Z_shARID1A_Input

city: Grand Rapids

first: Ronald

middle: L.

last: Chandler

state: MI

department: Obstetrics, Gynecology and Reproductive Biology

institute: Michigan State University

description: Eluted ChIP-seq input chromatin DNA from shARID1A lentiviral particle treated 12Z human endometriotic epithelial cells.

data_processing:
Raw reads for IPs and inputs were trimmed with cutadapt (Martin 2011) and Trim Galore! (http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/) followed by quality control analysis via FastQC (Andrews 2010) and MultiQC (Ewels, Magnusson et al. 2016).
Trimmed reads were aligned to GRCh38.p12 reference genome (Schneider, Graves-Lindsay et al. 2017) via Bowtie2 (Langmead and Salzberg 2012) with flag `--very-sensitive`. Aligned reads were sorted and indexed with samtools (Li, Handsaker et al. 2009).
Molecular complexity was estimated from duplicate rates by ATACseqQC (Ou, Liu et al. 2018) and preseqR (Daley and Smith 2013), and libraries were subsampled to equivalent molecular complexity within an experimental design based on these estimates with samtools.
Picard MarkDuplicates (http://broadinstitute.github.io/picard/) was used to remove PCR duplicates, followed by sorting and indexing.
For CHD4 binding analysis, MACS2 (Zhang, Liu et al. 2008) was used to call broad peaks on each ChIP replicate against the input chromatin control with FDR < 0.05 threshold. No peak calling was performed for H3.1/3.2 analysis.
The resulting CHD4 peaks were repeat-masked by ENCODE blacklist filtering and filtered for non-standard contigs (Amemiya, Kundaje et al. 2019).
A naive overlapping CHD4 peak set, as defined by ENCODE (Landt, Marinov et al. 2012), was constructed by calling peaks on pooled replicates followed by bedtools intersect (Quinlan and Hall 2010) to select for peaks of at least 50% overlap with each biological replicate.
ChIP-seq differential histone abundance analysis was performed with csaw (Lun and Smyth 2016). First, a consensus CHD4 peak set was constructed for each differential experiment from the union of replicate-intersecting, filtered MACS2 peak regions called in each condition. For H3.1/3.2, the shARID1A vs.c ontrol consensus H3.3 peak set was used (GSE190551). ChIP reads were counted in these query regions by csaw, then filtered for low abundance peaks with average log2CPM > -3. When comparing ChIP libraries, any global differences in IP efficiency observed between the two conditions were considered a result of technical bias to ensure a highly conservative analysis. As such, we employed a loess-based local normalization to the peak count matrix, as is implemented in csaw (Lun and Smyth 2016), to assume a symmetrical MA distribution. A design matrix was then constructed from one ‘condition’ variable, without an intercept term. The count matrix and loess offsets were then supplied to edgeR (Robinson, McCarthy et al. 2010) for estimating dispersions and fitting quasi-likelihood generalized linear models for differential abundance hypothesis testing. Nearby query regions were then merged up to 500 bp apart for a maximum merged region width of 5 kb, and the most significant probability was used to represent the merged region. Finally, FDR < 0.05 threshold was used to define significant differentially abundant regions.
Assembly: GRCh38.p12
Supplementary files format and content: Tabular blacklist-filtered broadPeak files reported by MACS2 corresponding to sites of significant CHD4 binding in 12Z cells from either or both ChIP replicates per condition. Tabular csaw results tables from differential CHD4 binding, and H3.1/3.2 abundance at H3.3-marked sites, for shARID1A vs. control conditions, across all tested genome-wide regions per assay.

source_name: 12Z endometriotic epithelial cells

growth_protocol: Human 12Z endometriotic epithelial cells were cultured in growth media (10% FBS, 1% L-glutamine, 1% Penicillin-Streptomycin).

extract_protocol:
Cells were treated with 1% formaldehyde in growth media for 10 minutes at ambient temperature. Formaldehyde was quenched by the addition of 0.125 M Glycine and incubation for 5 minutes at room temperature, followed by PBS wash and scraping. 1*10^7 crosslinked cells were used for each ChIP, and ChIP was performed in duplicate. Chromatin from crosslinked cells was fractionated by digestion with micrococcal nuclease using the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) according to the manufacturer protocol, followed by 30 seconds of sonication. ChIP was then performed according to the SimpleChIP Enzymatic Chromatin IP Kit (Cell Signaling) with the addition of 5 mM sodium butyrate to preserve histone acetylation. 1:250 anti-histone H2A.Z (ab4174, abcam) or 1:50 anti-acetyl-histone H4 (06-866, Millipore) was added to each, respective 1.25 mL IP. Crosslinks were reversed with 0.4 mg/mL Proteinase K (ThermoFisher) and 0.2 M NaCl at 65 °C for 2 hours. DNA was purified using the ChIP DNA Clean & Concentrator Kit (Zymo).
Libraries for input and IP samples were prepared by the Van Andel Research Institute Genomics Core. 10 ng of material was used for input samples, and the entire precipitated sample was used for IPs. Libraries were generated using the KAPA Hyper Prep Kit (v5.16) (Kapa Biosystems). Prior to PCR amplification, end-repaired and A-tailed DNA fragments were ligated to IDT for Illumina UDI Adapters (IDT DNA Inc.). Quality and quantity of the finished libraries were assessed using a combination of Agilent DNA High Sensitivity chip (Agilent Technologies), QuantiFluor® dsDNA System (Promega) and Kapa Illumina Library Quantification qPCR assays (Kapa Biosystems). Individually indexed libraries were pooled, and 100 bp, single-end sequencing was performed on an Illumina NovaSeq 6000 sequencer using a 100-cycle sequencing kit (Illumina). Each library was sequenced to minimum read depth of 80 million reads per input library and 40 million reads per IP library. Base calling was performed by Illumina NCS v2.0, and NCS output was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.9.0.

