title: Liver_TAA, AGO2, Abcom

city: chengdu

first: shuaijie

last: qian

state: sichuan

address: NO. 1, 4th Keyuan Road, Chengdu,

institute: West China Hospital, Sichuan University

data_processing:
Paired-end reads were harvested from Illumina HiSeq 4000 sequencer, and were quality controlled by Q30. After 3’ adaptor-trimming and low quality reads removing by cutadapt software (v1.9.3). The high quality trimmed reads were used to analyse circRNAs, LncRNAs and mRNAs.
The high quality reads were aligned to the reference genome/transcriptome with STAR software (v2.5.1b) and circRNAs were detected and identified with DCC software (v0.4.4). edgeR software (v3.16.5) was used to normalized the data and perform differentially expressed circRNA analysis.
Assembly: mm10
Supplementary files format and content: Matrix table with circRNA reads for each sample

extract_protocol:
RNA extracted using Trizol by following manufacturer’s instruction (Invitrogen)
rRNAs were removed from the immunoprecipitated RNA and input RNA samples by using Ribo-Zero™ rRNA Removal Kit (Illumina, San Diego, CA,  USA). RNA libraries were constructed by using rRNA-depleted RNAs with TruSeq Stranded Total RNA Library Prep Kit (Illumina, San Diego, CA,  USA) according to the manufacturer’s instructions. Libraries were controlled for quality and quantified using  the BioAnalyzer 2100 system (Agilent Technologies, Inc., USA).

value: Liver

tag: rip antibody

value: Argonaute-2 (Abcam, #ab186733)

value: 8-week thioacetamide i.p.


title: Patient 8 Slide B369 ROI 050

status: Public on Jun 28 2023

type: RNA

city: Seattle

first: Rich

middle: A

last: Klinghoffer

state: WA

address: 530 Fairview Ave N

country: USA

institute: Presage Biosciences

scan_protocol: Nanostring GeoMx Digital Spatial Profiling (DSP) Platform

data_processing: Raw probe level counts from the NanoString DSP machine were subjected to QC and normalization as follows. ROIs with deduplicated read counts of <10,000 were excluded. Count data was then normalized using TMM normalization(26) prior to performing limma analysis

molecule: total RNA

organism: Homo sapiens

source_name: head and neck carcinoma

label_protocol: Nanostring

extract_protocol: Tissue sections were baked, deparaffinized, washed in PBS, and targets were retrieved for 20 minutes in 1x Tris-EDTA pH 9.0 buffer (Invitrogen #00-4956-58) at 100 °C. Next, tissues were washed in PBS, incubated in 0.1 μg/ml proteinase K (Thermo Fisher Scientific, #AM2546) in PBS for 15 minutes at 37 °C and washed again in PBS. Protein targets were post-fixed in 10% neutral-buffered formalin for 5 minutes, followed by two 5-minute incubations in 12.25 mg/ml Tris base, 7.5 mg/ml Glycine stop buffer diluted in DEPC-treated water. Tissues were incubated overnight at 37 °C with hybridization solution (Human Cancer Transcriptome Atlas probe mix (NanoString #121400101), Buffer R (NanoString #121300313), and DEPC-treated water). During incubation, slides were covered with HybriSlip hybridization covers (Grace BioLabs #714022). After incubation, HybriSlip covers were gently removed by soaking in 2x SSC buffer. Two 25 minute stringent washes were performed using 50% formamide in 2x SSC at 37 °C. Tissues were washed for 5 minutes in 2× SSC and incubated in blocking buffer W (NanoString #121300313) for 30 minutes at room temperature in a humidity chamber. Primary antibody targeted against MIL113 was diluted in buffer W and incubated with the tissues for 1 hour followed by a 1 hour incubation with fluorescently-labeled secondary antibody diluted in buffer W. After the slides were washed twice for 5 minutes in 5x SSC buffer they were incubated for 1 hour in SYTO13 (50 nM) and fluorescently conjugated antibody targeting PanCK in blocking  8  buffer. Following staining the sections were washed for 5 minutes in fresh 2x SSC. Following whole slide imaging, multiple geometric ROIs of 400 μm2 were placed in regions of subasumstat drug exposure according to MIL113 signal intensity and regions of vehicle or background. Indexing oligonucleotides were then cleaved and quantified via next gen sequencing on a NovaSeq 6000 Illumina sequencer as previously described(25)

