title: G-CSF induced BMDMs_H3K27me3

city: Qingdao

first: zhao

last: zhan

state: Shandong

address: No.23 HongKong East Road,Laoshan District

department: School of Medicine and Pharmacy

institute: Ocean University of China

data_processing:
Basecalls performed using CASAVA version 1.4
ChIP-seq reads were aligned to the mm9 genome assembly using EasyAlign version 3.2 with the following configurations…
Data were filtered using the following specifications…
peaks were called using PeaksFind version 2.2 with the following setting: ChIP threshold (0.2), Enrichment Fold (2.5), Rescue Fold (3).
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

source_name: macrophage

growth_protocol: GM-CSF or M-CSF stimulated for 7 days

extract_protocol:
Lysates were clarified from sonicated nuclei and histone-DNA complexes were isolated with antibody.
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: untreated

value: bone marrow derived macrophage

value: G_CSF treated for 7 days

value: H3K4me3 (Active Motif, 39535 )


title: M-CSF induced BMDMs_input

status: Public on Nov 09 2024

type: SRA

country: China

library_source: genomic

molecule: genomic DNA

organism: Mus musculus

tag: cell type

tag: strain

tag: treatment

value: M_CSF treated for 7 days

tag: chip antibody


title: THP-1 cells, WT Legionella infection, 5 h post-infection, biol rep 2

city: Clayton

first: Kathleen

last: McCaffrey

state: VIC

address: 25-31 Wright Street

country: Australia

institute: Hudson Institute of Medical Research

library_source: transcriptomic

data_processing:
Image analysis was performed in real time by the NovaSeq Control Software (NCS) v1.6.0 and Real Time Analysis (RTA) v3.4.4, running on the instrument computer. RTA performs real-time base calling on the NovaSeq instrument computer. Then the Illumina bcl2fastq 2.20.0.422 pipeline was used to generate the sequence data.
Trimmed reads were mapped to GRCh38.90 using Tophat2 v2.1.1
Read counts were generated using featureCounts v1.5.0
Assembly: Homo sapiens genome (GRCh38.90)
Supplementary files format and content: tab delimited text file including raw counts for each Sample

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: THP-1 monocytes [Homo sapiens, male] (ATCC Cat#TIB-202) were cultured in RPMI 1640 supplemented with Glutamax (Gibco Cat#61870036) and 10 % foetal bovine serum (FBS) (Bovagen Cat#SFBS-AU) at 37C and 5 % CO2. THP-1 monocytes were seeded at 2.5x105 cells/cm2 in tissue-culture dishes and differentiated for 48 h prior to infection using 50 ng/mL phorbol 12-myristate 13-acetate (PMA) (Sigma Aldrich Cat#P8139).

extract_protocol:
At 5 h post-infection, RNA was extracted from cell monolayers using the ISOLATE II RNA Mini Kit (Bioline Cat# BIO-52073) according to the manufacturer’s instructions and analysed using a 2100 Bioanalyzer (Agilent).
cDNA libraries were prepared for three independent replicates per condition using the TruSeq® Stranded mRNA Library Prep (Illumina Cat# 20020594) according to the manufacturer’s instructions

treatment_protocol: THP-1 cell monolayers were infected with either L. pneumophila 130b or the deltalegC4 strain at a MOI of 10. At 2 h post-infection, cell monolayers were incubated with gentamicin at 100 ug/mL (Gibco Cat#15750060) for 1 h to kill any remaining extracellular bacteria followed by washing and the addition of fresh media.

tag: cell line

value: Monocyte

tag: genotype

value: WT

value: PMA differentiated, 48 h


title: THP-1 cells, deltaLegC4 Legionella infection, 5h post-infection, biol rep 3


title: G-CSF induced BMDMs_input


title: M-CSF induced BMDMs_H3K27me3


title: THP-1 cells, deltaLegC4 Legionella infection, 5 h post-infection, biol rep 2


title: M-CSF induced BMDM

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 mm9 whole genome using bowtie v0.12.2 with parameters -q -p 4 -e 100 -y -a -m 10 --best --strata
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript were counted and normalized by the size of the meta-transcript and by the size of the library.
Genome_build: mm9
Supplementary_files_format_and_content: peak text files

extract_protocol:
Cell nuclears were digested by Tn5 transposase
Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

value: M-CSF treated for 7 days


title: Control B

city: Milano

first: Andrea

last: Franceschini

state: Milano

address: via Ripamonti 435

country: Italy

institute: European Institute Of Oncology

description: 10x Genomics

library_source: transcriptomic single cell

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation was made using CellRanger 3.1.0
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: total RNA

source_name: Peripheral Blood

extract_protocol:
Peripheral blood mononuclear cells were isolated by Ficoll-Hypaque density gradient centrifugation, and isolated PBMCs were cryopreserved in liquid nitrogen according to standard protocols until use. After thawing of cryopreserved PBMC, to remove dead cells for sc-mRNAseq preparation, we took advantage of Dead Cell Removal Kit following manufacturer’s instruction.
10k alive cells were then processed with 10x Technology using V3.1 kit (10x Genomics), following manufacturer’s instructions. Finally library integrity was assessed by Hypersensitive (HS) Bioanalyzer run (Agilent).

tag: tissue

value: Peripheral Blood

tag: group

value: Control B

value: mononuclear cells


title: THP-1 cells, deltaLegC4 Legionella  infection, 5 h post-infection, biol rep 1


title: THP-1 cells, WT Legionella infection, 5h post-infection, biol rep 3


title: DN3(IK), treated with HDAC1 inhibitor MS-275 for 1 day, ChIP-seq

city: Hershey

first: Bing

last: He

state: PA

address: 500 University Dr

country: USA

institute: Penn State University

data_processing:
Sequencing reads were mapped to the mouse genome (mm9) using Bowtie2 (v2.2.2) with default parameter setting
Samtools and PICARD were used for QC of mapped reads (MAPQ>30).
ChIP-Seq peaks were called by MACS2 using default parameter setting
Assembly: mm9
Supplementary files format and content: bigWig

source_name: JE131 cell line (DN3 cells)

growth_protocol: cells were cultured in RPMI1640 with 10% FBS at 37℃ with 5% CO2

extract_protocol:
Lysates were clarified from sonicated nuclei and protein-DNA complexes were isolated with antibody.
Libraries were prepared according to instructions for Illumina ChIP-seq DNA sample prep kit or Quanta Bio sparQ DNA Library Prep Kit.

treatment_protocol: DN3 cells were transduced with retrovirus that contains HA-tagged wild-type murine Ikaros for 1 day, 2 days and 3 days.

value: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: DN3 cells transduced with Ikaros, treated with HDAC1 inhibitor MS-275 for 1 day


title: Naïve, PreCAR, Exp1, TR1 [RNA-seq]

status: Public on Nov 10 2024

city: Aurora

first: Terry

last: Fry

state: CO

institute: University of of Colorado Denver and Children's Hospital Col

description: Splenic CD8+ T cells were harvested from naïve mice.

data_processing:
Raw sequencing reads were de-multiplexed using bcl2fastq.
Quality of fastq files was accessed using FastQC (v.0.11.8) , FastQ Screen (v.0.13.0) and MultiQC (v.1.8).
Illumina adapters and low-quality reads were filtered out using BBDuk (v. 38.87).
Trimmed fastqc files were aligned to the mm10 murine reference genome and aligned counts per gene were quantified using STAR (v.2.7.9a).
Assembly: mm10
Supplementary files format and content: Tab-delimited text file includes raw counts.

source_name: Splenic T cells

growth_protocol: CD8+ T cells were maintained in RPMI1640 media supplemented with L-Glutamine, non-essential amino acids, sodium pyruvate, HEPES, antibiotics and 10% FBS.

extract_protocol:
For RNAseq, cells were homogenized in QIAzol Lysis Reagent and processed using the miRNeasy Micro Kit with on-column DNase treatment, both according to manufacturer protocols. RNA purity, quantity and integrity was determined with NanoDrop and TapeStation 4200 analysis.
The Universal Plus mRNA-Seq library preparation kit with NuQuant was used with an input of 200ng of total RNA to generate RNA-Seq libraries.

treatment_protocol: Vaccination was carried out with whole ovalbumin protein, anti-mouse CD40 and PolyI:C, with concurrent adoptive transfer of 5000 OT-I CD8+ T cells. OT-I T cells were isolated from vaccinated mice on day 28 post-vaccination from pooled vaccinated hosts (memory), or age-matched naïve mice (naïve). CD8+ T cells were activated using anti-CD3/anti-CD28 Dynabeads in the presence of IL-2 and IL-7, and transduced with a murine anti-mouse CD19 CAR containing CD28 costimulatory domain and CD3zeta domain. CAR T cells were infused into leukemia-bearing C57BL/6-background Rag1-/- mice at 1e6 CAR+ cells/mouse.

value: Splenic T cells

value: CD8+ T cell

value: Rag2-/- OT-I TCR transgenic


title: Monomer10

city: Chicago

first: D.

middle: James

last: Surmeier

state: IL

address: 303 E Superior Street, Lurie 8-220

department: Neuroscience

institute: Northwestern University

data_processing:
Adapters were trimmed from reads using cutadapt version 1.13
Trimmed reads were aligned using STAR version 020201
Gene counting was performed using htseq-count version 0.6.1p1
Differential expression was performed using DESeq2 version 1.14.1
Assembly: hg38
Supplementary files format and content: raw counts

source_name: Substantia nigra pars compacta (SNc)

growth_protocol: Mice were housed in groups of up to 5 animals per cage with food and water provided ad libitum on a 12-hour light/dark cycle. All animals were between two and three months old at the beginning of the experiments.

extract_protocol:
SNc tissue was dissected from brain slices and RiboTag immunoprecipitation was carried out with anti-Flag magnetic beads. RNA extraction was then performed using the RNA-easy Micro RNA extraction kit (QIAGEN).
RNA libraries for RNA-seq were prepared usingNEB Ultra II RNA DepletionLibrary Prep Kit following manufacturer's protocols.

treatment_protocol: Heterozygous DAT-Cre mice were injected with either aSYN PFFs or aSYN monomer protein into the SNc. 10 weeks after the initial injection, all mice were injected with an AAV vector carrying a DIO-RiboTag expression construct into the SNc.

value: Substantia nigra pars compacta (SNc)

value: dopaminergic neurons

value: heterozygous DAT-Cre

value: aSYN Monomer


title: THP-1 cells, WT Legionella infection, 5 h post-infection, biol rep 1

value: Monocyte


title: Asymptomatic A

description: 10x Genomics

value: Asymptomatic A


title: GM-CSF induced BMDM

value: bone marrow derived macrophage

value: GM-CSF treated for 7 days


title: DN3(IK), treated with HDAC1 inhibitor PTL for 2 days, ChIP-seq

value: DN3 cells transduced with Ikaros, treated with HDAC1 inhibitor Parthenolide (PTL) for 2 days


title: Asymptomatic B

description: 10x Genomics

value: Peripheral Blood

value: Asymptomatic B


title: Control A

description: 10x Genomics

value: Control A

value: mononuclear cells


title: DN3(IK), treated with HDAC1 inhibitor PTL for 1 day, ChIP-seq

value: JE131 cell line (DN3 cells)

value: an early T leukemia cell line that is derived from Ikaros knock-out mice

value: DN3 cells transduced with Ikaros, treated with HDAC1 inhibitor Parthenolide (PTL) for 1 day


title: Monomer9


title: Secondary B

description: 10x Genomics

value: Secondary B


title: Symptomatic B

description: 10x Genomics

value: Symptomatic B

value: Cyclophosphamide


title: Monomer6

value: Substantia nigra pars compacta (SNc)

value: dopaminergic neurons

value: heterozygous DAT-Cre


title: Monomer8

value: aSYN Monomer


title: Secondary A

description: 10x Genomics

value: Secondary A


title: DN3(IK), treated with HDAC1 inhibitor MS-275 for 2 days, ChIP-seq

value: DN3 cells transduced with Ikaros, treated with HDAC1 inhibitor MS-275 for 2 days


title: Monomer7


title: Monomer4


title: 3021 6-month

type: RNA

city: Boston

first: Margaret

last: Stefater-Richards

state: MA

address: 300 Longwood Ave

institute: Boston Children's Hospital

hyb_protocol: not provided

scan_protocol: not provided

data_processing: Affymetrix (Santa Clara, CA) HTA 2.0 arrays were processed using the 'oligo'(14) BioConductor package, quality-controlled with array QualityMetrics(15).  After exclusion of clear outliers, the remaining arrays were processed using the TAC4.0 software from Affymetrix/Thermo Fisher using their RMA-SST algorithm and imported back into this workflow. Non-coding and non-annotated genes were removed from the dataset; this strategy identified 25,049 of 70,523 probes for analysis.  These remaining probes were collapsed by taking the probeset for each gene with the maximum value for all samples; this strategy identified 23,327 genes which were included in the analysis represented here. Differentially expressed genes (as defined by a Benjamini-Hochberg FDR adjusted p-value of less than 0.05) were identified using limma(16) using a paired design.