treatment_protocol: Lentiviral shRNA particles were transduced into 12Z cells at a 100-fold multiplicity of infection, and media was replaced 24 hours later. Cells were harvested 72 hours following shRNA transduction.

tag: treatment/condition

value: shARID1A (lentiviral ARID1A shRNA particles)


title: ChIP-seq_Runx2-FLAG_Ob_rep1


title: 12Z_shARID1A_H3.1_rep1_ChIP

description: Eluted H3.1/3.2 ChIP DNA (replicate #1) from shARID1A lentiviral particle treated 12Z human endometriotic epithelial cells.

tag: antibody

value: anti-histone H3.1/3.2 (61629, Active Motif)


title: 12Z_shARID1A_H3.1_rep2_ChIP

description: Eluted H3.1/3.2 ChIP DNA (replicate #2) from shARID1A lentiviral particle treated 12Z human endometriotic epithelial cells.


title: Sample_116_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol

tag: age


title: Input_Runx2-FLAG_Cho_1

source_name: P1 rib chondrocytes

tag: cell type

value: Rib chondrocytes at P1


title: MDA2_T16

description: 10x Genomics

value: fresh tumor

value: surgical sample

value: Not Provided


title: 12Z_shARID1A_CHD4_rep1_ChIP

description: Eluted CHD4 ChIP DNA (replicate #1) from shARID1A lentiviral particle treated 12Z human endometriotic epithelial cells.

value: anti-CHD4 (D4B7, Cell Signaling)


title: Sample_115_RORg_MHCII

value: three weeks

value: RORgt+ MHCII+


title: ChIP-seq_Runx2-FLAG_Cho_rep1

tag: strain


title: 12Z_shARID1A_CHD4_rep2_ChIP

description: Eluted CHD4 ChIP DNA (replicate #2) from shARID1A lentiviral particle treated 12Z human endometriotic epithelial cells.


title: Control subject sample-2

description:
Ctrl_2
Human_Ataxia_normalized_counts.xlsx

value: Cerebellar vermis


title: Sample_114_RORg_MHCII


title: 12Z_Control_Input

description: Eluted ChIP-seq input chromatin DNA from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

value: Control (non-targeting shRNA treated)


title: 12Z_Control_H3.1_rep2_ChIP

description: Eluted H3.1/3.2 ChIP DNA (replicate #2) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.


title: 12Z_Control_CHD4_rep2_ChIP

description: Eluted CHD4 ChIP DNA (replicate #2) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.


title: THP-1 EMPTY rep10

city: Montréal

first: John

middle: D

last: Rioux

state: QC

address: 5000 Bélanger St.

department: Research Center

institute: Montreal Heart Institute

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 10

data_processing:
Illumina HiSeq2000 using HiSeq Control Software
Primary QC analysis was performed using FastQC (v0.11.5; https://www.bioinformatics.babraham.ac.uk/projects/fastqc)
Sequence filtering parameters set by Trimmomatic (v.0.36 ) Primer sequences were filtered out with provided TruSeq sequence data and a quality sliding window of Q over 20 for a 40-nucleotide window; only sequences longer than 70 nucleotides were kept in the filtered FASTQ files. Another FastQC run was performed on all filtered FASTQ files to validate Trimmomatic results.
Filtered FASTQ files were aligned to the human genome with STAR (v. 2.5.3a) using indexes built with STAR from H. sapiens GRCh Build 38 files (reference genome and GTF annotation files) provided by Illumina's iGenome repository.
Default values were selected except for the –quantMode flag that was set to TranscriptomeSAM for downstream quantification. Counts per gene for each sequenced sample were obtained using RSEM (v. 1.2.6)
Gene counts were transformed to FPKM as an approximation of gene relative abundance. Genes were filtered to keep only those with FPKM > 0.3 and count>8 in at least two samples.
Small RNAs and LOC genes without annotations were removed. Quality control of samples was performed, excluding strong outlier samples based on principal component analyses
The log-transformed FPKM were then normalized between samples with cyclicloess (normalizeCyclicloess from sva Bioconductor R package).
RNA-seq and cell culture batches effects were removed using ComBat (sva Bioconductor library v3.18.0).
Genome_build: GRCh 38
Supplementary_files_format_and_content: THP1_overexpression_processed_20210506.txt; tab delimited text file; normalized FPKM table

source_name: THP-1 cells

growth_protocol: THP-1 were maintained at 37°C with 5% atmospheric CO2 in RPMI 1600 supplemented with 10% FBS fetal bovine serum, 1% penicillin/streptomycin (Thermo Fisher Scientific)  and 0.05 mM beta-mercaptoethanol  (Invitrogen). THP-1 were grown for an average of 7 days (with a range of 4-16 days) to select successfully transduced cells and reach 1x106 cells/ml (3-5 x106 cells in total) before RNA extraction.