tag: tissue

value: head and neck carcinoma

tag: gender

value: Male

tag: anatomical location

value: Right parotid

tag: age

tag: tumor level

tag: treatment

value: Vehicle

value: negative


title: Patient 8 Slide B369 ROI 055

value: low


title: Patient 8 Slide B369 ROI 057


title: Patient 8 Slide B369 ROI 049


title: Patient 8 Slide B369 ROI 062

value: high


title: Patient 8 Slide C19 ROI 016

value: med


title: Liver_TAA, IgG, Abcom

type: SRA

country: China

library_source: transcriptomic

organism: Mus musculus

source_name: Liver

value: IgG (Abcam, #ab172730)


title: Patient 8 Slide B369 ROI 056


title: Patient 8 Slide B369 ROI 047


title: Cxcl13-Td+ stromal LNs cells from mice injected with 1 antigen-immunocomplex for 24 hours [CXCL13ICPE24h]

city: London

first: Pavel

last: Tolar

address: Institute of Immunity and Transplantation, Rowland Hill St

country: United Kingdom

institute: University College London

data_processing:
10X’s Cell Ranger software was used to de-multiplex Illumina BCL output, create fastq files and generate single cell feature counts for each library.
Assembly: GRCm38/mm10
Supplementary files format and content: Raw read count matrix for each sample in form of the Cell Ranger matrix, features and barcodes files.

source_name: FACS sorted Live/Death- Podoplanin+ CD31- CD45- CXCL13-TdTomato+

growth_protocol: LNs from immunised mice for 24h or 7 days were obtained after Schedule1.

extract_protocol:
LNs were dissociated to single cells by enzymatic treatment (0.4 mg/mL Collagenase D (Roche), 0.6 mg/mL Dispase II (Roche), 40 μg/mL DNase I (Roche)) for about 30-45 minutes at 37ºC. Cells were pelleted an stained for stromal, hematopoietic and endothelial markers and sorted using FACS Aria III and Fusion.
RNA libraries were prepared for sequencing using Chromium Single Cell 3' v3 protocol.

treatment_protocol: Tissue was digested with collagenase and DnaseI at single-cell level, stained form stromal, hematopoietic and endothelial markers and separated by FACS analysis based on surface markers expression.

tag: strain

tag: genotype

value: Injection with antigen-immunocomplex

tag: cell type

value: Cxcl13+ LN stromal cells


title: Patient 8 Slide B369 ROI 048


title: Patient 8 Slide B369 ROI 059


title: Patient 8 Slide B369 ROI 045


title: Cxcl13-Td+ stromal LNs cells from mice injected with 2 antigen-immunocomplex, for 7 days and 24 hours [Biotin24h]


title: XME1

city: Tianjin China

first: Miner

last: Xie

address: No.288, Nanjing Road

institute: State Key Laboratory of Experimental Hematology

data_processing:
Raw sequencing reads were demultiplexed and assigned to each single cell according to the unique barcode sequences pooled in sequencing libraries.
We next trimmed polyA tails, artificial sequences introduced during sequencing library construction, including TSO and UMI, and low quality bases from the 5’ prime or 3’ prime of each paired reads
Sequencing reads that passed quality control were aligned to the mouse reference genome (genome version: mm10) by using Tophat with default settings (version 2.0.12).
HTSeq package was used to summarize the uniquely aligned reads for each gene and duplicated transcripts were removed referring to UMI sequences. The number of transcripts for each gene was calculated as the number of different UMIs aligned.
Low quality cells were further removed based on the number of genes and transcripts detected in each cell referring to Scater R package.
We also removed genes with low expression abundance across all cells as described in Scater package.
Gene expression level was normalized as log2 (TPM/10 + 1), in which TPM is short for Transcripts per million and adding one is to avoid negative expression values.
Genome_build: mm10
Supplementary_files_format_and_content: tab-delimited text files include count values for each single cells.

growth_protocol: Single HSC1 (CD201+CD150+CD48-CD41-CD34-LSK) cells were cultured in serum-free media supplemented with 50ng/ml recombinant murine SCF, 50 ng/ml recombinant murine SCF plus 10 ng/ml recombinant human G-CSF, or 50 ng/ml recombinant murine SCF plus 50 ng/ml recombinant murine TPO for 7 days.