label: biotin

source_name: Roux limb (RL)

label_protocol: not provided

extract_protocol: RNA was extracted from frozen tissue samples by homogenization in trizol followed by chloroform separation and extraction in an RNAeasy mini column (Qiagen Inc., Germantown, MD) prior to cleaning using the RNase-Free DNaseSet (Qiagen Inc., Germantown, MD).  Microarray was performed using the GeneChip WT PLUS Reagent Kit (Affymetrix, Santa Clara, CA) to ampligy  250 g of RNA for each sample.  All RNA used for microarray had a minimum RNA Integrity Number (RIN) value of 6.5.

tag: Sex

value: Female

tag: diabetes status

value: Diabetic

value: Roux-en-Y gastric bypass surgery (RYGB)


title: Monomer5


title: 3015 baseline

value: Control


title: MG5 cells, BEX3

city: Nagoya

first: Makoto

last: Inoue

address: 1-100 Kusumoto-cho, Chikusa-ku, Nagoya

department: School of Pharmacy

country: Japan

institute: Aichi Gakuin University

data_processing:
Illumina bcl2fastq2-v2.20.0 software used for basecalling.
Trimmomatic program is used to remove adapter sequences and bases with base quality lower than three from the ends. Also using sliding window method, bases of reads that does not qualify for window size 4, and mean quality 15 are trimmed. Afterwards, reads with length shorter than 36bp are dropped to produce trimmed data.
Sequenced reads were mapped to mm10 whole genome by using HISAT2 version 2.1.0 with parameter -p 20 -dta --rna-strandness RF --novel-splicesite-outfile -x -1 -2
Fragment Per Kilobase of exon per Megabase of library size (FPKM) were calculated by using StringTie version 2.1.3b, with parameter --rf -p 20 -l -o -G -A -C -e
The reads were prepared for analysis using the Trimmomatic version 0.38 to remove adapter sequences and trim the low-quality bases. Subsequently, the processed reads were aligned to the Mus musculus reference genome (mm10) using HISAT2 version 2.1.0 by incorporating both HISAT2 and Bowtie2 for alignment. Reference genome sequences and gene annotation data were sourced from the NCBI Genome Assembly and NCBI RefSeq databases. Following alignment, data formatted in SAM was sorted and indexed using SAMtools version 1.9. Then, the StringTie version 2.1.3b tool was used to assemble and quantify the transcripts.
Assembly: mm10
Supplementary files format and content: tab-delimited text files include read count, FPKM, TPM values for each Sample

growth_protocol: Mouse astrocyte-like A1 cells were cultured in DMEM supplemeted with 10% FBS, 50 U/ml penicillin, and 50 µg/ml streptomycin at 37°C in a humidified atmosphere of 5% CO2 in air.  MG5 cells were cultured in a mixture of 30% DMEM supplemented with 10% FBS, 50 U/ml penicillin, and 50 µg/ml streptomycin, and 70% A1 cell-conditioned medium at 37°C in a humidified atmosphere of 5% CO2 in air.

extract_protocol:
Total RNA was extracted using RNAiso Plus (TaKaRa Bio Inc., Kusatsu, Japan).
A library was independently prepared with 1ug of total RNA for each sample by Illumina TruSeq Stranded mRNA Sample Prep Kit (Illumina, Inc., San Diego, CA, USA, #RS-122-2101). The first step in the workflow involves purifying the poly‐A containing mRNA molecules using poly‐T‐attached magnetic beads. Following purification, the mRNA is fragmented into small pieces using divalent cations under elevated temperature. The cleaved RNA fragments are copied into first strand cDNA using SuperScript II reverse transcriptase (Invitrogen, #18064014) and random primers. This is followed by second strand cDNA synthesis using DNA Polymerase I, RNase H and dUTP. These cDNA fragments then go through an end repair process, the addition of a single ‘A’ base, and then ligation of the adapters. The products are then purified and enriched with PCR to create the final cDNA library.

treatment_protocol: MG5 cells were treated with 6OHA or Bex at a concentration of 10 µM for 6 h.

value: microglial cells

value: WT

value: treated with BEX


title: MG5 cells, CTRL3

value: untreated


title: Sample5_6hrs_HU

city: Zurich

first: Ge

last: Tan

address: Winterthurerstrasse 190

department: Functional Genomics Center Zurich

country: Switzerland

institute: University of Zurich

data_processing:
Basecalls performed using illumina's bcl2fastq
Sequenced reads were trimmed for adaptor sequence, low complexity and low quality sequences. Then reads were aligned to Ensembl GRCh38.p10 genome assembly using STAR 2.7.8a with following parameters: '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
Counts were generated by Rsubread 2.8.0
Genome_build: GRCh38.p10
Supplementary_files_format_and_content: count file was generated by 'featureCounts' from Rsubread package. The numbers are raw counts.

source_name: Patient5 with Polycythemia vera

growth_protocol: CD34+ stem/progenitor cells from PV patients were incubated for 6 hours in X-VIVO medium (Lonza) with 2mM L-glutamine, 10ng/mL SCF, 50ng/mL TPO, 10ng/mL FLT3.

extract_protocol:
Total RNA was purified with the RNeasy Plus Micro Kit (Qiagen) following manufacturer’s instructions.
RNA-sequencing was performed as specified in Picelli et al 2014 using the NovaSeq sequencing platform (Illumina).

treatment_protocol: The PV stem/progenitor cells were treated with clusterin (CLU) (20µg/mL) or IKK-16 (2µM) or both, CLU (20µg/mL) and IKK-16 (2µM), or HU (100µM) or solvent control for 6 hours.

tag: disease state

value: Polycythemia vera

tag: patient number

value: Peripheral blood

value: Hematopoietic stem/progenitor cells

tag: ex vivo treatment

value: HU treated


title: MG5 cells, 6OHA2

value: treated with 6OHA


title: Symptomatic A

description: 10x Genomics

value: Peripheral Blood

value: Symptomatic A

value: mononuclear cells

value: Methotrexate


title: Sample5_6hrs_IKK16

value: IKK-16 treated


title: KO, replicate 2, scRNA seq

city: Baltimore

first: Yijun

last: Xu

state: MD

address: 733 N Broadway

institute: Johns Hopkins University School of Medicine

description: 10X Gemomics

data_processing:
The raw fastq files were demultiplexed, barcoded and counted by CellRanger 7.0.0
Assembly: GRCm39
Supplementary files format and content: The h5 files with gene count matrix, annotated with cell barcode and gene symbols

source_name: Cochlear tissue

extract_protocol:
P21 male mice (3 Tmie-/-, 4 Tmie+/- controls) were anesthetized, sacrificed by decapitation, and temporal bones were isolated and dissected in ice-cold Leibovitz’s L-15 medium. Dissected tissue consisted of the spiral ganglion, spiral limbus, inner sulcus, organ of Corti, and outer sulcus and was pooled in tubes containing ice-cold L-15. Pooled tissue was centrifuged and the supernatant was replaced with a prewarmed solution of Leibovitz containing 200 units/mL of collagenase IV (ThermoFisher, 17104-019) and incubated for 30 min at 37°C. Collagenase solution was replaced with a prewarmed solution of Earle’s Balanced Salt Solution (EBSS) containing 20 units/mL papain (Worthington, LK003150), 1mM L-cysteine, 0.5mM EDTA, 15 mM HEPES, 10units/mL DNAse I (StemCell Technologies, 7900), and 8 µL/mL RNAse inhibitor (Lucigen, 30281-1). Single cell solutions were obtained by incubation for 30 min at 37°C and gentle trituration every 10 min via pipette. Then, an equal volume of L-15 medium containing 10 mg/mL ovomucoid inhibitor, 10 mg/mL BSA (Worthington), and 8 µL/mL RNAse inihibtor was added, and the suspension was passed through a 20 µm filter to remove debris. Cells were re-pelleted at 350g for 5 min, washed twice with DMEM/F12 containing 0.04% BSA and 8 µL/mL RNase inhibitor, and pelleted again. Lastly, cells were resuspended in 60 µL of DMEM/F12 containing 0.04% BSA and 8 µL/mL RNase inhibitor.
Cell counts and viability were determined using the Cell Countess II with Trypan Blue. Cells were combined with RT reagents and loaded onto Next GEM Chip G along with 3’ v3.1 gel beads (10X Genomics, PN-1000121). The NextGEM protocol was run on the 10X Chromium Controller to create Gel Beads in emulsion (GEMs), composed of a single cell, uniquely barcoded gel bead, and reverse transcriptase reagents. Next, 100 µL of emulsion was retrieved from the chip and incubated (45 min at 53°C , 5 min at 85°C, cool to 4°C), generating barcoded cDNA from each cell. The GEMs were broken using Recovery Agent and cDNA was cleaned, following manufacturer’s instructions using MyOne SILANE beads (Invitrogen, 37002D). cDNA was amplified for 11-12 cycles based on input cell number (3 min at 98°C, 11-12 cycle:  15 sec at 98°C, 20 sec at 63°C, 1 min at 72°C; 1 min at 72°C, cool to 4°C) and samples were cleaned using 0.6X SPRIselect beads (Beckman Coulter, B23317). QC was completed using Qubit and Bioanalyzer to determine size and concentrations. 10 µL of amplified cDNA (containing 172-222 ng cDNA) was carried into library prep. Fragmentation, end repair and A-tailing were completed, and samples were cleaned up using double sided size selection (0.6X, 0.8X) with SPRIselect beads.  Adaptor ligation (15 min at 20°C, cool to 4°C), 0.8X cleanup and amplification were performed, with PCR using unique i7 index sequences.  Libraries underwent a final cleanup using double sided size selection (0.6X, 0.8X) with SPRIselect beads.  Library QC was performed using Qubit, Bioanalyzer and KAPA library quantification qPCR kit.  Libraries were sequenced on the geSa using v1.5 kits, targeting 50K reads/cell, at read lengths of 28 (R1), 8 (i7), 91 (R2).

value: Cochlear tissue

value: Tmie-/-

tag: age


title: 3020 baseline

value: Female

value: Diabetic

value: Roux-en-Y gastric bypass surgery (RYGB)


title: MG5 cells, BEX2

value: microglial cells

value: WT

value: treated with BEX


title: 3021 baseline


title: MG5 cells, BEX1


title: 3015 6-month

value: Control


title: Monomer2

value: Substantia nigra pars compacta (SNc)

value: dopaminergic neurons

value: heterozygous DAT-Cre

value: aSYN Monomer


title: Sample5_6hrs_Clu

value: Polycythemia vera

value: Peripheral blood

value: Hematopoietic stem/progenitor cells

value: CLU treated


title: Sample5_6hrs_CluIKK16

value: CLU and IKK-16 treated


title: 3021 1-month


title: Monomer1


title: 3011 baseline

value: Male


title: 3020 1-month

value: Female


title: PFF10

value: aSYN PFF


title: 3010 baseline

value: Diabetic

value: Roux-en-Y gastric bypass surgery (RYGB)


title: 3020 6-month


title: PFF9


title: Sample5_6hrs_control

value: Solvent control


title: 3011 6-month


title: 3011 1-month


title: PFF8


title: Colonic tissue, M-1, IP

city: hefei

first: duo

last: ma

address: No.81 Meishan Road, Shushan District

institute: Anhui Medical University

data_processing:
Basecalls performed using CASAVA version 1.8
circRNA-seq reads were mapped to human genome by BWA-MEM software by circRNA-seq reads were mapped to human genome by BWA-MEM software by default parameters except -T = 19
circRNAs were detected and annotated with CIRI software
Assembly: hg19
Supplementary files format and content: excel format

source_name: colon

growth_protocol: Male C57BL/6J mice (6–8 weeks old, 20–22 g)

extract_protocol:
Retinas were removed, flash frozen on dry ice, and RNA was harvested using Trizol reagent. Illumina TruSeq RNA Sample Prep Kit (Cat#FC-122-1001) was used with 1 ug of total RNA for the construction of sequencing libraries.
RNA libraries were prepared for sequencing using standard Illumina protocols

treatment_protocol: C57 mice in the model group were injected with 5% w/v TNBS by anal insertion into the colon

value: colon

value: WT

value: TNBS-induced IBD


title: Colonic tissue, M-2, IP


title: 3015 1-month

value: Control


title: Colonic tissue, N-2, IP

value: Normal feeding


title: Colonic tissue, M-3, IP


title: Colonic tissue, N-3, IP


title: PFF7

value: Substantia nigra pars compacta (SNc)

value: dopaminergic neurons

value: heterozygous DAT-Cre


title: Colonic tissue, N-1, IP


title: Sample4_6hrs_IKK16

source_name: Patient4 with Polycythemia vera

value: Polycythemia vera

value: Peripheral blood

value: Hematopoietic stem/progenitor cells

value: IKK-16 treated


title: Sample4_6hrs_Clu

value: CLU treated


title: Monomer3

value: aSYN Monomer


title: Colonic tissue, M-3, input


title: 3009 baseline

value: Female


title: 3010 6-month

value: Diabetic

value: Roux-en-Y gastric bypass surgery (RYGB)


title: PFF6

value: aSYN PFF


title: Sample4_6hrs_control

value: Solvent control


title: Sample4_6hrs_CluIKK16

value: CLU and IKK-16 treated


title: Colonic tissue, M-2, input

value: colon

value: WT

value: TNBS-induced IBD


title: Sample4_6hrs_HU

value: HU treated


title: PFF4

value: Substantia nigra pars compacta (SNc)