extract_protocol:
Total RNA was extracted from stably transduced THP-1 cultures using the RNeasy Plus Mini kit (Qiagen) according to manufacturer’s protocol. The RNA samples were quantified, and quality controlled using an Agilent RNA 6000 Nano kit (Agilent) on an Agilent Bioanalyzer 2100 system. Samples with RNA Integrity Number (RIN) below 8 were discarded.
RNA samples were transformed into barcoded DNA libraries using TruSeq Stranded mRNA library preparation kits (Illumina), which were then paired-end sequenced, generating 2x100bp reads, using an Illumina HiSeq2000 sequencer

treatment_protocol: THP-1 cells were transduced in triplicate via spinoculation by open reading frames (ORFs) for 42 genes cloned into a modified GATEWAY® compatible polycistronic lentiviral expression vector, pLVX-EF1a-IRES-PURO/eGFP

value: Monocytic leukemia

tag: overexpressed gene

value: EMPTY plasmid

tag: sampleID

tag: plasmid

tag: infection date

tag: days in culture

tag: sequencing batch

value: B


title: Sample_112_RORg_MHCII

tag: tissue


title: non-senescent HDFs, Nintedanib for 13 days, bio rep 3

city: Daegu

first: Young-Sam

last: Lee

address: 333 Technojungang-Daero, Hyeonpung-Eup, Dalsung-Gun

department: Department of New Biology

country: South Korea

institute: DGIST

description:
with-for 10d-1
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 13 days.

data_processing:
The adaptor sequences were trimmed by the trimmomatic (v0.38) and then aligned to the reference human genome (hg38) using the HISAT2 aligner(ver 2.1.0).
The align data were quantified to the gene features (NCBI_109.20200522) in gene count using StringTie (ver 2.1.3b).
Assembly: GRCh38 (hg38)
Supplementary files format and content: Excel files include FPKM values, TPM values, and read counts.

source_name: HDF

growth_protocol: Human dermal fibroblasts (HDFs) were cultured in growth medium composed of DMEM supplemented with 10% FBS and 100 units/mL penicillin, 10 μg/mL streptomycin, and 25 ng/mL amphotericin B. Cells were maintained at 37 °C in 5% CO2 and routinely split at ratios of 1:4 during early passages (up to passage 15) or 1:2 during late passages (passages 50-51).

extract_protocol:
Total RNA was extracted from HDFs using the QIAzol Lysis Reagent on ice, following the manufacturer’s protocol. RNA purity and concentration were determined using NanoDrop One spectrophotometer. Integrity of RNA was also confirmed by gel electrophoresis and BioAnalyzer before RNA-Seq.
Isolated RNA was fragmented using TruSeq Stranded mRNA LT Sample Prep Kit according to the manufacturer’s protocol, and libraries for sequencing were then generated based on NovaSeq 6000 S4 Reagent Kit and the protocols in Microgen Inc. (Seoul, South Korea). The libraries were sequenced using NovaSeq 6000 system.

treatment_protocol: 1. Drug treatment for 1 day on HDFs; 2. Nintedanib (5 micromolar) treatment for 3 days on HDFs; 3. Change to complete growth media when 3 days after nintedanib treatment and culture for 10 days after withdrawal (wd) of the drug; and 4. Nintedanib (5 micromolar) treatment for 13 days on HDFs (with, w).

tag: cell line

value: HDF

value: Human dermal fibroblast, passage 10 (non-senescent)

tag: genotype

value: WT

value: 5 micromolar of Nintedanib for 13 days


title: Sample_113_RORg_MHCII

value: mesenteric lymph nodes (MLN)


title: THP-1 EMPTY rep11

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 11


title: 12Z_Control_CHD4_rep1_ChIP

description: Eluted CHD4 ChIP DNA (replicate #1) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.


title: non-senescent HDFs, Nintedanib for 3 days then 10 day after withdrawal of the drug, bio rep 3

description:
wd-for 10d-3
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 3 days, then withdrawal of the drug for 10 days.

tag: treatment

value: 5 micromolar of Nintedanib for 3 days, then withdrawal


title: THP-1 EMPTY rep9

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 9


title: non-senescent HDFs, Nintedanib for 3 days, bio rep 2

description:
Nin-for 3d-3
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 3 days.

value: 5 micromolar of Nintedanib for 3 days


title: Sample_111_RORg_MHCII


title: THP-1 EMPTY rep8

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 8


title: Sample_110_RORg_MHCII


title: THP-1 EMPTY rep6

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 6


title: THP-1 EMPTY rep7

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 7


title: non-senescent HDFs, control (DMSO for 3 days), bio rep 2

description:
con3
Gene expression in non-senescent HDFs treated with DMSO for 3 days.

value: DMSO for 3 days


title: non-senescent HDFs, Nintedanib for 3 days then 10 day after withdrawal of the drug, bio rep 2

description:
wd-for 10d-2
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 3 days, then withdrawal of the drug for 10 days.


title: non-senescent HDFs, Nintedanib for 13 days, bio rep 2

description:
with-for 10d-2
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 13 days.


title: 12Z_Control_H3.1_rep1_ChIP

description: Eluted H3.1/3.2 ChIP DNA (replicate #1) from non-targeting shRNA lentiviral particle treated (control) 12Z human endometriotic epithelial cells.

value: anti-histone H3.1/3.2 (61629, Active Motif)


title: Sample_109_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: non-senescent HDFs, sunitinib, bio rep 3

description:
HDFy-suni3
Gene expression in non-senescent HDFs treated with sunitinib (10 micromolar) for 1 day.

value: 10 micromolar of Sunitinib


title: non-senescent HDFs, Nintedanib for 3 days, bio rep 1

description:
Nin-for 3d-2
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 3 days.


title: non-senescent HDFs, MP470, bio rep 3

description:
HDFy-MP470-3
Gene expression in non-senescent HDFs treated with MP470 (20 micromolar) for 1 day.