extract_protocol:
Single cells were picked up by micromanipulator and were placed directly into cell lysis buffer. The reverse transcription and template switch steps were then performed following the modified Smart-seq2* protocol. Amplified cDNA was sonicated to ~300-base-pair (bp) fragments by the Covaris S2 system. The 3' ends of the transcripts are enriched by Dynabeads Myone streptavidin C1 beads (invitrogen) after biotin-primer PCR.
The cDNA libraries were generated using a KAPA Hyper Prep Kit for Illumina (KAPA). Finally, the samples were ready for sequencing on an Illumina Hiseq platform (Novogene).
Modified Smart-seq2

treatment_protocol: Single HSC1 cells were treated with different cytokine combinations for 7 days.

value: 8-10 weeks

value: Bone marrow

value: SCF, SCF+TPO


title: XME2

value: SCF+G-CSF


title: Cxcl13-Td+ stromal LNs cells from mice injected with 2 antigen-immunocomplex, for 7 days and 24 hours [Biotin7d]


title: Patient 8 Slide B369 ROI 042


title: Patient 8 Slide B369 ROI 043


title: Patient 8 Slide B369 ROI 041


title: Patient 8 Slide B369 ROI 040


title: Patient 8 Slide B369 ROI 046


title: Patient 8 Slide B369 ROI 044


title: Patient 8 Slide B369 ROI 039


title: Patient 8 Slide B369 ROI 037


title: Patient 8 Slide B369 ROI 038


title: pair10_L

city: Princeton

first: Kristina

middle: Marie

last: Garske

email: kmgarske@ucla.edu, kg8086@princeton.edu

state: New Jersey

address: Carl Icahn Lab, South Drive, Princeton University

department: Lewis-Sigler Institute for Integrative Genomics; Ecology & Evolutionary Biology

institute: Princeton University

data_processing:
Reads were aligned to hg19 with STAR v2.7.0e, using the 2-pass method and the following parameters: --outFilterMultimaNmax 1, --outFilterMismatchNmas 6, --alignIntronMin 20, --alignIntronMax 500000, --chimSegmentMin 15.
Gene counts were obtained using the featureCounts function of Subread v1.6.4 and the gencode v19 annotation.
We corrected the log2-transformed gene transcripts per million mapped reads (TPMs) for pair ID (as a random effect), age, sex, and median 3' bias, using the lme4 v1.1 R package.
Assembly: hg19
Supplementary files format and content: geneCounts_allSamples.txt: tab-delimited file includes raw counts for each sample
Supplementary files format and content: geneTPMs_normalized_corrected.txt: tab-delimited file includes the log2-transformed TPMs corrected for covariates and technical factors

molecule: polyA RNA

source_name: Primary preadipocytes from subcutaneous adipose tissue

growth_protocol: Preadipocytes were seeded into PromoCell Preadipocyte Growth Medium (PromoCell C-27410) with 1% Penicillin-Streptomycin and maintained in a monolayer at <90% confluency at 37°C and 5% CO2.

extract_protocol:
Cells were washed once with PBS before lysing with TriZol (Invitrogen 15596026) and RNA was purified using the Direct-Zol RNA Mini-Prep (Zymo Research R2061).
Libraries were prepared using the Illumina TruSeq Stranded mRNA kit.