value: dopaminergic neurons

value: heterozygous DAT-Cre


title: Sample3_6hrs_HU

source_name: Patient3 with Polycythemia vera

value: Polycythemia vera

value: Peripheral blood

value: Hematopoietic stem/progenitor cells


title: Colonic tissue, M-1, input


title: Sample3_6hrs_CluIKK16


title: Colonic tissue, N-3, input

value: Normal feeding


title: PFF3


title: 3009 6-month

value: Female

value: Control


title: Colonic tissue, N-2, input


title: PFF5


title: 3009 1-month

value: Roux-en-Y gastric bypass surgery (RYGB)


title: Sample3_6hrs_Clu

value: CLU treated


title: 3008 baseline

value: Diabetic


title: PFF2

value: aSYN PFF


title: Colonic tissue, N-1, input

value: colon


title: 3010 1-month


title: 3008 6-month


title: Sample2_6hrs_IKK16

source_name: Patient2 with Polycythemia vera

value: IKK-16 treated


title: APAP-WT-Saline-r3

city: Shanghai

first: Gufa

last: Lin

address: 1239 Siping road Tongji university

department: Key Laboratory of Spine and Spinal Cord Injury Repair and Regeneration of Ministry of Education, Orthopaedic Department of Tongji Hospital, School of Life Sciences and Technology, Tongji University

institute: Tongji University

description:
RNA298
FPKM_anno.xlsx

data_processing:
The libraries were sequenced on an llumina Novaseq 6000 platform and 150 bp paired-end reads were generated.Raw reads of fastq format were firstly processed using fastp and the low quality reads were removed to obtain the clean reads.
The clean reads were mapped to the reference genome (mm10) using HISAT2.
FPKM of each gene was calculated and the read counts of each gene were obtained by HTSeq-count. PCA analysis were performed using R (v 3.2.0) to evaluate the biological duplication of samples.
Assembly: mm10
Supplementary files format and content: format: xlsx content:gene_name,description,GO_id,GO_term,pathway,pathway_description,TF_family

source_name: Liver

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol. RNA purity and quantification were evaluated using the NanoDrop 2000 spectrophotometer (Thermo Scientific, USA). RNA integrity was assessed using the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA).
The libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

value: Liver

value: wild type

tag: injection

value: APAP

value: Saline


title: Sample3_6hrs_control

value: Solvent control


title: Sample2_6hrs_Clu

value: Polycythemia vera


title: Sample3_6hrs_IKK16

value: Peripheral blood


title: APAP-WT-Saline-r2

description:
RNA296
FPKM_anno.xlsx


title: 3006 baseline

value: Male


title: Sample2_6hrs_control

value: Hematopoietic stem/progenitor cells


title: BGC pel-1

city: Hong Kong

first: GAO

last: Ying

state: China

address: Hong Kong

department: Chemistry

institute: The university of Hong Kong

data_processing:
kneaddata v0.12.0; bowtie 2.3.5.1; featureCounts v1.6.2; DESeq2
Sequence reads were trimmed for adaptor sequence/low-quality sequence/rRNA sequence using kneaddata v0.12.0 (parameters: -db SILVA_128_LSUParc_SSUParc_ribosomal_RNA --trimmomatic-options ILLUMINACLIP:TruSeq3-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:60 --run-trim-repetitive --reorder --bowtie2-options '--very-sensitive --dovetail' --bypass-trf)
Trimmed sequence reads were mapped to GCF_010692905.1 using bowtie 2.3.5.1 (default parameters)
Read count extraction were performed using featureCounts v1.6.2 (parameters: -s 2 -p -B -C -t CDS -g gene_id)
Differential expression analysis was performed using DESeq2
Assembly: GCF_010692905.1
Supplementary files format and content: tab-delimited text file includes raw counts for each sample

organism: Haloferax volcanii

source_name: bacterial cell

growth_protocol: All the strains were cultured in Hv-Ca medium at 45 °C and 200 r.p.m for 20 hours

extract_protocol:
The experiment group of heterologous expression strain with the plasmid pTA 1228 harboring BGC pel in Hv-Ca medium was collected after 20 hours at 45 °C and 200 r.p.m.
The total RNA of all the samples was extracted using RNAprep Pure Cell/Bacteria Kit (Tiangen Biotech, Beijing, China)
RNA libraries were constructed using the Fast RNA-seq Lib Prep Kit V2 (ABclonal, Cat. RK20306)

tag: strain name

value: bacterial cell

tag: genetic modification

tag: time


title: BGC pel-3

tag: cell type


title: APAP-WT-Saline-r1

description:
RNA297
FPKM_anno.xlsx

tag: treatment


title: 3006 6-month


title: BGC cib2-3

extract_protocol:
The experiment group of heterologous expression strain with the plasmid pTA 1228 harboring BGC cib2 in Hv-Ca medium was collected after 20 hours at 45 °C and 200 r.p.m.
The total RNA of all the samples was extracted using RNAprep Pure Cell/Bacteria Kit (Tiangen Biotech, Beijing, China)
RNA libraries were constructed using the Fast RNA-seq Lib Prep Kit V2 (ABclonal, Cat. RK20306)


title: PFF1

value: Substantia nigra pars compacta (SNc)

value: dopaminergic neurons

value: heterozygous DAT-Cre


title: BGC pel-2


title: 3008 1-month

value: Female

value: Diabetic

value: Roux-en-Y gastric bypass surgery (RYGB)


title: APAP-Adipor2KO-Saline-r1

description:
RNA279
FPKM_anno.xlsx

value: Adipor2 knock-out


title: 3004 baseline

value: Control


title: APAP-Adipor2KO-Saline-r2

description:
RNA294
FPKM_anno.xlsx

value: Liver


title: Sample1_6hrs_HU

source_name: Patient1 with Polycythemia vera

value: HU treated


title: 3004 6-month


title: BGC cib2-2


title: 3003 6-month


title: Sample1_6hrs_CluIKK16

value: CLU and IKK-16 treated


title: APAP-Adipor2KO-Leo-r2

description:
RNA365
FPKM_anno.xlsx

value: APAP

value: Leo


title: BGC cib2-1


title: Sample1_6hrs_IKK16

value: Polycythemia vera

value: Peripheral blood

value: IKK-16 treated


title: Sample1_6hrs_Clu

value: Hematopoietic stem/progenitor cells

value: CLU treated


title: Control-3

extract_protocol:
The control group of the heterologous expression strain with empty plasmid pTA 1228 in Hv-Ca medium was collected after 20 hours at 45 °C and 200 r.p.m.
The total RNA of all the samples was extracted using RNAprep Pure Cell/Bacteria Kit (Tiangen Biotech, Beijing, China)
RNA libraries were constructed using the Fast RNA-seq Lib Prep Kit V2 (ABclonal, Cat. RK20306)

value: bacterial cell


title: APAP-WT-Leo-r2

description:
RNA300
FPKM_anno.xlsx

value: wild type


title: 3002 baseline

value: Female


title: APAP-Adipor2KO-Leo-r1

description:
RNA363
FPKM_anno.xlsx


title: Sample1_6hrs_control

value: Solvent control


title: Control-2


title: APAP-WT-Leo-r1

description:
RNA299
FPKM_anno.xlsx


title: Control-1


title: 3002 6-month

value: Roux-en-Y gastric bypass surgery (RYGB)


title: UW1211DNABLD

status: Public on Nov 08 2024

type: genomic

city: New Haven

first: Sameet

last: Mehta

state: CT

address: 300 Cedar St.

institute: Yale University

hyb_protocol: Bisulphite converted DNA was amplified, fragmented, and hybridized to human Infinium MethyEPIC BeadChip (Illumina standard protocol)

scan_protocol: Illumina’s iScan system according to the manufacturer’s protocol

data_processing:
Sesame package in R 4.3.1 environment
Average beta

label: Cy3 and Cy5

source_name: blood

label_protocol: According to manufacturer's protocol

growth_protocol: DNA from CSF cell pellets were extracted using the Qiagen AllPrep Micro kit (catalog # 80284), whereas RNA and DNA from PBMCs were extracted from the Qiagen AllPrep DNA/RNA/miRNA Universal Kit (catalog # 80224), both per manufacturer instructions.  Due to lower number of CSF cells, all CSF cells were used.  For PBMCs, 10 million cells were lysed in 700µL of RLT buffer, with half stored at a temperature of -80°C as backup.

extract_protocol: DNA was extracted from CSF cell pellet and from PBMC using the low yield nucleic acid extraction kit from Qiagen

value: blood

tag: timepoint

tag: subject

tag: disease

value: syphilis


title: UW1211DNACSF

source_name: csf

tag: tissue

value: csf


title: UW1210WK52CSFDNA

value: neurosyphilis

tag: group


title: UW1210WK12CSFDNA


title: UW1192DNABLD

tag: hiv


title: UW1210DNACSF


title: UW1192WK12CSFDNA


title: UW1210DNABLD


title: UW1188WK24CSFDNA


title: UW1192DNACSF


title: UW1200DNABLD


title: UW1200DNACSF


title: UW1188DNACSF


title: UW1188WK12CSFDNA


title: UW1184DNACSF


title: 3002 1-month

tag: Sex

tag: diabetes status

value: Control


title: 3001 baseline


title: 3003 1-month


title: UW1141DNABLD


title: UW1141DNACSF


title: UW1167DNABLD


title: UW1167DNACSF


title: 3001 6-month


title: UW1139DNACSF


title: 3003 baseline


title: UW1113WK52CSFDNA


title: 3001 1-month


title: UW1113WK12CSFDNA


title: UW1108WK52CSFDNA


title: UW1108DNACSFWK12


title: UW1122DNACSF


title: UW1108DNACSFWK24


title: UW1107DNACSF


title: UW1103DNACSFWK12


title: UW1105DNACSF


title: UW1105DNABLD


title: UW1108DNABLD


title: UW1107DNABLD


title: UW1108DNACSF


title: UW1122DNABLD


title: UW1103DNABLD


title: UW1042DNACSF


title: UW1042WK52CSFDNA


title: UW1113DNACSF


title: UW1042WK24CSFDNA


title: UW1042DNABLD


title: UW1100DNACSF


title: UW1042WK12CSFDNA


title: B78_DT_ADT

city: San Francisco

first: Bushra

last: Samad

state: CA

address: 505 Parnassus Ave

institute: USCF Immunoprofiler

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v4.0.0 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10

source_name: tumor

extract_protocol:
Tumors were sectioned while live using a compresstome (Precisionary Instruments VFZ-310-0Z) to generate ~160 μm sections.
The sectioning, imaging, spatial barcoding, tumor dissociation, sorting, 10X encapsulation and library construction were identical to the methods described in (Hu et al., 2020).

value: tumor


title: UW1036WK12CSFDNA


title: B78_DT_GEX


title: UW1036DNACSF


title: UW1103DNACSF


title: UW1008DNACSF


title: UW1008DNACSFWK12


title: Cuprizone Vehicle 8

city: Cambridge

first: Timothy

middle: R

last: Hammond

address: 350 Water Street

institute: Sanofi

data_processing:
Omicsoft Aligner 4 (OSA4); ArrayStudio_V10.1
Assembly: Mouse.B38 (GenCodeV19)
Supplementary files format and content: FPKM counts matrix

source_name: brain (corpus callosum)

extract_protocol:
Qiagen RNeasy Micro kit
TruSeq stranded mRNA library prep Kit

value: brain (corpus callosum)

value: Cuprizone Vehicle


title: Cuprizone Vehicle 6


title: Cuprizone Vehicle 4


title: Cuprizone Vehicle 7


title: UW999DNABLD


title: Cuprizone Vehicle 5


title: UW999DNACSF


title: Cuprizone Vehicle 3


title: UW989DNABLD


title: Cuprizone Vehicle 2


title: UW989DNACSF


title: Cuprizone Vehicle 1


title: UW962DNACSF


title: UW719DNABLD


title: Cuprizone BTKi 8

value: Cuprizone BTKi


title: UW719DNACSF


title: PDS_excision

city: Dallas

first: Jason

middle: C

last: Klein

state: TX

address: 5323 Harry Hines Blvd

institute: University of Texas Southwestern Medical Center

description: Additional raw read file sequenced with NextSeq2K, P3, 28 and 90bp reads

data_processing:
Reads from both sequencing runs were trimmed and analyzed together with Cell Ranger Multi v7.2.0
CellBender was performed with 5,000 expected cells, 15,000 droplets, and an fpr of 0.1.
Filtering and normalization was performed in Scanpy with python 3.10.
Samples were aggregated and batch corrected using Scanorama v1.7.4.
Assembly: Chromiium Flex Human Probe Panel
Supplementary files format and content: h5

source_name: Tumor

extract_protocol:
“Sample Preparation from FFPE Tissue Sections for Chromium Fixed RNA Profiling,” CG000632 Rev C
“Chromium Fixed RNA Profiling Reagent Kits For Singleplexed Samples,” CG000691 Rev A