value: 20 micromolar of MP470


title: Sample_107_RORg_MHCII

value: three weeks

value: RORgt+ MHCII+


title: non-senescent HDFs, Nintedanib for 13 days, bio rep 1

description:
with-for 10d-1
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 13 days.


title: non-senescent HDFs, control (DMSO for 3 days), bio rep 1

description:
con2
Gene expression in non-senescent HDFs treated with DMSO for 3 days.


title: THP-1 EMPTY rep4

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 4


title: THP-1 EMPTY rep5

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 5


title: Sample_108_RORg_MHCII


title: Sample_106_RORg_MHCII


title: Sample_105_RORg_MHCII


title: THP-1 EMPTY rep2

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 2


title: Sample_104_RORg_MHCII


title: non-senescent HDFs, Nintedanib, bio rep 3

description:
HDFy-Nin3
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 1 day.

value: 5 micromolar of Nintedanib


title: senescent HDFs, sunitinib, bio rep 3

description:
HDFO-suni3
Gene expression in senescent HDFs treated with sunitinib (10 micromolar) for 1 day.

value: Human dermal fibroblast, passage 50 (senescent)


title: senescent HDFs, MP470, bio rep 3

description:
HDFO-MP470-3
Gene expression in senescent HDFs treated with MP470 (20 micromolar) for 1 day.


title: senescent HDFs, ABT263, bio rep 3

description:
HDFO-ABT3
Gene expression in senescent HDFs treated with ABT263 (5 micromolar) for 1 day.

value: 5 micromolar of ABT263


title: Sample_103_RORg_MHCII


title: senescent HDFs, Nintedanib, bio rep 3

description:
HDFO-Nin3
Gene expression in senescent HDFs treated with Nintedanib (5 micromolar) for 1 day.


title: non-senescent HDFs, Nintedanib for 3 days then 10 day after withdrawal of the drug, bio rep 1

description:
wd-for 10d-1
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 3 days, then withdrawal of the drug for 10 days.


title: THP-1 ORF THADA rep3

description: THP-1 stable cell line overexpressing THADA gene / replicate 3

value: Monocytic leukemia

value: THADA

value: A


title: non-senescent HDFs, sunitinib, bio rep 2

description:
HDFy-suni2
Gene expression in non-senescent HDFs treated with sunitinib (10 micromolar) for 1 day.

value: HDF

value: Human dermal fibroblast, passage 10 (non-senescent)

value: WT


title: THP-1 ORF THADA rep2

description: THP-1 stable cell line overexpressing THADA gene / replicate 2


title: senescent HDFs, control, bio rep 3

description:
HDFO-con3
Gene expression in senescent HDFs treated with DMSO for 1 day.

value: DMSO


title: Sample_101_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol

value: mesenteric lymph nodes (MLN)


title: non-senescent HDFs, ABT263, bio rep 2

description:
HDFy-ABT2
Gene expression in non-senescent HDFs treated with ABT263 (5 micromolar) for 1 day.


title: non-senescent HDFs, MP470, bio rep 2

description:
HDFy-MP4702
Gene expression in non-senescent HDFs treated with MP470 (20 micromolar) for 1 day.


title: Sample_102_RORg_MHCII


title: THP-1 ORF THADA rep1

description: THP-1 stable cell line overexpressing THADA gene / replicate 1


title: non-senescent HDFs, ABT263, bio rep 3

description:
HDFy-ABT3
Gene expression in non-senescent HDFs treated with ABT263 (5 micromolar) for 1 day.


title: Sample_100_RORg_MHCII


title: non-senescent HDFs, control, bio rep 3

description:
HDFy-con3
Gene expression in non-senescent HDFs treated with DMSO for 1 day.


title: non-senescent HDFs, Nintedanib, bio rep 2

description:
HDFy-Nin2
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 1 day.


title: non-senescent HDFs, control, bio rep 2

description:
HDFy-con2
Gene expression in non-senescent HDFs treated with DMSO for 1 day.


title: THP-1 EMPTY rep3

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 3

value: EMPTY plasmid

value: B


title: THP-1 EMPTY rep1

description: THP-1 stable cell line transduced bt an EMPTY gene / replicate 1


title: Sample_98_RORg_MHCII


title: Sample_99_RORg_MHCII


title: senescent HDFs, MP470, bio rep 2

description:
HDFO-MP470-2
Gene expression in senescent HDFs treated with MP470 (20 micromolar) for 1 day.


title: senescent HDFs, ABT263, bio rep 2

description:
HDFO-ABT2
Gene expression in senescent HDFs treated with ABT263 (5 micromolar) for 1 day.


title: senescent HDFs, Nintedanib, bio rep 2

description:
HDFO-Nin2
Gene expression in senescent HDFs treated with Nintedanib (5 micromolar) for 1 day.


title: THP-1 ORF TAGAP rep1

description: THP-1 stable cell line overexpressing TAGAP gene / replicate 1

value: TAGAP


title: Sample_97_RORg_MHCII


title: THP-1 ORF SYT11 rep3

description: THP-1 stable cell line overexpressing SYT11 gene / replicate 3


title: non-senescent HDFs, MP470, bio rep 1

description:
HDFy-MP470-1
Gene expression in non-senescent HDFs treated with MP470 (20 micromolar) for 1 day.

value: 20 micromolar of MP470


title: Sample_96_RORg_MHCII

value: three weeks


title: non-senescent HDFs, sunitinib, bio rep 1

description:
HDFy-suni1
Gene expression in non-senescent HDFs treated with sunitinib (10 micromolar) for 1 day.

value: 10 micromolar of Sunitinib


title: non-senescent HDFs, ABT263, bio rep 1

description:
HDFy-ABT1
Gene expression in non-senescent HDFs treated with ABT263 (5 micromolar) for 1 day.