tag: pair

tag: status

value: lower BMI MZ sibling


title: pair7_L

value: Primary preadipocytes from subcutaneous adipose tissue


title: pair8_L


title: pair8_H

value: higher BMI MZ sibling


title: pair7_H


title: pair9_H


title: pair10_H


title: pair9_L


title: Patient 8 Slide B349 ROI 048

value: head and neck carcinoma

value: Male

value: Background


title: Patient 8 Slide B349 ROI 049

value: Right parotid

value: negative


title: Patient 8 Slide B349 ROI 050


title: Patient 8 Slide B369 ROI 036


title: pair6_L


title: pair5_L


title: pair4_L


title: pair6_H


title: pair5_H


title: Patient 8 Slide C19 ROI 022


title: pair4_H


title: Patient 8 Slide B349 ROI 047


title: pair3_H


title: Patient 8 Slide C19 ROI 021


title: Patient 8 Slide C19 ROI 017


title: Patient 8 Slide C19 ROI 018


title: Patient 8 Slide C19 ROI 019

value: high


title: Patient 8 Slide C19 ROI 020


title: Patient 8 Slide B349 ROI 040


title: pair2_H


title: pair1_L


title: pair3_L


title: pair9_L_D1

library_source: genomic

data_processing:
Reads were aligned to hg19 with Bowtie2 v2.2.9 using the following parameters: --k 4, -X 2000 --local.
Unpaired unmapped reads, duplicate reads, sex chromosome reads, and reads with MAPQ < 30 were filtered out
We called consensus peaks on all samples combined, using MACS2 v2.2.7.1 and peaks not in blacklisted regions, with an FDR<0.05 and counts per million mapped reads (CPM) >=1 in >=10% of samples were retained
Peak counts were obtained using the featureCounts function of Subread v1.6.4 and the ATAC-seq peaks called from MACS2
We performed a differential accessiblity (DA) analysis between the PAd and D1 time points using limma v3.34.9 and the voom method. We used the duplicateCorrelation function in limma to account for the repeated measures from the same individual. We included age, sex and fraction of reads in peaks (FRiP) in the model. We tested for PAd vs. D1 DA in the lower and higher BMI sibling subgroups separately. We used an FDR<0.05 as the cutoff to define significant DA peaks for these comparisons.
100-kb bin counts were obtained using the featureCounts function of Subread v1.6.4 and 100-kb genomic bins with blacklisted regions removed
The preadipocyte A compartment counts were obtained using the featureCounts function of Subread v1.6.4 and A compartments called in the preadipocytes
We corrected the log2-transformed ATAC peak bins per million mapped reads (BPMs), 100-kb BPMs, and A compartment BPMs for pair ID (as a random effect), age, sex, and fraction of reads in peaks (FRiP), using the lme4 v1.1 R package.
Assembly: hg19
Supplementary files format and content: peakCounts_allSamples.txt: tab-delimited file includes raw counts for each sample
Supplementary files format and content: DApeaks_PAdvD1.txt: tab-delimited file includes the differentially accessible (DA) peaks called in the lower and higher BMI siblings separately, with positive log2 fold-change (FC) corresponding to peaks that are more accessible at D1 and negative log2FC corresponding to peaks that are more accessible in PAd
Supplementary files format and content: peakTPMs_normalized_corrected_allSamples.txt: tab-delimited file includes the log2-transformed BPMs corrected for covariates and technical factors
Supplementary files format and content: binTPMs_100kbBins_normalized_corrected_PAdsamples.txt: tab-delimited file includes the PAd log2-transformed 100-kb bin BPMs corrected for covariates and technical factors
Supplementary files format and content: AcompTPMs_normalized_corrected_PAdsamples.txt: tab-delimited file includes the log2-transformed PAd A compartment BPMs corrected for covariates and technical factors

molecule: genomic DNA

extract_protocol:
Following the omni-ATAC protocol, cells were treated with DNase I, trypsinized, and DNA was tagmented and purified with the Qiagen minElute kit.
Illumina sequencing adapters were added to the tagmented DNA samples to create the sequencing libraries.

treatment_protocol: For the adipogenic differentiation (D1 samples), preadipocytes were grown to 100% confluency and the differentiation was initiated using the PromoCell Preadipocyte Differentiation Medium (PromoCell C-27436) for 24 hours