value: Tumor


title: Cuprizone BTKi 6


title: Cuprizone BTKi 7


title: Cuprizone BTKi 5


title: Cuprizone BTKi 3


title: PDS1


title: PDS2


title: Cuprizone BTKi 2


title: UW1036DNABLD


title: UW1008DNABLD


title: Cuprizone BTKi 1


title: AFX2


title: AFX3


title: AFX1


title: Naive BTKi 2

value: Naive BTKi


title: Naive BTKi 4


title: IPIKID059.T2.rna.live

data_processing:
The remaining reads were aligned to the Ensembl GRCh38.85 transcriptome build using STAR
Assembly: GRCh38
Supplementary files format and content: FASTQ files

source_name: Primary tumor

extract_protocol:
The mRNA was isolated via DinaBead Direct, then converted into amplified
The dsDNA went through tagmentation, amplification and clean up with  AMPure XP beads steps, using the Illumina Nextera XT DNA Library Prep Kit. Quality control analysis was performed on the resulting pooled libraries with the Agilent Bioanalyzer HS DNA chip to assess fragment size distribution and concentration
RNAseq reads were first aligned to reference of rRNA and mitochondrial rRNA using BWA-mem

value: Primary tumor


title: Naive BTKi 3


title: Naive Vehicle 3

value: Naive Vehicle


title: IPIKID082.T1.rna.live


title: Naive Vehicle 4


title: IPILUNG057.T1.rna.live


title: IPIKID046.T1.rna.live


title: Cuprizone BTKi 4


title: IPIHNSC097.T1.rna.live


title: Naive Vehicle 1


title: IPIHNSC095.T1.rna.live


title: Naive Vehicle 2


title: IPIHNSC091.T1.rna.live


title: IPIHNSC093.T1.rna.live


title: BTKi EAE 3

data_processing:
cellranger-7.1.0
Assembly: mm10-2020-A
Supplementary files format and content: .h5 matrix files

source_name: lumbar spinal cord

extract_protocol:
10x Genomics Nuclei Isolation Kit
Chromium Next GEM Single Cell 3ʹ Reagent Kits v3.1 (Dual Index)

value: lumbar spinal cord

tag: strain


title: IPIHNSC081.T1.rna.live


title: BTKi EAE 2


title: BTKi EAE 4


title: BTKi EAE 5


title: IPIHNSC088.T1.rna.live


title: BTKi EAE 1


title: Naive BTKi 1


title: IPIHNSC080.T1.rna.live


title: Vehicle EAE 4


title: Vehicle EAE 3


title: IPIHNSC066.T1.rna.live


title: IPIGYN152.T1.rna.live


title: IPIGYN148.T1.rna.live


title: IPIGYN140.T1.rna.live


title: IPIGYN142.T1.rna.live


title: IPIGYN145.T1.rna.live


title: Vehicle EAE 1


title: BTKi naïve 3


title: Vehicle naïve 4


title: IPIGYN137.T1.rna.live


title: IPIGYN133.T1.rna.live


title: IPIGYN131.T1.rna.live


title: Vehicle naïve 3


title: Vehicle naïve 2


title: IPIGYN130.T1.rna.live


title: IPIGYN129.T1.rna.live


title: Vehicle naïve 1


title: cy_epi_d20_sr

city: Philadelphia

first: Andy

last: Minn

address: 421 Curie Blvd

institute: University of Pennsylvania

description: 10x scRNA-seq

data_processing:
CellRanger was used for demultiplexing cell barcodes and aligning reads.
Seurat and scDblFinder were used to perform quality control of the expression matrices and remove doublets, respectively.
Assembly: GRCm38
Supplementary files format and content: cell_anova.rds: Processed Seurat object contains in vivo experiment gene-by-cell count matrix, UMAP coordinates, and cell barcode metadata.

source_name: Small Intestine

extract_protocol:
Single cells were pooled and loaded onto a 10X Genomics Chromium controller for generation of 10X scRNA-seq libraries
scRNA-seq library preparation was performed following the Chromium Next GEM single-cell 3' v3.1 (dual index) kit (10x Genomics, #PN-100268)

value: Small Intestine

value: Small Intestine Epithelium

tag: genotype

value: Wildtype

value: SR


title: cy_lp_d20_sr

description: 10x scRNA-seq

value: Small Intestine Lamina Propria


title: IPIGYN123.T1.rna.live


title: cy_lp_d20_control

description: 10x scRNA-seq


title: Vehicle EAE 2


title: IPIGYN121.T1.rna.live


title: cy_epi_d20_control

description: 10x scRNA-seq


title: IPIGYN114.T1.rna.live


title: ll_epi_d10_sr

description: 10x scRNA-seq


title: cy_lp_d10_sr

description: 10x scRNA-seq


title: BTKi naïve 2


title: BTKi naïve 1


title: cy_epi_d10_sr

description: 10x scRNA-seq


title: IPIGYN111.T1.rna.live


title: IPIGYN112.T1.rna.live


title: cy_lp_d10_control

description: 10x scRNA-seq


title: IPIGYN090.T1.rna.live


title: cy_epi_d10_control

description: 10x scRNA-seq


title: IPIGYN072.T1.rna.live


title: ll_epi_d3_sr_2

description: 10x scRNA-seq


title: IPIGYN073.T1.rna.live


title: IPIGYN062.T1.rna.live


title: ll_epi_d3_control_2

description: 10x scRNA-seq


title: IPIGYN126.T1.rna.live


title: IPIGYN055.T1.rna.live


title: IPIGYN056.T1.rna.live


title: IPIGYN038.T1.rna.live


title: ll_epi_d3_control_1

description: 10x scRNA-seq


title: cy_lp_d2_sr

description: 10x scRNA-seq


title: cy_epi_d2_control

description: 10x scRNA-seq


title: IPIGYN120.T1.rna.live


title: cy_lp_d2_control

description: 10x scRNA-seq


title: IPIGYN037.T1.rna.live


title: IPIGYN030.T1.rna.live


title: IPIKID081.T1.rna.live


title: IPIGYN036.T1.rna.live


title: IPICRC125.T1.rna.live


title: IPIGYN024.T1.rna.live


title: IPICRC117.T1.rna.live


title: sample10; Mouse brain; PE-high; snRNAseq; replication 2

city: Houston

first: Li

last: Yang

address: 6565 Fannin Street

department: Department of System Medicine and Bioengineering (SMAB)

institute: METHODIST HOSPITAL RESEARCH INSTITUTE

description: 10X Genomics

data_processing:
Demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software (v7.1.0).
Assembly: mm10-2020-A
Supplementary files format and content: Tab-separated values files and matrix files (barcodes.tsv,  features.tsv, matrix.mtx).

molecule: nuclear RNA

source_name: Brain

extract_protocol:
Fresh mouse brains were cryopreserved using OCT and sectioned into slides. Nuclei were then isolated following the manufacturer's protocol using the 10X Genomics Chromium Nuclei Isolation Kit with RNase Inhibitor (1000494).
To prepare a cDNA library using the 10X Genomics Chromium Next GEM Single Cell 3' Kit v3.1 (1000269), the workflow typically involves the following key steps: Cell or Nuclei Preparation: Single cells or nuclei are partitioned into Gel Bead-In-Emulsions (GEMs) using the Chromium Controller. Each GEM contains unique molecular identifiers (UMIs) that label each cell’s RNA individually. Reverse Transcription: Within the GEMs, reverse transcription occurs, converting RNA to cDNA while incorporating the UMIs and barcodes that tag each transcript to its respective cell. cDNA Amplification: After GEM disruption, cDNA is purified and amplified via PCR to generate sufficient material for library construction. Library Construction: Amplified cDNA is fragmented, end-repaired, and ligated with Illumina sequencing adapters. Dual indexing can be applied if needed, enabling multiplexing during sequencing. Quality Control: The final libraries are quantified using tools like the Agilent Bioanalyzer or TapeStation and prepared for sequencing on an Illumina platform.

value: Brain

value: whole brain nuclei

value: PE-high EVs


title: sample8; Mouse brain; PE-high; snRNAseq; replication 1

description: 10X Genomics


title: ll_epi_d3_sr_1

description: 10x scRNA-seq


title: IPICRC111.T1.rna.live


title: sample4; Mouse brain; PE-low; snRNAseq; replication 2

description: 10X Genomics

value: PE-low EVs


title: WGBS4_3ppm_TP40-2_M_WT

city: Leuven

first: Lehua

last: Chen

address: Herestraat 49

country: Belgium

institute: KU Leuven

description:
3ppm_KOvsWT.dmrs.bed
WT_30vs3ppm.dmrs.bed
3ppm_KOvsWT_hyper.bed
3ppm_KOvsWT_hypo.bed
WT_30vs3ppm_hyper.bed
WT_30vs3ppm_hypo.bed

data_processing:
TrimGalore (v0.6.10) was used to trim reads based on quality (PHRED < 30) and to remove adapter sequences. Further, from both read 1 and read 2, 15 bp were trimmed from the 5’ end and 5 bp from the 3’ end. Only reads with a minimum length of 20 bp were kept. Using Bismark (v0.23.1), the trimmed reads were aligned to GENCODE mm10 GRCm38.p6 with a maximal insert size of 500 bp, followed by deduplication and methylation extraction. Using a custom script the CpG counts were merged to one strand. The DSS package was used, using a standard workflow, to call differentially methylated loci, which were used to find differentially methylated regions (DMRs). We kept DMRs with a minimal difference of 10% in methylation, that contained minimal 3 CpGs and had a minimal length of 100 bp. DMRs were annotated using AnnotatR (v1.16.0) and ChIPseeker (v1.26.2) packages in R (v4.0.5) using UCSC gene feature and CpG island (CpGi) locations. Genes were associated with DMRs using the rGREAT (v1.22.0) package. GO term enrichment was performed using Cluster Profiler (v3.18.1).
Assembly: mm10
Supplementary files format and content: .meth files of individual samples
Supplementary files format and content: .bam files of individual samples
Supplementary files format and content: bed file with DMRs
Supplementary files format and content: bed file with hyperDMRs
Supplementary files format and content: bed file with hypoDMRs

source_name: embryonic brain

extract_protocol:
Genomic DNA (gDNA) was extracted from embryonic brains using the Purelink Genomic DNA mini kit (Invitrogen, K182001) from individual E11.5 brains . DNA quality was assessed with NanoDdrop One (Thermo Fisher) , and absence of RNA contamination was confirmed with a 0.8% agarose gel stained with SYBR Safe.
400 ng of genomic DNA was sonicated on a Covaris LE220 with settings targeting an average size of 400 bp. Prior to bisulfite conversion, 0.5% unmethylated Lambda gDNA was spiked in and DNA quantification performed using Picogreen. 400 ng of sheared DNA was bisulfite converted with the Zymo EZ DNA Methylation Gold kit (cat# D5005, VWR) following the product manual. Estimating a 75% recovery rate, 50 ng of deaminated DNA was used for library prep with the IDT xGen™ Methyl-Seq DNA library prep kit (cat#10009824). Briefly, gDNA was heat-denatured and the single stranded DNA was used as template for proprietary adaptase stub tailing and adapter ligation prior to full-length adapter addition during the indexing PCR amplification of the library. Following product purification, the resulting libraries were quantitated by Picogreen and fragment size assessed with the Agilent 2100 Bioanalyzer. All samples were pooled equimolarly and re-quantitated by qPCR using the Applied Biosystems ViiA7 Quantitative PCR instrument and a KAPA Library Quant Kit (p/n KK4824). Using the concentration from the ViiA7™ qPCR machine above, 150 pM of equimolarly pooled library was loaded onto one lane of the NovaSeq S4 flowcell (Illumina p/n 20028312) following the XP Workflow protocol (Illumina kit p/n 20043131) and amplified by exclusion amplification onto a nanowell-designed, patterned flowcell using the Illumina NovaSeq 6000 sequencing instrument. PhiX Control v3 adapter-ligated library (Illumina p/n FC-110-3001) was spiked-in at 2% by weight to ensure balanced diversity and to monitor clustering and sequencing performance. A paired-end 150 bp cycle run was used to sequence an average of 400 million read pairs (~40X coverage) per sample.