title: Sample_95_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol

value: RORgt+ MHCII+


title: THP-1 ORF TAGAP rep3

description: THP-1 stable cell line overexpressing TAGAP gene / replicate 3


title: senescent HDFs, sunitinib, bio rep 2

description:
HDFO-suni2
Gene expression in senescent HDFs treated with sunitinib (10 micromolar) for 1 day.

value: Human dermal fibroblast, passage 50 (senescent)


title: THP-1 ORF SYT11 rep1

description: THP-1 stable cell line overexpressing SYT11 gene / replicate 1


title: THP-1 ORF SYT11 rep2

description: THP-1 stable cell line overexpressing SYT11 gene / replicate 2


title: senescent HDFs, sunitinib, bio rep 1

description:
HDFO-suni1
Gene expression in senescent HDFs treated with sunitinib (10 micromolar) for 1 day.


title: non-senescent HDFs, control, bio rep 1

description:
HDFy-con1
Gene expression in non-senescent HDFs treated with DMSO for 1 day.


title: THP-1 ORF TAGAP rep2

description: THP-1 stable cell line overexpressing TAGAP gene / replicate 2


title: THP-1 ORF STAT3 rep3

description: THP-1 stable cell line overexpressing STAT3 gene / replicate 3


title: senescent HDFs, MP470, bio rep 1

description:
HDFO-MP470-1
Gene expression in senescent HDFs treated with MP470 (20 micromolar) for 1 day.


title: Sample_94_RORg_MHCII


title: non-senescent HDFs, Nintedanib, bio rep 1

description:
HDFy-Nin1
Gene expression in non-senescent HDFs treated with Nintedanib (5 micromolar) for 1 day.

value: 5 micromolar of Nintedanib


title: senescent HDFs, ABT263, bio rep 1

description:
HDFO-ABT1
Gene expression in senescent HDFs treated with ABT263 (5 micromolar) for 1 day.

value: 5 micromolar of ABT263


title: senescent HDFs, Nintedanib, bio rep 1

description:
HDFO-Nin1
Gene expression in senescent HDFs treated with Nintedanib (5 micromolar) for 1 day.


title: Sample_93_RORg_MHCII


title: THP-1 ORF STAT3 rep2

description: THP-1 stable cell line overexpressing STAT3 gene / replicate 2

value: Monocytic leukemia


title: Sample_92_RORg_MHCII


title: THP-1 ORF STAT3 rep1

description: THP-1 stable cell line overexpressing STAT3 gene / replicate 1

value: A


title: senescent HDFs, control, bio rep 1

description:
HDFO-con1
Gene expression in senescent HDFs treated with DMSO for 1 day.

value: HDF


title: Sample_91_RORg_MHCII


title: NHBE, mock-infected, 24hpi, rep1

city: Provo

first: Brett

middle: E

last: Pickett

state: UT

department: Microbiology and Molecular Biology

institute: Brigham Young University

description:
Mock_24hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_24hr-treatmentMock_24hr_entrez.tsv
edgeR_dge_results_treatmentWA_24hr-treatmentMock_24hr_entrez.tsv

data_processing:
Trimming: TrimGalore v0.6.4, default parameters
Mapping & Quantification: Salmon v1.2.0, default parameters
Quality Control: FastQCv0.11.8, default parameters
Differential Expression: edgeRv3.32.0, default parameters
Assembly: GRCh38.98
Supplementary files format and content: tab-delimited text files include CPM values, log2 fold-change values, and FDR-corrected p-values for each sample

molecule: polyA RNA

source_name: NHBE

growth_protocol: NHBE cells were grown in triplicate to near confluency, then separated prior to infection or mock-infection.

extract_protocol:
Total RNA was extracted from cells using Trizol reagent according to manufacturer’s protocol.
RNA libraries were prepared for sequencing using standard Illumina NextSeq protocols.

treatment_protocol: NHBE cells were incubated with the indicated virus (or mock) at an MOI of 2, washed in PBS, and incubated at 37⁰C with 5% CO2 prior to harvesting at 6, 12, or 24 hpi.

value: NHBE

value: Normal Human Bronchial Epithelial Cells

tag: infection

value: Mock-infected

tag: time


title: NHBE, mock-infected, 24hpi, rep3

description:
Mock_24hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_24hr-treatmentMock_24hr_entrez.tsv
edgeR_dge_results_treatmentWA_24hr-treatmentMock_24hr_entrez.tsv


title: NHBE, mock-infected, 24hpi, rep2

description:
Mock_24hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_24hr-treatmentMock_24hr_entrez.tsv
edgeR_dge_results_treatmentWA_24hr-treatmentMock_24hr_entrez.tsv


title: Sample_90_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol

value: mesenteric lymph nodes (MLN)


title: THP-1 ORF TMEM135 rep2

description: THP-1 stable cell line overexpressing TMEM135 gene / replicate 2


title: NHBE, mock-infected, 12hpi, rep1

description:
Mock_12hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_12hr-treatmentMock_12hr_entrez.tsv
edgeR_dge_results_treatmentWA_12hr-treatmentMock_12hr_entrez.tsv


title: Sample_89_RORg_MHCII


title: NHBE, mock-infected, 12hpi, rep3

description:
Mock_12hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_12hr-treatmentMock_12hr_entrez.tsv
edgeR_dge_results_treatmentWA_12hr-treatmentMock_12hr_entrez.tsv