value: adipogenic differentiation, 24 hours


title: pair9_H_PAd

value: no adipogenic differentiation


title: pair2_L


title: pair1_H


title: pair8_H_D1


title: pair9_L_PAd


title: Patient 8 Slide B349 ROI 037

value: low


title: Patient 8 Slide B349 ROI 034


title: Patient 8 Slide B349 ROI 038


title: Patient 8 Slide B349 ROI 035

value: med


title: Patient 8 Slide B349 ROI 039


title: Patient 8 Slide B349 ROI 036


title: Patient 8 Slide B349 ROI 033


title: pair8_H_PAd


title: pair8_L_D1


title: pair8_L_PAd


title: Patient 8 Slide B349 ROI 032


title: pair7_H_PAd


title: pair9_H_D1


title: Patient 8 Slide B349 ROI 031


title: Patient 8 Slide B349 ROI 028


title: Patient 8 Slide B349 ROI 029


title: Patient 8 Slide B349 ROI 030


title: pair7_L_PAd


title: pair6_H_D1


title: pair6_H_PAd


title: Patient 8 Slide B19 ROI 067


title: pair6_L_PAd


title: pair6_L_D1


title: Patient 8 Slide B19 ROI 066


title: pair4_H_PAd


title: pair5_L_PAd


title: pair5_H_PAd


title: Patient 8 Slide B19 ROI 061


title: Patient 8 Slide B19 ROI 062


title: pair4_L_PAd


title: Patient 8 Slide B19 ROI 064


title: pair3_H_PAd


title: Patient 8 Slide B19 ROI 063


title: pair3_L_D1


title: Patient 8 Slide B19 ROI 060


title: Patient 8 Slide B19 ROI 059


title: Patient 8 Slide B349 ROI 027


title: pair2_H_D1


title: Patient 8 Slide B19 ROI 065


title: Patient 8 Slide B19 ROI 056


title: Patient 8 Slide B19 ROI 057


title: Patient 8 Slide B19 ROI 055


title: Patient 8 Slide B19 ROI 054


title: Patient 8 Slide B19 ROI 053


title: pair2_L_D1


title: pair1_H_D1


title: pair2_H_PAd


title: Patient 8 Slide B19 ROI 048

value: Vehicle


title: pair3_H_D1


title: Patient 8 Slide B19 ROI 047


title: pair3_L_PAd


title: pair2_L_PAd


title: pair1_L_PAd


title: pair1_H_PAd


title: pair1_L_D1


title: Patient 8 Slide B349 ROI 046


title: Patient 8 Slide B19 ROI 046


title: Patient 8 Slide B349 ROI 045


title: Patient 8 Slide B19 ROI 044


title: Patient 8 Slide B349 ROI 043


title: Patient 8 Slide B349 ROI 044


title: Patient 8 Slide B349 ROI 042


title: Patient 8 Slide B19 ROI 058


title: Patient 8 Slide B19 ROI 045


title: HeyA8 A2-1

city: Singapore

first: Tuan Zea

last: Tan

address: 14 Medical Drive, #11-01, Singapore

department: Cancer Science Institute Singapore

country: Singapore

institute: National University of Singapore

description: Mesenchymal subtype

data_processing:
Reads were mapped to Homo sapiens genome assembly GRCh37/hg19 using STAR alignment software and read counts obtained with RSEM.
Data was filtered to exclude lowly-expressed genes (count per million > 1 in 25% or more samples). Next, data was filtered for known protein-coding genes and normlized using TMM.
Next, data was adjusted for heteroskedasticity using limma package (R version 4.2).
Assembly: hg19
Supplementary files format and content: tab-delimited text files include log2 normalized values for each Sample

source_name: Ovarian Cancer

growth_protocol: SKOV3 cell line was maintained using Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 10% (v/v) fetal bovine serum (FBS). HeyA8 cell line was maintained using Roswell Park Memorial Institute 1640 media (RPMI) supplemented with 10% (v/v) FBS

extract_protocol: Cells were first harvested by trypsinization and cell pellet was subjected to RNA extraction according to the protocol provided in AllPrep DNA/RNA mini kit (Qiagen). RNA was then quantified using NanoDrop™ 2000 Spectrophotometer. RNA samples were prepared for library preparation at 2.0ug per sample.