value: embryonic brain

tag: cell line

value: 129S6.cg Tet1<tm1Koh>

value: E11.5 brain

value: WT


title: IPICRC106.T1.rna.live


title: IPICRC105.T1.rna.live


title: cy_epi_d2_sr

description: 10x scRNA-seq


title: WGBS2_30ppm_TP43-7_M_WT

description:
30ppm_KOvsWT.dmrs.bed
WT_30vs3ppm.dmrs.bed
30ppm_KOvsWT_hyper.bed
30ppm_KOvsWT_hypo.bed
WT_30vs3ppm_hyper.bed
WT_30vs3ppm_hypo.bed


title: WGBS3_3ppm_TP57-5_M_KO

description:
3ppm_KOvsWT.dmrs.bed
KO_30vs3ppm.dmrs.bed
3ppm_KOvsWT_hyper.bed
3ppm_KOvsWT_hypo.bed
KO_30vs3ppm_hyper.bed
KO_30vs3ppm_hypo.bed

value: KO


title: IPICRC101.T1.rna.live

value: Primary tumor


title: IPICRC103.T1.rna.live


title: IPICRC099.T1.rna.live


title: WGBS1_30ppm_TP38-6_M_KO

description:
30ppm_KOvsWT.dmrs.bed
KO_30vs3ppm.dmrs.bed
30ppm_KOvsWT_hyper.bed
30ppm_KOvsWT_hypo.bed
KO_30vs3ppm_hyper.bed
KO_30vs3ppm_hypo.bed


title: IPICRC096.T1.rna.live


title: ChIP_WT_d3_anti-H3K4me3_rep2

city: Freiburg im Breisgau

first: Sebastian

last: Arnold

address: Albertstraße 25

department: Institute of Experimental and Clinical Pharmacology and Toxicology

country: Germany

institute: University Freiburg

data_processing:
Low-quality reads and adapter reads were trimmed from raw data using Galaxy platform Trim Galore! (Galaxy Version 0.4.3.1).
ChIP-seq reads were mapped to the mm10 genome using Galaxy platform Bowtie2 (v2.3.4.3+galaxy0) with paired end settings.
PCR duplicates were removed using RmDup (v2.0.1) with default settings.
IGV track BigWig files were generated using bamCoverage (v3.3.2.0.0) with bin size 10 bases and normalization to RPKM, with paired-end extension of the fragments. BigWig files of biological duplicates were merged using bigwigCompare (v3.3.2.0.0) by computing the mean of the signal in the two files.
The enriched regions of EOMES ChIP were detected using MACS2 (v2.1.1.20160309.6) with pooled treatment files from two biological replicates using the BAMPE format as an input file and DSGInput BAM file (GSM3676129) as control with the following settings for the shifting model: confidence enrichment ratio against background 5-50; band width 300 and q-value of 0.01.
High confidence peak list for EOMES-ChIP was generated by filtering MACS2 output file peaks in tabular format for pileup values ≥25.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwig

source_name: A2lox.Cre mouse embryonic stem cells

growth_protocol: Mouse embryonic stem cells were maintained on mitotically inactivated STO feeder monolayer in 2i medium in humidified atmosphere with 5% CO2 at 37°C. 2i medium is composed of DMEM supplemented with 15% ESC-grade FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 1xNEAA, 1mM sodium pyruvate, 100µM β-mercaptethanol with 1000 U/ml LIF, 3 mM CHIR99021 and 1 mM PD0325901.

extract_protocol:
Embryoid bodies were harvested and singularized using trysine digest. Cells were fixed with 2mM DSG for 20 minutes and additional fixation with 1% MeOH-free formaldehyde for 10 minutes for EOMES and SMARCA4 (BRG1) and GFP ChIP-seq. A fixation with 1% MeOH-free formaldehyde for 9 min was performed for histone ChIP-seq experiments. After quenching and cell lysis using iDeal ChIP-seq kit for transcription factors (diagenode), chromatin was sonicated using a  Bioruptor Pico (diagenode). 20µg chromatin was incubated with anti-body coupled magnatic beads over night. Elution, decross-linking and DNA purification was performed after manufactures instruction.
ChIP-seq libraries were prepared with NEBNext Ultra II DNA Library Prep Kit for Illumina (NEB, E7645S). Libraries were amplified using 6-12 cycles on the thermocycler dependent on input amount and sample type. Post amplification libraries were size selected at 150-500bp in length using SPRIselect beads (Beckman Coulter). Libraries were validated using the Agilent High Sensitivity D1000 ScreenTape System.

treatment_protocol:
Embryoid Body formation was induced by culturing approximately 100.000 mESCs in 60 mm dishes under non-adhesive conditions in ESGRO Complete Basal medium  for total of 3.5 days. Mesoderm and endoderm differentiation was stimulated by treatment with human recombinant Activin A (30ng/ml) from day 2 onwards. Expression of EomesGFP from dKOEoGFP cells was induced by treatment with 5ug/ml doxyxycline from day 2 onwards. Nodal and WNT pathway is inhibited by treatment with 10 mM SB431542 (Tocris) and 2 uM XAV939 (Torcis) for 24h.
Expression of EomesGFP from dKOEoGFP cells or EomesER from dKOEoER cells was induced by treatment with 5µg/ml doxyxycline from day 2 onwards. Nodal and WNT pathway is inhibited by treatment with 10 µM SB431542 (Tocris) and 2 µM XAV939 (Torcis) for 24h. SMARCA4 activity is inhibited by treatement with BRM014 (10µM, Biozol). Polymerase II inhibition is induced by alpha-Amanitin (3µg/ml, Sigma-Aldrich) treatment for 18h from day 2.

value: A2lox.Cre mouse embryonic stem cells

value: embryonic stem cells

value: Activin A


title: ChIP_WT_d3_anti-H3K4me3_rep1


title: ChIP_WT_d3_anti-H3K4me1_rep1


title: ChIP_WT_d3_anti-H3K27ac_rep2


title: IPIKID128.T1.rna.myeloid


title: ChIP_WT_d3_anti-H3K27ac_rep1


title: IPILUNG049.T1.rna.myeloid


title: sample1; Mouse brain; PE-low; snRNAseq; replication 1

description: 10X Genomics


title: IPIKID127.T1.rna.myeloid


title: ChIP_WT_d3_anti-EO_rep2


title: ChIP_WT_d3_anti-H3K4me1_rep2


title: IPIKID126.T1.rna.myeloid


title: ChIP_WT_d3_anti-Brg1_rep1


title: IPIKID120.T1.rna.myeloid


title: ChIP_WT_d3_anti-Brg1_rep2


title: IPIKID123.T1.rna.myeloid


title: ChIP_WT_d2_anti-H3K4me3_rep1

value: no Treatment


title: ChIP_WT_d2_anti-H3K4me3_rep2


title: IPIKID116.T1.rna.myeloid


title: ChIP_WT_d2_anti-H3K4me1_rep2


title: IPIKID114.T1.rna.myeloid


title: IPIKID115.T1.rna.myeloid


title: IPIKID106.T3.rna.myeloid


title: ChIP_WT_d2_anti-H3K27ac_rep2


title: IPIKID106.T2.rna.myeloid


title: ChIP_WT_d2_anti-H3K27ac_rep1


title: IPIKID119.T1.rna.myeloid


title: IPIKID082.T1.rna.myeloid


title: ChIP_WT_d3_anti-EO_rep1


title: ChIP_dKOEoGFP_d3_nodox_ActA_anti-H3K27ac_rep2

value: dKOEoGFP


title: IPIKID048.T1.rna.myeloid


title: ChIP_WT_d2_anti-Brg1_rep4


title: ChIP_dKOEoGFP_d3_nodox_ActA_anti-H3K27ac_rep1


title: ChIP_WT_d2_anti-Brg1_rep3


title: IPIKID081.T1.rna.myeloid


title: IPIKID046.T1.rna.myeloid


title: IPIHNSC097.T1.rna.myeloid


title: ChIP_dKOEoGFP_d3_dox_SB_XAV_anti-H3K27ac_rep2

value: dox/SB/XAV


title: ChIP_dKOEoGFP_d3_dox_SB_XAV_anti-H3K27ac_rep1


title: IPIHNSC095.T1.rna.myeloid


title: IPIKID116.T2.rna.myeloid


title: ChIP_dKOEoGFP_d3_dox_BRM017_24h_anti-GFP_rep2

value: dox/Activin A/ BRM017


title: IPIHNSC094.T1.rna.myeloid


title: ChIP_WT_d2_anti-H3K4me1_rep1


title: ChIP_dKOEoGFP_d3_dox_BRM017_24h_anti-GFP_rep1


title: IPIHNSC093.T1.rna.myeloid


title: IPIHNSC091.T1.rna.myeloid


title: ChIP_dKOEoGFP_d3_dox_anti-Brg1_rep2

value: dox/Activin A


title: IPIHNSC090.T1.rna.myeloid


title: IPIHNSC088.T1.rna.myeloid


title: IPIHNSC081.T1.rna.myeloid


title: ChIP_dKOEoGFP_d3_dox_anti-Brg1_rep1


title: ChIP_dKOEoGFP_d3_dox_ActA_anti-H3K27ac_rep2


title: IPIHNSC066.T1.rna.myeloid


title: ChIP_dKOEoGFP_d3_dox_ActA_anti-H3K27ac_rep1


title: IPIHNSC056.T1.rna.myeloid


title: IPIHNSC080.T1.rna.myeloid


title: IPIGYN152.T1.rna.myeloid


title: ChIP_dKO_d3_anti-H3K4me3_rep2

value: dKO


title: ChIP_dKOEoGFP_d2_anti-H3K27ac_rep2


title: IPIHNSC030.T1.rna.myeloid


title: ChIP_dKO_d3_anti-H3K4me1_rep2


title: ChIP_dKO_d3_anti-H3K4me3_rep1


title: ChIP_dKO_d3_anti-H3K4me1_rep1


title: IPIGYN145.T1.rna.myeloid


title: IPIGYN140.T1.rna.myeloid


title: IPIGYN142.T1.rna.myeloid


title: ChIP_dKO_d3_anti-H3K27ac_rep2


title: ChIP_dKO_d3_anti-H3K27ac_rep1


title: ChIP_dKOEoGFP_d3_dox_BRM014_24h_anti-GFP_rep2

value: dox/Activin A/ BRM014


title: ChIP_dKOEoGFP_d3_dox_BRM014_24h_anti-GFP_rep1


title: IPIGYN139.T1.rna.myeloid


title: ChIP_dKO_d3_anti-Brg1_rep2


title: IPIGYN137.T1.rna.myeloid


title: ChIP_dKO_d3_anti-Brg1_rep1


title: IPIGYN136.T1.rna.myeloid


title: ChIP_dKOEoGFP_d2_anti-H3K27ac_rep1


title: RNAseq_WT_d3_rep3

data_processing:
Untrimmed FASTQ raw files were mapped into BAM using the Rsubread package (conda version 1.25.2) with the mm10 iGenomes FASTA/GTF reference/annotation files.
Differential expression analysis was performed using DESeq2 (v.18.1), with counts first normalized by library size and then by gene-wise dispersion.
A negative binomial generalized linear model fitting was performed using Wald statistics on the normalzied count data, and the results were filtered for the adjusted p < 0.05 and log2 FC>2
Assembly: GRCm38/mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

growth_protocol: Mouse embryonic stem cells were maintained on mitotically inactivated STO feeder monolayer in 2i medium in humidified atmosphere with 5% CO2 at 37°C. 2i medium is composed of DMEM supplemented with 15% ESC-grade FBS, 2mM L-Glutamine, 50U/ml Penicillin/Streptomycin, 1xNEAA, 1mM sodium pyruvate, 100µM β-mercaptethanol additioned with 1000 U/ml LIF and two inhibitors: 3 mM CHIR99021 and 1 mM PD0325901.

extract_protocol:
Total RNA was harvested using Rneasy mini plus kit (Qiagen) with on column DNAse digest.
Libraries were prepared from 10 ng of RNA with the Ovation SoLo RNA-seq Systems kit (NuGEN).

treatment_protocol:
Embryoid body formation was induced by culturing approximately 100.000 ESCs in 60 mm dishes under non-adhesive conditions in ESGRO Complete Basal medium  for total of up to 3.5 days. Mesoderm and endoderm differentiation was stimulated by treatment with human recombinant Activin A (30ng/ml) from day 2 onwards.
Expression of EomesGFP from dKOEoGFP cells or EomesER from dKOEoER cells was induced by treatment with 5µg/ml doxyxycline from day 2 onwards. Nodal and WNT pathway is inhibited by treatment with 10 µM SB431542 (Tocris) and 2 µM XAV939 (Torcis) for 24h. SMARCA4 activity is inhibited by treatement with BRM014 (10µM, Biozol). Polymerase II inhibition is induced by alpha-Amanitin (3µg/ml, Sigma-Aldrich) treatment for 18h from day 2.