title: NHBE, mock-infected, 6hpi, rep3

description:
Mock_6hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_6hr-treatmentMock_6hr_entrez.tsv
edgeR_dge_results_treatmentWA_6hr-treatmentMock_6hr_entrez.tsv


title: THP-1 ORF TMEM135 rep1

description: THP-1 stable cell line overexpressing TMEM135 gene / replicate 1


title: NHBE, mock-infected, 6hpi, rep2

description:
Mock_6hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_6hr-treatmentMock_6hr_entrez.tsv
edgeR_dge_results_treatmentWA_6hr-treatmentMock_6hr_entrez.tsv


title: NHBE, mock-infected, 12hpi, rep2

description:
Mock_12hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_12hr-treatmentMock_12hr_entrez.tsv
edgeR_dge_results_treatmentWA_12hr-treatmentMock_12hr_entrez.tsv


title: NHBE, USA-WA1/2020, 24hpi, rep3

description:
WA_24hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_24hr-treatmentMock_24hr_entrez.tsv


title: THP-1 ORF SLC7A10 rep2

description: THP-1 stable cell line overexpressing SLC7A10 gene / replicate 2


title: NHBE, USA-WA1/2020, 24hpi, rep2

description:
WA_24hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_24hr-treatmentMock_24hr_entrez.tsv


title: NS_3

city: Guangzhou

first: Yanjuan

last: Chen

state: Guangdong

address: Guangzhou

department: Department of Geriatrics and Division of Rheumatology and Research

institute: The Second Clinical Medical College, Jinan University (Shenzhen People's Hospital)

data_processing:
The sequencing data was filtered with SOAPnuke (v1.5.2)by removing reads containing sequencing adapter.
Removing reads whose low-quality base ratio (base quality less than or equal to 5) is more than 20%.
Removing reads whose unknown base ('N' base) ratio is more than 5%, afterwards clean reads were obtained and stored in FASTQ format
The clean reads were mapped to the reference genome using HISAT2 (v2.0.4)
Bowtie2 (v2.2.5) was applied to align the clean reads to the reference coding gene set, then expression level of gene was calculated by SEM (v1.2.12).
Assembly: HISAT2 (v2.0.4)
Supplementary files format and content: excel files include FPKM values for each Sample

source_name: HMC3 cells

growth_protocol: Human microglia cell HMC3 was cultured in Minimum Essential Medium (MEM) containing 10% FBS and 1mM sodium pyruvate. Cells were seeded into 6 cm plate and grown at 37℃ in a saturated humidity atmosphere of 5% CO2.

extract_protocol:
Total RNA was extracted from the cells of each group using Trizol (Invitrogen, Carlsbad, CA, USA) according to manual instruction.
Total RNA was qualified and quantified using a Nano Drop and Agilent 2100 bioanalyzer (Thermo Fisher Scientific, MA, USA).The final library was amplified with phi29 to make DNA nanoball (DNB) which had more than 300 copies of one molecular, DNBs were loaded into the patterned nanoarray and single end 50 bases reads were generated on BGIseq500 platform (BGI-Shenzhen, China).

treatment_protocol:
When the confluency of cells became up to 80-90%, we changed media to fresh MEM supplemented with 10% GCNY medicated serum (GCNY) and 10% normal saline medicated serum (NC), respectively.
Simultaneously, the cells were treated with normal serum and 200μM H2O2 (NS) for 4h.

value: HMC3 cells

value: human microglial cells

value: Immortalization of human fetal brain-derived primary microglia

value: normal serum + H2O2

value: 4 hours


title: Sample_88_RORg_MHCII

city: New York

last: Brown

institute: Memorial Sloan Kettering Cancer Center

data_processing:
base-calling was performed using HiSeq Control Software HD v3.4.0.38
samples were demultiplexed using bcl2FASTQ v2.20.0.422
FASTQ files from demultiplexed samples were aligned to GRCm38 (mm10) using STAR v2.7.7a with ‘--twopassMode Basic --outFilterMultimapNmax 1 --quantMode TranscriptomeSAM’
The alignments of each sample were name-sorted using Samtools v1.11
The count matrix for all cells was created by counting alignments using featureCounts (subread v2.0.1)
Low-quality cells/genes were filtered and downstream analyses (normalization, PCA, etc.) was performed using Seurat v3.2.3.
Cells were clustered using PhenoGraph and UMAP embedding was computed using Seurat v3.2.3.
Genome_build: mm10
Supplementary_files_format_and_content: the count matrix (tab-delimited table) includes raw counts for all cells (smart-seq2 samples).
Supplementary_files_format_and_content: the cell metadata (csv table) includes clusters, annotations, etc. for all cells (corresponding to rows in the count matrix).