treatment_protocol: SKOV3 cell line was treated with DMSO and R428 for 24 hrs

value: Ovarian Cancer

tag: cell line

value: WT

value: no treatment


title: HeyA8 A211-2

description: Mesenchymal subtype

value: AXL Knockout


title: HeyA8 A112-2

description: Mesenchymal subtype


title: HeyA8 A211-1

description: Mesenchymal subtype


title: HeyA8 S8-1

description: Mesenchymal subtype

value: SAM68 Knockout


title: HeyA8 S8-2

description: Mesenchymal subtype


title: HeyA8 A2-2

description: Mesenchymal subtype


title: HeyA8 A112-1

description: Mesenchymal subtype


title: HeyA8 S7-2

description: Mesenchymal subtype


title: Patient 8 Slide B19 ROI 032


title: HeyA8 C1-1

description: Mesenchymal subtype


title: HeyA8 S7-1

description: Mesenchymal subtype


title: Patient 8 Slide B19 ROI 031


title: HeyA8 C1-2

description: Mesenchymal subtype


title: SKOV3, R428-1

description: Mesenchymal subtype


title: Patient 8 Slide B19 ROI 042


title: Patient 8 Slide B19 ROI 041


title: Patient 8 Slide B19 ROI 040


title: SKOV3, R428-2

description: Mesenchymal subtype


title: SKOV3, DMSO-2

description: Mesenchymal subtype

value: DMSO


title: Patient 8 Slide B19 ROI 030

value: head and neck carcinoma


title: Patient 8 Slide B19 ROI 038

value: Male


title: SKOV3, DMSO-1

description: Mesenchymal subtype


title: Patient 8 Slide B19 ROI 037


title: Patient 7 Slide C18 ROI 015

value: Left parotid

value: Background


title: Patient 8 Slide B19 ROI 029

value: Right parotid

value: negative


title: Patient 8 Slide B19 ROI 039


title: Patient 7 Slide C18 ROI 014


title: Patient 7 Slide C18 ROI 017


title: Patient 7 Slide C18 ROI 016

value: high


title: Patient 7 Slide B19 ROI 065


title: SINV-infected U87 cells, biol rep 3

city: Sherbrooke

first: Martin

last: Bisaillon

state: QC

address: 3201 rue Jean-Mignault

department: Département de biochimie et de génomique fonctionnelle

country: Canada

institute: Université de Sherbrooke

description:
processed_data_gene_expression.xlsx
processed_data_alternative_splicing.xlsx

data_processing:
Reads were trimmed using Trimmomatic 0.32 to remove adapter sequences as well as nucleotides with low quality scores (TRAILING: 30). The quality of output reads was verified using FastQC 0.11.5.
Reads were aligned to the reference genome (hg38 and viral genomes) using STAR 2.5.1b with default parameters except for --outFilterMismatchNmax 5.
Aligned reads were then assigned to genes and quantified using Rsubread.FeatureCounts 1.20.6 with options isGTFAnnotationFile=TRUE, countChimericFragments=FALSE, largestOverlap=TRUE, isPairedEnd=TRUE, useMetaFeatures=TRUE, requireBothEndsMapped=TRUE, strandSpecific=1, minOverlap=10, autosort=TRUE.
Differential gene expression analysis was performed with DESeq2 using default parameters.
Alternative splicing analysis was performed using rMATS 3.2.5 with options -len 93 -a 3 -t paired -analysis U. ΔPSI values for each alternative splicing event were calculated by subtracting the PSI value in infected cells from the PSI value in non-infected cells.
Assembly: hg38
Supplementary files format and content: Processed data files (excel workbooks) for gene expression and alternative splicing include TPM/log2(fold-change) values and PSI/ΔPSI values for each sample, respectively.

growth_protocol: U87 cells were grown in complete Dulbecco’s modified Eagle’s Medium (cDMEM) containing 10% fetal bovine serum and L-glutamine, and cells were incubated at 37°C in humidified incubators supplemented with 5% CO2.

extract_protocol:
Cells were harvested and homogenized using QIAshredder (Qiagen). RNA was isolated using the RNeasy kit (Qiagen) following the manufacturer’s recommended protocols.
PolyA-RNA was purified from 5µg total RNA using NEB magnetic mRNA Isolation Kit (NEB, #S1550S) and eluted into a final volume of 25µl. Sequencing libraries were prepared using 9µl of isolated mRNA and ScriptSeq RNA-Seq Library Preparation Kit (Epicentre, SSV21124).

treatment_protocol:
50% confluent U87 in T150 cells were either infected at a multiplicity of infection (MOI) of 5 or treated with cell-conditioned media for 24h.
Kunjin virus (strain FLSDX, GenBank AY274504.1), Zika virus (strain PRVABC59, GenBank KU501215.1), Yellow Fever virus (strain 17D, GenBank X03700.1), and Sindbis virus (strain TE3’2J, NCBI reference sequence NC_001547.1) were used for viral infections.