title: RNAseq_WT_d3_rep2


title: IPIGYN148.T1.rna.myeloid


title: IPIGYN131.T1.rna.myeloid


title: RNAseq_WT_d3_rep1


title: IPIGYN130.T1.rna.myeloid


title: IPIGYN129.T1.rna.myeloid


title: RNAseq_WT_d3.5_rep3


title: RNAseq_WT_d3.5_rep2


title: RNAseq_WT_d3.5_rep4


title: IPIGYN126.T1.rna.myeloid


title: IPIGYN120.T1.rna.myeloid


title: IPIGYN121.T1.rna.myeloid


title: RNAseq_WT_d3.5_rep1


title: RNAseq_WT_d2_rep1


title: IPIGYN112.T1.rna.myeloid


title: RNAseq_WT_d2_rep2


title: RNAseq_WT_d2.5_rep4


title: RNAseq_WT_d2_rep3


title: IPIGYN114.T1.rna.myeloid


title: IPIGYN111.T1.rna.myeloid


title: IPIGYN134.T1.rna.myeloid


title: RNAseq_WT_d2.5_rep3


title: IPIGYN073.T1.rna.myeloid


title: IPIGYN133.T1.rna.myeloid


title: IPIGYN072.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_nodox_BRM017_24h_rep3

value: Activin A/BRM017


title: RNAseq_WT_d2.5_rep2


title: IPIGYN090.T1.rna.myeloid


title: IPIGYN062.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_nodox_BRM017_24h_rep1


title: IPIGYN123.T1.rna.myeloid


title: IPIGYN056.T1.rna.myeloid


title: RNAseq_WT_d2_rep4


title: IPIGYN038.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_nodox_BRM017_24h_rep2


title: IPIGYN055.T1.rna.myeloid


title: IPIGYN037.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_nodox_ActA_rep2


title: IPIGYN036.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_nodox_ActA_rep1


title: IPICRC125.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_dox_SB_XAV_rep3


title: RNAseq_WT_d2.5_rep1


title: RNAseq_dKOEoGFP_d3_dox_SB_XAV_rep2


title: RNAseq_dKOEoGFP_d3_dox_SB_XAV_rep1


title: IPIGYN030.T1.rna.myeloid


title: IPIGYN024.T1.rna.myeloid


title: IPICRC117.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_dox_BRM017_24h_rep3

value: dox/Activin A/BRM017


title: RNAseq_dKOEoGFP_d3_dox_BRM014_24h_rep3

value: dox/Activin A/BRM014


title: RNAseq_dKOEoGFP_d3_dox_BRM017_24h_rep1


title: IPICRC106.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_dox_BRM017_24h_rep2


title: IPICRC111.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_dox_BRM014_24h_rep2


title: IPICRC103.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_dox_ActA_rep3


title: RNAseq_dKOEoGFP_d3_dox_BRM014_24h_rep1


title: RNAseq_dKOEoGFP_d3_nodox_ActA_rep3


title: IPICRC101.T1.rna.myeloid


title: IPICRC096.T1.rna.myeloid


title: IPICRC099.T1.rna.myeloid


title: IPICRC035.T1.rna.myeloid


title: RNAseq_dKOEoGFP_d3_dox_ActA_rep2


title: RNAseq_dKOEoGFP_d3_dox_ActA_rep1


title: RNAseq_dKOEoGFP_d2_rep3


title: RNA_dKOEoER_C4_d2.75_dox_no4OHT_noAMA_rep3

value: dKOEoER


title: RNA_dKOEoER_C4_d2.75_dox_no4OHT_noAMA_rep2


title: RNAseq_dKOEoGFP_d2_rep2


title: RNAseq_dKOEoGFP_d2_rep1


title: RNA_dKOEoER_C4_d2.75_dox_4OHT_noAMA_rep3

value: dox/Activin A/4-Hydroxy-Tamoxifen


title: RNA_dKOEoER_C4_d2.75_dox_4OHT_noAMA_rep2


title: RNA_dKOEoER_C4_d2.75_dox_no4OHT_noAMA_rep1


title: RNA_dKOEoER_C4_d2.75_dox_4OHT_noAMA_rep1


title: RNA_dKOEoER_C4_d2.75_dox_4OHT_3ug_AMA_18h_rep2


title: IPICRC105.T1.rna.myeloid


title: RNA_dKOEoER_C4_d2.75_dox_4OHT_3ug_AMA_18h_rep1


title: RNAseq_dKO_d3_rep4


title: RNA_dKOEoER_C4_d2.75_dox_4OHT_3ug_AMA_18h_rep3


title: RNAseq_dKO_d3_rep3


title: RNAseq_dKO_d3_rep1


title: ATAC_WT_d3_rep2

data_processing:
Low-quality reads and adapter reads were trimmed from raw data using Galaxy platform Trim Galore! (Galaxy Version 0.4.3.1).
Sequencing reads were mapped to the mm10 genome using Galaxy platform Bowtie2 (v2.3.4.3+galaxy0) using paired end settings and duplicates were removed using RmDup (v2.0.1) with default settings.
IGV track BigWig files were generated using bamCoverage (v3.3.2.0.0) with bin size 10 bases and normalization to RPKM, with paired-end extension of the fragments. BigWig files of biological duplicates were merged using bigwigCompare (v3.3.2.0.0) by computing the mean of the signal in the two files.
Peak calling of accessible sites was performed using MACS2 (v2.1.1.20160309.6) with the following settings for the shifting model: confidence enrichment ratio against background 5-50; band width 300 and q-value of 0.01.
Assembly: GRCm38/mm10
Supplementary files format and content: bigwigs

extract_protocol:
The protocol was modified from Kaestner Lab, 2020.  After EB formation, cells were harvested and singularized using 0.05% Trypsine for a single cell suspension. Cells were washed with PBS and 50.000 cells were lysed in 50 µl ATAC-seq lysis buffer. Isolated nuclei were mixed with 50 µl of transposition reaction mix containing Tagment DNA Enzyme 1 (Nextra DNA Library Preparation Kit, Illumina). Samples were incubated at 37°C, 600 rpm for 30 min. Tagmented DNA was purified using the Qiagen MinElute Kit (Qiagen, 28004).
Eluted fragments were amplified by PCR with an appropriate number of PCR-cycles (5-8) using Custom Nextera PCR primer and the NEBNext High-Fidelity 2x PCR Master Mix (Nextera DNA Library Preparation Kit (New England BioLabs, E7530L)). Amplified DNA was purified using Qiagen MinElute Kit. A size-selection using SPRI select beads (Beckman, B23318) for fragments <1.000 following manufacture´s instruction. Size distribution of the libraries was determined with a BioAnalyzer 2100 (Agilent) using High sensitivity DNA Kit (Agilent, 5067-4626).

value: WT


title: ATAC_WT_d3.5_rep2


title: ATAC_WT_d2_rep1


title: ATAC_WT_d3.5_rep1


title: ATAC_WT_d2_rep2


title: ATAC_WT_d2.5_rep2


title: ATAC_WT_d2.5_rep1


title: Ctrl_2_S4

city: Bern

first: Nadia

last: Mercader

address: Baltzerstrasse 2

institute: University of Bern

data_processing:
FastQ files for each sample were obtained using cellranger mkfastq pipeline (10x Genomics).
For bioinformatics analysis we used the Mus musculus genome assembly v106 from Ensembl followed by cellranger pipeline.
Cell doublets info were removed using Scrublet algorithm
The counts were then processed using the Seurat pipeline (v4.0) in R
Assembly: Mus musculus genome assembly v106 from Ensembl
Supplementary files format and content: *barcodes.tsv, tab seprated values, barcode of the GEMs
Supplementary files format and content: *features.tsv, tab seprated values, features of 10x
Supplementary files format and content: *matrix.mtx, matrix, counts matrix

source_name: Heart

extract_protocol:
The cardiac tissue was homogenized and Ter119 antibody (BioLegend, 1:200) was used to exclude blood cells. After sorting, nuclei integrity was assessed on 5µl sample diluted 1:2 in Trypan blue and on the Countess III cell counter (Thermofisher). Each nuclei suspension was loaded into one port of a Chromium Next GEM Chip G (10x Genomics) with a target output of 10,000 nuclei.
Single nuclei were encapsulated into emulsion droplets using the Chromium Controller (10x Genomics). SnRNA-seq libraries were prepared using the Chromium Next GEM Single Cell 3' Kit v3.1 (10x Genomics) following the manufacturer instructions and each library was amplified using a SureCycler 8800 thermal cycler (Agilent Technologies). The average size of each library was then calculated using a High sensitivity DNA chip on a 2100 Bioanalyzer (Agilent Technologies) and the concentration was determined using the Qubit fluorometer (Thermofisher). Individual libraries were diluted to 10 nM and pooled for sequencing. Library pool was sequenced at 650 pM in paired-end reads (28bp Read1, 10bp Index1, 10 pb Index 2 and 90bp Read2) on a P3 flow cell (100 cycles) of the NextSeq 2000 (Illumina).

value: Heart


title: ATAC_dKOEoGFP_d3_nodox_BRM017_24h_rep2

value: A2lox.Cre mouse embryonic stem cells


title: CI_2_S2

description: Library pool was sequenced at 650 pM in paired-end reads (28bp Read1, 10bp Index1, 10 pb Index 2 and 90bp Read2) on a P3 flow cell (100 cycles) of the NextSeq 2000 (Illumina).


title: CI_1_S1


title: Ctrl_1_S3


title: ATAC_dKOEoGFP_d3_nodox_BRM017_24h_rep1

value: embryonic stem cells


title: Trifoliate_leaf3, replicate 3, sNucRNAseq

city: Tucson

first: Sergio Alan

last: Cervantes-Perez

state: Arizona

address: 1140 E South Campus Dr

department: School of Plant Sciences

institute: University of Arizona

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v6.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
The integration of the replicates and the processing of the data was generated in Seurat.
Assembly: Glycine_max_v2.1.52 From: http://ftp.ensemblgenomes.org/pub/plants/release-52/gtf/; http://ftp.ensemblgenomes.org/pub/plants/release-52/fasta/glycine_max/

organism: Glycine max

source_name: leaf

extract_protocol:
Tissues were chopped and passed through a 30µm cell strainer. The filtered nuclei were purified by cell sorting using FACSAria II™ cell sorter (BD Biosciences). An average of 80-100,000 nuclei were collected for each sample, centrifuged, and re-suspended in phosphate buffered saline-bovine serum albumin 0.5%-RNA-inhibitor solution.
Libraries were performed according to the manufacturer's instructions (single cell 3’ v2 protocol, 10x Genomics).

value: leaf

value: Williams 82


title: Chip-BRD3-KD-TYRO3

city: Tainan

first: Shaw-Jenq

last: Tsai

address: 1 , University Road

department: Department of Physiology, College of Medicine

country: Taiwan

institute: National Cheng Kung University

data_processing:
bcl2fastq version 2.19.1 (no lane splitting) software used for basecalling
ChIP-seq reads were aligned to the hg19 genome assembly using bwa     0.7.17     mem, -M with the following configurations…
peaks were called using CLC Workbanch 8.5.1 with the ChIP-Seq Analysis (legacy) setting: Windows size = 300, Filter peaks on read orientation = Yes
Genome_build: hg19
Supplementary_files_format_and_content: peak text files

source_name: Carcinoma; Colorectal

growth_protocol: HCT116 cells were routinely cultured in McCoy's medium supplemented with 10% FBS.

extract_protocol:
Lysates were clarified from sonicated nuclei and BRD3-DNA complexes were isolated with antibody. 10 ng of BRD3-DNA was used for the construction of sequencing.
DNA libraries were prepared for sequencing using the KAPA Hyper Prep Kit (KR0961 – v6.17, Kapa Biosystems)

treatment_protocol: ICD-TYRO3 or KD-TYRO3 were overexpressed in HCT116 cells

value: epithelial

tag: genotype/variation

value: kinase-dead TYRO3 overexpressing

tag: chip antibody

value: BRD3 (Proteintech-Cat# 11859-1-AP, RRID:AB_206)


title: Chip-BRD3-ICD-TYRO3

value: nuclear TYRO3 overexpressing


title: ATAC_dKOEoGFP_d3_nodox_ActA_rep2

value: dKOEoGFP

value: Activin A


title: ATAC_dKOEoGFP_d3_nodox_ActA_rep1


title: RNAseq_dKO_d3_rep2

value: dKO


title: ATAC_dKOEoGFP_d3_dox_SB_XAV_rep2

value: dox/SB/XAV


title: 012323-OJO001

city: New Orleans

first: Jovanny

last: Zabaleta

state: LA

address: 1700 Tulane Ave

department: Interdisciplinary Oncology

institute: LSUHSC

data_processing:
Bowtie 2.2.5 to remove contaminants (rDNA, tRNA, mtrDNA)
Aligned to STAR 2.7.8a
Quantification with RefSeq Transcripts 93
Filtered out features with <10 reads across all samples
TMM normalization
Differential expression with DESEQ2
Biological tissue samples were obtained from patients categorized overexpression and basal groups for ID1 and ID3 genes. Raw data underwent initial quality processing to remove low-quality reads and artifacts, followed by alignment to the reference genome using STAR. Data normalization was achieved using the Trimmed Mean of M-values (TMM) method to adjust for sequencing depth variations and technical biases among samples. Gene expression data were preprocessed to ensure quality, including normalization, filtering, and correction of undesired effects.
Assembly: hg38
Supplementary files format and content: txt files containing raw counts

source_name: Bome Marrow

extract_protocol:
The Allprep DNA/RNA Mini Kit (QIAGEN) was used for RNA isolation and the manufacturer's protocol was followed using the Qiacube. The extraction process was performed on LC (CD19+), non-leukemic cells (CD19-), and the whole cell population (cells without separation). RNA quantification was performed using Qubit™ RNA High Sensitivity and Nanodrop according to the manufacturer's protocols.
RNA obtained from the CD19 negative fraction of the samples was used to prepare the libraries. Libraries were generated using Illumina Stranded Total RNA prep with Ribo-Zero Plus library preparation kit according to manufacturer’s instructions. Briefly, ribosomal RNA was first depleted from total RNA (100 ng). Following purification, the RNA was fragmented, and first- and second-strand cDNA synthesized.  Libraries were created from the cDNA by first adenylating the 3′ end and ligating anchors to the ends. An amplification step of 13 cycles of PCR was then performed to add unique indexes to the ligated products. Resulting libraries were quantified using the Qubit dsDNA High Sensitivity Assay Kit and the size and purity assessed with the Agilent 2100 bioanalyzer. Sequencing was performed on Illumina’s NextSeq 2000 instrument using a NextSeq 2000 P2 200 cycles kit with pair-end 76 bp reads. FASTQ files were uploaded to Partek Flow for analysis, as follows: contaminants (rDNA, tRNA, mtDNA) were removed with Bowtie 2 (v2.2.5) and the reads aligned to hg38 with STAR v2.7.8a and quantified with RefSeq Transcripts 93.