extract_protocol:
RORgt+MHCII+ cells were enriched from a pool of MLN from 3-week-old RorcVenus-CreERT2 mice. Cells were depleted of Lineage (TCRb, TCRgd, CD19, B220, NK1.1)+ cells via staining with biotinylated antibodies followed by magnetic bead negative selection. Live, Lin(CD3, TCRb, TCRgd CD19, B220, NK1.1)–CD64–Ly6C–MHCII+RORgt(Venus)+ cells were then sorted into single wells. Cells were also stained for CD90, CD11c and CD11b for acquiring index sorting information on cell surface expression. Aire+ mTECs were enriched from a pool of thymi from 3-week old mice via staining with biotinylated antibodies against CD45 followed by magnetic bead negative selection. CD45–Epcam+MHCII+Aire(GFP)+ cells were sorted into single wells. Aire+ DCs were enriched from a pool of MLN from the same 3-week old mice. Cells were depleted of Lin+ cells as described above and live, Lin(CD3, TCRb, TCRgd CD19, B220, NK1.1)–CD90–CD64–Ly6C–CD11c+MHCII+Aire(GFP)+ cells were then sorted into single wells.
Single cells were sorted into Buffer RLT (Qiagen). Cell lysates were immediately sealed and spun down before transferring to dry ice and storing at -80 ºC. RNA was purified using the Agencourt RNAClean XP beads (Beckman Coulter) at a 2.2X ratio. First-strand cDNA synthesis was achieved using Maxima H Minus Reverse Transcriptase (ThermoFisher) according to the manufacturer’s protocol using oligo dT primers, with the addition of a custom template-switch oligo in a 1mM final concentration. cDNA was amplified for 24 cycles using KAPA HiFi HotStart ReadyMix (Kapa Biosystems KK2601). After PicoGreen quantification, 0.1-0.2ng of cDNA was used to prepare libraries with the Nextera XT DNA Library Preparation Kit (Illumina) in a total volume of 6.25µL with 12 cycles of PCR. Indexed libraries were pooled by volume and cleaned by aMPure XP beads (Beckman Coulter) at a 1X ratio. Pools were sequenced on a HiSeq 4000 in a PE50 or PE100 run using the HiSeq 3000/4000 SBS Kit (Illumina).

value: three weeks


title: Sample_86_RORg_MHCII

value: RORgt+ MHCII+


title: Sample_87_RORg_MHCII


title: THP-1 ORF SLC7A10 rep3

description: THP-1 stable cell line overexpressing SLC7A10 gene / replicate 3


title: NS_2


title: THP-1 ORF SLC7A10 rep1

description: THP-1 stable cell line overexpressing SLC7A10 gene / replicate 1


title: THP-1 ORF TMEM135 rep3

description: THP-1 stable cell line overexpressing TMEM135 gene / replicate 3


title: NS_1


title: NHBE, USA-WA1/2020, 24hpi, rep1

description:
WA_24hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_24hr-treatmentMock_24hr_entrez.tsv


title: Sample_85_RORg_MHCII


title: THP-1 ORF SLC39A11 rep3

description: THP-1 stable cell line overexpressing SLC39A11 gene / replicate 3


title: THP-1 ORF SLC39A11 rep2

description: THP-1 stable cell line overexpressing SLC39A11 gene / replicate 2


title: Sample_84_RORg_MHCII

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: NHBE, USA-WA1/2020, 12hpi, rep2

description:
WA_12hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_12hr-treatmentMock_12hr_entrez.tsv


title: Sample_83_RORg_MHCII


title: NHBE, mock-infected, 6hpi, rep1

description:
Mock_6hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_6hr-treatmentMock_6hr_entrez.tsv
edgeR_dge_results_treatmentWA_6hr-treatmentMock_6hr_entrez.tsv


title: NHBE, USA-WA1/2020, 12hpi, rep1

description:
WA_12hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_12hr-treatmentMock_12hr_entrez.tsv


title: Sample_82_RORg_MHCII


title: THP-1 ORF SLC39A11 rep1

description: THP-1 stable cell line overexpressing SLC39A11 gene / replicate 1


title: NC_1

value: normal serum


title: NC_3


title: NC_2


title: THP-1 ORF SLC2A13 rep3

description: THP-1 stable cell line overexpressing SLC2A13 gene / replicate 3


title: Sample_81_RORg_MHCII


title: senescent HDFs, control, bio rep 2

description:
HDFO-con2
Gene expression in senescent HDFs treated with DMSO for 1 day.

value: Human dermal fibroblast, passage 50 (senescent)

value: WT

value: DMSO


title: GCNY_2

value: GCNY-medicated serum + H2O2


title: THP-1 ORF SLC2A13 rep1

description: THP-1 stable cell line overexpressing SLC2A13 gene / replicate 1

value: Monocytic leukemia

value: A


title: NHBE, USA-WA1/2020, 6hpi, rep2

description:
WA_6hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_6hr-treatmentMock_6hr_entrez.tsv

value: NHBE

value: Normal Human Bronchial Epithelial Cells


title: NHBE, USA-WA1/2020, 6hpi, rep1

description:
WA_6hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_6hr-treatmentMock_6hr_entrez.tsv


title: Sample_80_RORg_MHCII

value: mesenteric lymph nodes (MLN)


title: Sample_79_RORg_MHCII


title: GCNY_1

value: HMC3 cells


title: Sample_78_RORg_MHCII


title: THP-1 ORF SLC22A4 rep2

description: THP-1 stable cell line overexpressing SLC22A4 gene / replicate 2


title: NHBE, USA-WA1/2020, 12hpi, rep3

description:
WA_12hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_12hr-treatmentMock_12hr_entrez.tsv


title: Sample_77_RORg_MHCII


title: THP-1 ORF SLC22A4 rep3

description: THP-1 stable cell line overexpressing SLC22A4 gene / replicate 3


title: NHBE, New York 1-PV08001/2020, 24hpi, rep3

description:
NY_24hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_24hr-treatmentMock_24hr_entrez.tsv


title: NHBE, New York 1-PV08001/2020, 24hpi, rep1

description:
NY_24hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_24hr-treatmentMock_24hr_entrez.tsv


title: NHBE, USA-WA1/2020, 6hpi, rep3

description:
WA_6hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentWA_6hr-treatmentMock_6hr_entrez.tsv


title: mMoDCs, infected, rep3

city: Madrid

first: Isabel

last: García-García

state: Madrid

address: Calle José Antonio Novais, 12

department: Genética, Fisiología y Microbiología

country: Spain

institute: Universidad Complutense de Madrid (UCM)