value: Bome Marrow

tag: id1 expression_level

value: Basal

tag: id3 expression_level

tag: remission

value: yes

tag: relapse

tag: survival status

value: Death


title: 012323-MKH015

value: Overexpression

value: no

value: Alive


title: Trifoliate_leaf2, replicate 2, sNucRNAseq

value: leaf


title: 012323-FUM013


title: 012323-D-B017


title: 012323-B-R005


title: ATAC_WT_d3_rep1

value: A2lox.Cre mouse embryonic stem cells

tag: cell type

value: embryonic stem cells

value: WT

tag: treatment


title: 012323-AMM016

tag: tissue


title: ATAC_dKOEoGFP_d3_dox_BRM017_24h_rep2

value: dox/Activin A/BRM017


title: ATAC_dKOEoGFP_d3_dox_BRM017_24h_rep1


title: CMT2 with V1200R mutation in cc Line15 Rep1

city: St Louis

first: Xuehua

last: Zhong

state: MO

address: One Brookings Drive

department: Biology

institute: Washington University in St. Louis

data_processing:
Reads were filtered using fastp and then aligned to TAIR10 genome using HISAT2 (v.2.0.0-beta).
Transcripts were assembled using StringTie.
Quantification of gene expression and the identification of DEGs were performed with DESeq2.
Assembly: TAIR10

organism: Arabidopsis thaliana

source_name: whole seedling

growth_protocol: Seedlings were grown on 1/2 MS medium containing 1% sucrose for 10 days in long-day growth conditions (16 hrs light: 8 hours dark) at 22°C.

extract_protocol:
Total RNA was extracted using PureLink RNA Mini Kit and treated with Dnase I.
Library was constructed using a TruSeq RNA Library Preparation Kit (Illumina); messenger RNA was purified using RNA purification beads and fragmented by sonication using a Covaris S220 focused-ultrasonicator. One microgram of total RNA was reverse-transcried into cDNA with ProtoScript II. End-repair, 3'-end adenylation, ligation of adaptors and PCR amplification for 13 cycles were then performed.

value: whole seedling


title: CMT2 with V1200R mutation in cc Line15 Rep2


title: CMT2 with V1200R mutation in cc Line9 Rep1


title: ATAC_dKOEoGFP_d3_dox_BRM014_24h_rep2

value: dKOEoGFP

value: dox/Activin A/BRM014


title: CMT2 in cc Line19 Rep2


title: ATAC_dKOEoGFP_d3_dox_BRM014_24h_rep1


title: CMT2 in cc Line1 Rep1


title: CMT2 in cc Line1 Rep2


title: ATAC_dKOEoGFP_d3_dox_ActA_rep2

value: dox/Activin A


title: ATAC_dKOEoGFP_d3_dox_ActA_rep1


title: cmt2 cmt3 mutant Rep2


title: cmt2 cmt3 mutant Rep1


title: Col-0 Rep2


title: IPIKID125.T1.rna.myeloid

value: Primary tumor


title: Lhasa-0 accession of A. thaliana

data_processing:
For all samples in Col-0 background, sequencing raw reads were trimmed using FASTP and aligned to the Arabidopsis thaliana TAIR10 genome using bsmap version 2.9; allowing 4% mismatches, trimmed anything with a quality score of 33 or less, and removed any reads with more than five N's. Methylation at every cytosine was determined by bsmap's methratio.py script, processing only unique reads and removing duplicates. Differentially methylated regions (DMRs) were identified using methylKit with the cutoffs: 40% difference for CG, 20% for CHG and 10% difference for CHH DMRs, and a p-value <0.01.
For Lhasa-0 BS-seq, reads were filtered for < 5 N, quality trimmed (Phred score >= 30) and alignment was allowed proceed with up to 8% read mismatch. Methylation tracks were created by calling cytosine methylation in all contexts via the methratio.py script removing duplicated reads and including zeros. After alignment via BSMap, 100 bp DMRs were called against 54 wildtype high confidence Arabidopsis libraries via hcDMR caller, accepting only unique mappings and using the -Steve filter.
Assembly: TAIR10
Supplementary files format and content: bigwig file of DNA methylation

source_name: leaf tissue

growth_protocol: Seedlings were grown on 1/2 MS medium containing 1% sucrose for 10 days in long-day growth conditions (16 hrs light: 8 hours dark) at 22°C. For leaf tissues in Lhasa-0 sample, plants were grown 4 weeks in long-day growth conditions.

extract_protocol:
DNA was extracted using conventional CTAB method.
For bisulfite sequencing, the genomic DNA was fragmented to a mean size of 100-300 bp by sonication using a Covaris S220 focused-ultrasonicator, followed by end-repair, 3'-end adenylation and methylated adaptor ligation using Illumina TruSeq DNA kit. Then, bisulfite conversion was performed using a Zymo EZ DNA Methylation-Lightning kit, and the bisulfite-converted, adaptor-ligated DNA was enriched by PCR for 12 cycles using KAPA HiFi HotStart Uracil+ Kit, purified with Agencourt beads and quantified by Qubit HS dsDNA kit.

value: leaf tissue


title: Col-0 Rep1


title: ATAC_dKOEoGFP_d2_rep2

value: no Treatment


title: spleen DicerTG LCMV TrapR 50302

city: Prague

first: Filip

last: Horvat

address: Videnska 1083

country: Czech Republic

institute: Institute of Molecular Genetics of the ASCR

description: small RNA

data_processing:
Small RNA-seq reads were trimmed in two rounds using bbduk.sh version 38.87. First, NEXTflex adapter were trimmed from right end: bbduk.sh -Xmx20G threads=6 in=${FILE}.fastq.gz out=${FILE}.atrim.fastq.gz literal=TGGAATTCTCGGGTGCCAAGG stats=${FILE}.atrim.stats overwrite=t ktrim=r k=19 rcomp=f mink=10 hdist=1 minoverlap=8 Next, 4 random bases from both sides of reads were trimmed: bbduk.sh -Xmx20G threads=6 in=${FILE}.atrim.fastq.gz out=${FILE}.trimmed.fastq.gz stats=${FILE}.ftrim.stats overwrite=t forcetrimright2=4 forcetrimleft=4 minlength=18
The genome index was created by joining mouse genome .fasta file (GCA_000001635.2, mm10) with individual viral genomes (JN048469.1, NC_001479.1, NC_004291.1, NC_004294.1, U39292.1). Trimmed reads were mapped to such genome index with STAR version 2.7.10b with the following parameters: STAR --readFilesIn ${FILE}.fastq.gz --genomeDir ${GENOME_INDEX} --runThreadN 12 --genomeLoad LoadAndRemove --limitBAMsortRAM 20000000000 --readFilesCommand unpigz –c --outFileNamePrefix ${FILENAME} --outSAMtype BAM SortedByCoordinate --outReadsUnmapped Fastx --outFilterMismatchNoverLmax 0.1 --outFilterMatchNmin 16 --outFilterMatchNminOverLread 0 --outFilterScoreMinOverLread 0 --outFilterMultimapNmax 99999 --outFilterMultimapScoreRange 0 --alignIntronMax 1 --alignSJDBoverhangMin 999999999999
Genome browser coverage tracks in bigWig format were produced using bedtools v2.26.0 and wigToBigWig v4 from UCSC: genomeCoverageBed -ibam ${FILENAME}.bam -bg -split > ${FILENAME}.bedGraph wigToBigWig ${FILENAME}.bedGraph chrNameLength.txt ${FILENAME}.bw
Assembly: mm10
Supplementary files format and content: .bigWig
Supplementary files format and content: coverage genome browser tracks files: - bigWig format - generated in a non-stranded mode - not normalized for library size

source_name: spleen

extract_protocol:
Spleen collected from sacrificed animals were either directly used for analysis or stored at -80° C for later use. Mouse organs were washed with PBS, homogenized in Qiazol lysis reagent (Qiagen) and total RNA was isolated by Qiazol-chloroform extraction and ethanol precipitation method. Fresh Infected spleens (wahsed in PBS) were also used for isolation of RISC complexes by by Trans-kingdom, rapid, affordable Purification of RISCs (TrapR, Lexogen, Austria). RISC-associated small RNAs were extracted by a mixture of acidic phenol, chloroform and isoamylalcohol and precipitated by cold isopropanol. RISC-associated small RNAs were immediately used for small RNA library preparation.
After isolation, RNA quality was verified by electrophoresis on 1% agarose gel and RNA concentration was determined by Qubit Broad Range Assay (Invitrogen). Small RNA libraries were prepared using NEXTFLEX® Small RNA-Seq Kit v3 for Illumina (PerkinElmer) according to the manufacturer’s protocol; 3′ adapter ligation was performed overnight at 20 °C, 15 cycles were used for PCR amplification and gel purification was performed for size selection. For gel purification, libraries were separated on a 2.5% agarose gel using 1× lithium borate buffer and visualized with ethidium bromide. The 150–160 bp fraction was cut off the gel and DNA was isolated using the MinElute Gel Extraction Kit (Qiagen). Final libraries were sequenced by 75-nucleotide single-end reading using the Illumina NextSeq500/550 platform.

treatment_protocol: Viral infections LCMV: Viral stocks of LCMV, strains Armstrong (Arm) and Clone 13 (C13), were propagated in BHK-21 cells as described previously (49). These strains were obtained from Prof. Daniel Pinschewer (University Hospital Basel, Switzerland). The viral titer in aliquots were determined by LCMV Focus Forming Assay. Briefly, 3T3 cells were infected with different dilutions of the virus supernatant. Viral antigens were detected with rat anti-LCMV nucleoprotein antibody (Clone VL-4; BioXCell, Cat. N.: BE0106, Lot: 787521S1, diluted 1:500), and visualized by a color reaction using secondary goat anti-rat IgG HRP antibody (diluted 1:500) 48 h after infection.. For LCMV acute infection, each mouse was injected intraperitoneally 2x105 or 2.5x106 PFUs of LCMV Arm. At 3 dpi or 8 dpi, mice were euthanized by cervical dislocation and organ samples were collected for total RNA isolation. All used animals had the C57Bl/6 background. For LCMV chronic infection, each mouse was injected intraperitoneally 106 PFUs of LCMV C13. At 30 dpi, mice were euthanized by cervical dislocation and organ samples were collected for total RNA isolation.

value: spleen

value: Dicertg(O-HA)/tg(O-HA)

value: LCMV infected

tag: age

value: adult (12 weeks)

tag: experiment year_month


title: spleen DicerTG LCMV TrapR 50041

description: small RNA


title: ATAC_dKOEoGFP_d3_dox_SB_XAV_rep1

value: dox/SB/XAV


title: spleen WT LCMV TrapR 50070

description: small RNA

value: Dicerwt/wt


title: ATAC_dKOEoER_C4_d2.75_dox_no4OHT_noAMA_rep2

value: A2lox.Cre mouse embryonic stem cells

value: dKOEoER


title: CMT2 with V1200R mutation in cc Line9 Rep2


title: ATAC_dKOEoGFP_d2_rep1

value: embryonic stem cells


title: spleen WT LCMV TrapR 50069

description: small RNA


title: spleen DicerTG LCMV Qiazol 50041

description: small RNA


title: spleen WT LCMV Qiazol 50069

description: small RNA


title: ATAC_dKOEoER_C4_d2.75_dox_4OHT_noAMA_rep2

value: dox/Activin A/4-Hydroxy-Tamoxifen


title: ATAC_dKOEoER_C4_d2.75_dox_4OHT_noAMA_rep1


title: spleen WT LCMV Qiazol 50070

description: small RNA


title: CMT2 in cc Line19 Rep1

value: whole seedling


title: Wells Syndrome 001

city: Lausanne

first: JEREMY

last: DI DOMIZIO

state: Vaud

address: Av Boveresses 155, 1066 Epalinges

institute: CHUV

description:
internal positive and negative controls were used
WELL_001

hyb_protocol: standard protocol

scan_protocol: standard protocol

data_processing: Data were normalized and log2 transformed using nSolver® 4.0 (Nanostring Technologies). Basically, housekeeping probes to be used for normalization are selected based on the geNorm algorithm as implemented in the NormqPCR R library

label: NanoString indexing

source_name: skin biopsy

label_protocol: NanoString indexing

extract_protocol: mRNA expression of 600 targets was analysed with the nCounter Human Immunology V2 panel including 20 customized probes (Nanostring Technologies, Seattle, WA, USA) on the nCounter® platform (Nanostring Technologies) using 100 ng of RNA per skin sample.

treatment_protocol: samples were snap-frozen without any treatment

tag: disease

value: Wells Syndrome


title: ATAC_dKOEoER_C4_d2.75_dox_no4OHT_noAMA_rep1


title: Wells Syndrome 003

description:
internal positive and negative controls were used
WELL_003


title: Unclear Rash 020

description:
internal positive and negative controls were used
UR_020

value: Unclear Rash


title: Wells Syndrome 002

description:
internal positive and negative controls were used
WELL_002


title: ATAC_dKOEoER_C4_d2.75_dox_4OHT_3ug_AMA_18h_rep2


title: Unclear Rash 019

description:
internal positive and negative controls were used
UR_019


title: Unclear Rash 017

description:
internal positive and negative controls were used
UR_017


title: ATAC_dKOEoER_C4_d2.75_dox_4OHT_3ug_AMA_18h_rep1


title: Unclear Rash 018

description:
internal positive and negative controls were used
UR_018


title: spleen DicerTG LCMV Qiazol 50302

description: small RNA


title: Unclear Rash 016

description:
internal positive and negative controls were used
UR_016


title: Unclear Rash 015

description:
internal positive and negative controls were used
UR_015


title: Unclear Rash 013

description:
internal positive and negative controls were used
UR_013


title: ATAC_dKO_d3_rep1

value: dKO

value: Activin A


title: IPIGYN037.T1.rna.tcell

value: Primary tumor


title: AL8810, TCR

city: New York

first: Amaia

last: Lujambio

state: New York

address: 1470 Madison Avenue

institute: Icahn School of Medicine at Mount Sinai

description:
10x Genomics
srt_obj.rds

data_processing:
Raw features by cells matrices were generated with CellRanger > v.5.0.1
Assembly: mm10
Supplementary files format and content: seurat objects including raw count matrices, represents all data (15 total samples RNA(15) + TCR(15))
Supplementary files format and content: contig files of TCR-seq

source_name: Hepatocellular carcinoma

extract_protocol:
Mice were sacrificed and then the liver was perfused with PBS+EDTA 2mM through the inferior cava vein. Individual tumor nodules were visually inspected and selected to avoid healthy adjacent tissue and normalize for both size and level of expected necrosis across all samples. The selected tumor was then extracted from the liver using a sterile scalpel, weighed, and manually minced with sterile instruments. Minced tumor nodules were then enzymatically digested with 2.5mL enzymatic digestion mix (Miltenyi Biotech,Tumor dissociation Kit) in DMEM medium in a gentleMACS C Tube (Miltenyi Biotech) and then placed on gentleMACS Octo Dissociator (Miltenyi Biotech) for enzymatic and further mechanical dissociation with the “37°C_m_TDK1” program. Lysates were strained through a 70-µm cell strainer (Miltenyi) and resultant single cells were pelleted at 300g for 5 min at 4°C. From this point onward, cells were kept at 4°C. Elimination of red blood cells using “Red blood cell lysis solution” (Miltenyi Biotech) for 2 min on ice followed by elimination of dead cells using the “Dead Cell Removal” kit (Miltenyi Biotech) was performed according to manufacturer protocols. CD45 positive cells (immune cells) were separated from CD45 negative cells (tumor and non-immune stromal cells) using the CD45 microbeads mouse kit (Miltenyi Biotech) and each fractions were counted manually using a hemacytometer, then recombined at 1:1 ratio. This step was performed to ensure sufficient numbers of immune cells were sequenced from the bulk tumor samples. Only samples with a viability >80% were used.
Single-cell RNA sequencing (scRNA-seq) sample processing was immediately performed after cell extraction/isolation by the HIMC core facility at the Icahn School of Medicine at Mount Sinai. Two single-cell suspensions were counted (Nexcelom Cellometer Auto 2000) and each loaded on one lane of the 10x Genomics NextGem 5’v2.0 assay as per the manufacturer’s protocol with a targeted cell recovery of 10,000 cells per lane. Gene expression (5’Gex) and TCR libraries were generated as per the 10x Genomics demonstrated protocol (https://assets.ctfassets.net/an68im79xiti/57JaTECQNBPSpyDz8 oucdi/ced6aa8eaf73d6ee18dea8fdbd945faa/CG000331_Chromium_Next_GEM_Single_Cell_5-v2_UserGuide_RevD.pdf). All libraries were quantified via Agilent Technologies 4200 Tapestation and KAPA library quantification kit (Roche). Gene expression libraries were sequenced at a targeted depth of 25,000 reads per cell and TCR libraries at a targeted read depth of 5,000 reads per cell. Libraries were sequenced on the Illumina NovaSeq S2 100 cycle kit with run parameters set to 26x10x10x90 (R1xi7xi5xR2).

value: Hepatocellular carcinoma

tag: Sex

value: M

value: MycLucOS, NICD

tag: library type

value: TCR


title: Unclear Rash 012

description:
internal positive and negative controls were used
UR_012


title: Unclear Rash 014

description:
internal positive and negative controls were used
UR_014


title: Unclear Rash 011

description:
internal positive and negative controls were used
UR_011


title: Unclear Rash 009

description:
internal positive and negative controls were used
UR_009


title: AL8809, TCR

description:
10x Genomics
srt_obj.rds

tag: genotype


title: Unclear Rash 008

description:
internal positive and negative controls were used
UR_008


title: Unclear Rash 010

description:
internal positive and negative controls were used
UR_010


title: Unclear Rash 006

description:
internal positive and negative controls were used
UR_006


title: Unclear Rash 007

description:
internal positive and negative controls were used
UR_007


title: AL7361-T2, TCR

description:
10x Genomics
srt_obj.rds

value: F

value: MycLucOS, sgp53


title: Unclear Rash 004

description:
internal positive and negative controls were used
UR_004


title: AL7361-T1, TCR

description:
10x Genomics
srt_obj.rds


title: Unclear Rash 005

description:
internal positive and negative controls were used
UR_005


title: AL7317, TCR

description:
10x Genomics
srt_obj.rds

value: MycLuc, sgp53


title: Unclear Rash 002

description:
internal positive and negative controls were used
UR_002


title: Unclear Rash 003

description:
internal positive and negative controls were used
UR_003


title: Unclear Rash 001

description:
internal positive and negative controls were used
UR_001


title: ATAC_dKO_d3_rep2

tag: cell line

value: A2lox.Cre mouse embryonic stem cells


title: Sweet's syndrome 002

description:
internal positive and negative controls were used
SW_002

value: Sweet's syndrome


title: AL7316, TCR

description:
10x Genomics
srt_obj.rds


title: Psoriasis 055

description:
internal positive and negative controls were used
PsO_055

value: Psoriasis


title: Psoriasis 054

description:
internal positive and negative controls were used
PsO_054


title: AL7312, TCR

description:
10x Genomics
srt_obj.rds


title: Psoriasis 052

description:
internal positive and negative controls were used
PsO_052


title: AL7282, TCR

description:
10x Genomics
srt_obj.rds

value: MycLuc, NICD


title: Psoriasis 051

description:
internal positive and negative controls were used
PsO_051


title: Psoriasis 049

description:
internal positive and negative controls were used
PsO_049


title: AL7244, TCR

description:
10x Genomics
srt_obj.rds

value: MycLucNICD


title: Psoriasis 048

description:
internal positive and negative controls were used
PsO_048


title: AL7228, TCR

description:
10x Genomics
srt_obj.rds


title: Psoriasis 050

description:
internal positive and negative controls were used
PsO_050


title: AL7246, TCR

description:
10x Genomics
srt_obj.rds


title: BTKi 3, triculture

data_processing:
Quantification was performed at gene level to obtain count-level information using the Expectation-Maximization (EM) algorithm54. Differential expression. Analysis was performed using DESeq2 (version 1.30.1) in RStudio (R 4.0.2).
Assembly: Human B38 reference genome, GenCode.V24
Supplementary files format and content: Normalized counts matrix

source_name: iPSC-derived neurons, astrocytes, and neurons

extract_protocol:
RLT buffer (Qiagen)
Illumina Stranded mRNA Prep Ligation

value: BTKi


title: AL7305, TCR

description:
10x Genomics
srt_obj.rds


title: AL7232, TCR

description:
10x Genomics
srt_obj.rds


title: Psoriasis 045

description:
internal positive and negative controls were used
PsO_045


title: Psoriasis 044

description:
internal positive and negative controls were used
PsO_044


title: Psoriasis 046

description:
internal positive and negative controls were used
PsO_046


title: AL7122, TCR

description:
10x Genomics
srt_obj.rds


title: BTKi 2, triculture

value: iPSC-derived neurons, astrocytes, and neurons


title: Psoriasis 043

description:
internal positive and negative controls were used
PsO_043


title: Sweet's syndrome 001

description:
internal positive and negative controls were used
SW_001


title: AL7237, TCR

description:
10x Genomics
srt_obj.rds


title: Psoriasis 042

description:
internal positive and negative controls were used
PsO_042


title: BTKi 1, triculture


title: Psoriasis 041

description:
internal positive and negative controls were used
PsO_041


title: Psoriasis 039

description:
internal positive and negative controls were used
PsO_039


title: AL8810, GEX

description:
10x Genomics
srt_obj.rds

value: GEX


title: Psoriasis 053

description:
internal positive and negative controls were used
PsO_053


title: AL8809, GEX

description:
10x Genomics
srt_obj.rds


title: IgG + BTKi 2, triculture

value: IgG + BTKi


title: Psoriasis 038

description:
internal positive and negative controls were used
PsO_038


title: Psoriasis 037

description:
internal positive and negative controls were used
PsO_037


title: Psoriasis 047

description:
internal positive and negative controls were used
PsO_047


title: Psoriasis 036

description:
internal positive and negative controls were used
PsO_036


title: AL7361-T2, GEX

description:
10x Genomics
srt_obj.rds


title: Psoriasis 035

description:
internal positive and negative controls were used
PsO_035


title: IgG 3, triculture

value: IgG+Vehicle


title: Psoriasis 033

description:
internal positive and negative controls were used
PsO_033


title: Psoriasis 034

description:
internal positive and negative controls were used
PsO_034


title: IgG + BTKi 1, triculture


title: AL7361-T1, GEX

description:
10x Genomics
srt_obj.rds

value: Hepatocellular carcinoma


title: Psoriasis 032

description:
internal positive and negative controls were used
PsO_032


title: IgG 2, triculture


title: IgG 1, triculture


title: AL7305, GEX

description:
10x Genomics
srt_obj.rds


title: IgG + BTKi 3, triculture


title: Psoriasis 029

description:
internal positive and negative controls were used
PsO_029


title: Psoriasis 028

description:
internal positive and negative controls were used
PsO_028


title: Psoriasis 027

description:
internal positive and negative controls were used
PsO_027


title: Psoriasis 031

description:
internal positive and negative controls were used
PsO_031


title: Psoriasis 040

description:
internal positive and negative controls were used
PsO_040


title: AL7316, GEX

description:
10x Genomics
srt_obj.rds


title: Vehicle 3, triculture

value: Vehicle


title: Vehicle 2, triculture


title: Psoriasis 026

description:
internal positive and negative controls were used
PsO_026


title: Psoriasis 025

description:
internal positive and negative controls were used
PsO_025


title: AL7282, GEX

description:
10x Genomics
srt_obj.rds


title: Vehicle 1, triculture


title: AL7312, GEX

description:
10x Genomics
srt_obj.rds


title: Psoriasis 024

description:
internal positive and negative controls were used
PsO_024


title: Psoriasis 023

description:
internal positive and negative controls were used
PsO_023


title: IgG + BTKi 4

data_processing:
Quantification was performed at gene level to obtain count-level information using the Expectation-Maximization (EM) algorithm54. Differential expression. Analysis was performed using DESeq2 (version 1.30.1) in RStudio (R 4.0.2).
Assembly: Human B38 reference genome, GenCode.V24
Supplementary files format and content: Counts matrix

source_name: iPSC-derived microglia

value: iPSC-derived microglia


title: Psoriasis 022

description:
internal positive and negative controls were used
PsO_022


title: AL7244, GEX

description:
10x Genomics
srt_obj.rds


title: 6M2DZ

city: Newark

last: Weinstein

state: NJ

address: New Jersey Medical School Cancer Center 205 South Orange Ave

department: Center for Immunity and Inflmmation

institute: Rutgers New Jersey Medical School

description: 6M DZ2

data_processing:
Base calling (bcl2fastq v2.20.0.422)
QC (FASTQC v0.11.8, Picard v2.21.1, Samtools v1.9, Preseq v2.0.3, RseQC v3.0.1, edgeR v3.26.5, Qualimap v2.2.2-dev)
Trimming and Alignment (Cutadapt v2.5, STAR vSTAR_2.6.1.d)
Counting hit counts and transcripts (featureCounts v1.6.4, StringTie v2.0)
Differential gene expression (DESeq2 v1.22.1)
Assembly: Genome_build: GRCm38
Supplementary files format and content: Comma delimited file (csv) for differential gene expression counts via DESeq2.

source_name: Spleen

extract_protocol:
RNA was extracted using the RNAeasy plus mini kit (Qiagen)
Paired end strand-specific RNA libraries were prepared for sequencing using standard Illumina protocols at Genewiz.

value: Spleen


title: IgG + BTKi 3


title: Psoriasis 030

description:
internal positive and negative controls were used
PsO_030


title: Psoriasis 021

description:
internal positive and negative controls were used
PsO_021


title: AL7317, GEX

description:
10x Genomics
srt_obj.rds

value: F


title: AL7228, GEX

description:
10x Genomics
srt_obj.rds

value: MycLucOS, NICD


title: IgG + BTKi 2


title: Psoriasis 020

description:
internal positive and negative controls were used
PsO_020


title: 6M1DZ

description: 6M DZ1


title: AL7246, GEX

description:
10x Genomics
srt_obj.rds


title: Psoriasis 019

description:
internal positive and negative controls were used
PsO_019