data_processing:
Quality control checks for raw sequence data from each sample were performed, using FastQC v.0.11.9 (Babraham Bioinformatics)
Low quality reads (mean quality score <15; reads length <36) were removed using Trimmomatic v.0.39
Mapping of the quality-filtered reads to the Ovis aries reference genome was performed using subread-align (Subread v.2.0.1)
Cuffdiff (Cufflinks v.2.2.1) was used to perform gene count summarization and to identify differentially expressed genes (DEGs) between the PPRV-infected mMoDC samples and their mock-infected counterparts
False discovery rate (FDR) correction was used to discard false positive results. Threshold: 0.05
Assembly: Oar_rambouillet_v1.0
Supplementary files format and content: Tab-delimited text file, it includes FPKM values for all samples

organism: Ovis aries

source_name: mMoDC

extract_protocol:
RNeasy Mini Kit + DNase set (Qiagen)
mRNA was captured through the polyA tail and libraries were constructed with a NEB-Next Ultra-II RNA Library Prep kit (NE BioLabs)

value: mMoDC

value: PPRV-infected


title: THP-1 ORF SLC22A4 rep1

description: THP-1 stable cell line overexpressing SLC22A4 gene / replicate 1


title: mMoDCs, infected, rep4


title: Sample_75_RORg_MHCII

first: Chrysothemis

description:
RORgt+ MHCII+ from 3-week old mice
smart-seq2 protocol


title: NHBE, New York 1-PV08001/2020, 12hpi, rep3

description:
NY_12hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_12hr-treatmentMock_12hr_entrez.tsv


title: NHBE, New York 1-PV08001/2020, 24hpi, rep2

description:
NY_24hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_24hr-treatmentMock_24hr_entrez.tsv


title: Sample_74_RORg_MHCII


title: THP-1 ORF RTEL1 rep3

description: THP-1 stable cell line overexpressing RTEL1 gene / replicate 3


title: mMoDCs, mock, rep3

value: mock-infected


title: mMoDCs, infected, rep2


title: THP-1 ORF RTEL1 rep2

description: THP-1 stable cell line overexpressing RTEL1 gene / replicate 2


title: GCNY_3

value: human microglial cells

value: Immortalization of human fetal brain-derived primary microglia

value: 4 hours


title: mMoDCs, mock, rep4


title: THP-1 ORF C21orf33 rep3

description: THP-1 stable cell line overexpressing C21orf33 gene / replicate 3


title: THP-1 ORF RTEL1 rep1

description: THP-1 stable cell line overexpressing RTEL1 gene / replicate 1


title: mMoDCs, infected, rep1


title: NHBE, New York 1-PV08001/2020, 6hpi, rep3

description:
NY_6hpi_rep3
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_6hr-treatmentMock_6hr_entrez.tsv


title: THP-1 ORF C21orf33 rep2

description: THP-1 stable cell line overexpressing C21orf33 gene / replicate 2


title: Sample_76_RORg_MHCII

value: three weeks

value: RORgt+ MHCII+


title: Sample_72_RORg_MHCII


title: Sample_71_RORg_MHCII


title: NHBE, New York 1-PV08001/2020, 6hpi, rep2

description:
NY_6hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_6hr-treatmentMock_6hr_entrez.tsv


title: NHBE, New York 1-PV08001/2020, 12hpi, rep2

description:
NY_12hpi_rep2
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_12hr-treatmentMock_12hr_entrez.tsv


title: mMoDCs, mock, rep2


title: NHBE, New York 1-PV08001/2020, 12hpi, rep1

description:
NY_12hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_12hr-treatmentMock_12hr_entrez.tsv


title: mMoDCs, mock, rep1


title: THP-1 ORF SLC2A13 rep2

description: THP-1 stable cell line overexpressing SLC2A13 gene / replicate 2


title: THP-1 ORF C21orf33 rep1

description: THP-1 stable cell line overexpressing C21orf33 gene / replicate 1


title: Sample_70_RORg_MHCII


title: NHBE, New York 1-PV08001/2020, 6hpi, rep1

description:
NY_6hpi_rep1
Cells infected with SARS-CoV-2 isolate at MOI of 2.
edgeR_dge_results_treatmentNY_6hr-treatmentMock_6hr_entrez.tsv


title: MB49_Batf3-/-_POM1_1

city: Wu Han

first: Junyi

last: Hu

address: No. 1277 Liberation Avenue

department: Urology

institute: Union Hospital, Tongji Medical College, Huazhong University of Science and Technology

data_processing:
Single-cell RNA sequencing data was collected on a Hiseq X Ten Illumina instrument.
Alignment using Cell Ranger (5.0.0) from 10x Genomics.
Genome_build: mm10 (GRCm38)
Supplementary_files_format_and_content: *.tar: Tar archives include barcodes.tsv.gz, features.tsv.gz, and matrix.mtx.gz files.

source_name: bladder cancer

growth_protocol: MB49 Subcutaneous tumors.

extract_protocol:
After single cell suspension, CD45+ cells were sorted.
Barcoded scRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3 Reagent Kit.

treatment_protocol: 5 mg/kg of the NTPDase inhibitor sodium polyoxotungstate (POM-1/CD39i, purchased from Santa Cruz Biotechnology, Inc., Dallas, Texas, USA) once per day from day 6 to day 22.

value: MB49 Subcutaneous tumors

tag: marker

value: CD45+ sorted

value: POM-1 treated


title: Sample_69_RORg_MHCII


title: MB49_Batf3-/-_untreated_1

value: untreated