value: glioblastoma cell line

value: Sindbis virus, MOI=5

tag: time


title: ZIKV-infected U87 cells, biol rep 1

value: Zika virus, MOI=5


title: KUNV-infected U87 cells, biol rep 3

value: Kunjin virus, MOI=5


title: KUNV-infected U87 cells, biol rep 2


title: Patient 7 Slide B19 ROI 064


title: Patient 7 Slide B19 ROI 063


title: KUNV-infected U87 cells, biol rep 1


title: Mock-infected U87 cells, biol rep 2

value: cell-conditioned media


title: YFV-infected U87 cells, biol rep 1

value: Yellow fever virus, MOI=5


title: SINV-infected U87 cells, biol rep 1


title: YFV-infected U87 cells, biol rep 2


title: YFV-infected U87 cells, biol rep 3


title: SINV-infected U87 cells, biol rep 2


title: ZIKV-infected U87 cells, biol rep 3


title: Mock-infected U87 cells, biol rep 1


title: SNCA-Tg _14M_Epi_17

city: Tübingen

first: Jakob

last: Admard

address: Calwerstr. 7

department: Institut für Medizinische Genetik und Angewandte Genomik

country: Germany

institute: Universitätsklinikum Tübingen

data_processing:
Basecalling of raw sequencing output was performed with Illumina bcl2fastq version 2.19.1.
For adapter sequence trimming in FASTQ files, ngs-bits SeqPurge version 2018_04 was used.
Trimmed read sequences were aligned with STAR version 2.5.4a
Read counting for exonic regions was performed with subread featureCounts version 2.0.0.
Assembly: Rnor6
Supplementary files format and content: subread featureCounts tab-separated, per-gene raw counts

organism: Rattus norvegicus

source_name: colon

extract_protocol: NEBNext Ultra II Directional RNA, NEBNext Poly(A) mRNA Magnetic Isolation

value: colon

value: >12 months

value: colon epithelial

value: transgenic


title: Patient 7 Slide C18 ROI 012

value: head and neck carcinoma

value: low


title: Patient 7 Slide B19 ROI 059

value: Male

value: Left parotid


title: Patient 7 Slide B19 ROI 060


title: Patient 7 Slide C18 ROI 011


title: ZIKV-infected U87 cells, biol rep 2


title: SNCA-Tg _14M_Epi_16


title: SNCA-Tg _14M_Epi_14


title: Patient 7 Slide B19 ROI 062


title: 14M_Epi_WT_19_1P

value: wild type


title: Patient 7 Slide B19 ROI 061

value: med


title: Patient 7 Slide C18 ROI 013


title: WT_14M_Epi_20


title: Patient 7 Slide B19 ROI 042

value: high


title: Patient 7 Slide B19 ROI 068

value: Background

value: negative


title: Patient 7 Slide C18 ROI 010


title: Patient 7 Slide B19 ROI 067


title: Patient 7 Slide B19 ROI 043


title: Patient 7 Slide B19 ROI 041


title: Mock-infected U87 cells, biol rep 3

value: glioblastoma cell line


title: PfPRMT5KO, 46h

city: Tampa

first: JUN

last: MIAO

state: Florida

address: 3720 Spectrum Boulevard, MDC84

department: Internal Medicine

institute: University of South Florida

data_processing:
Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained.
Reads were then mapped to the P. falciparum 3D7 strain reference genome with HISAT2
Differentially expressed genes are determined by DESeq2  with Padj < 0.01 and absolute log2 fold change higher than 1.
The transcriptional profiles are normalized by TPM for multi-time points or condition comparisons.
Assembly: pf3D7_V3.0.fasta
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

organism: Plasmodium falciparum

source_name: Plasmodium parasite

growth_protocol: 3D7 strains of P. falciparum were cultured in type O+ human RBCs at 5% hematocrit in RPMI 1640 medium supplemented with 25 mM HEPES, 50mg/L hypoxanthine, 25 mM NaHCO3, 0.5% Albumax II and 40 mg/ml gentamicin sulfate. The culture was maintained at 37°C in a gas mixture of 5% CO2, 3% O2 and 92% N2.

extract_protocol:
Parasites of designated developmental stages were harvested after lysis of the RBC membrane with 0.1% (v/v) saponin in PBS. Total RNA was isolated from the purified parasites using Quick-RNA MiniPrep kit (Zymo Research). The RNA was treated with the ezDNaseTM Enzyme (Invitrogen) to remove contaminating genomic DNA. RNA pellets were dissolved in 50 µL RNase-free water, and the RNA integrity was checked using the Agilent Bioanalyzer.
RNA sequencing libraries were prepared using the KAPA stranded RNA-seq library preparation kit (Roche) with 500 ng RNA from each sample. RNA was fragmented by heating at 94 °C for 8 min, and cDNA was synthesized using reverse transcriptase with random primers. Afterward, 3’ dTMP adapters were ligated to the 3’ dAMP library fragments. The quality of the barcoded libraries was validated using the Agilent Bioanalyzer. The DNA 1000 Reagents were used to quantify the library sizes and confirm the absence of primer dimers. Libraries were quantified using a KAPA Universal Library Quantification Kit (Roche), and library concentrations were adjusted for library size. Libraries were sequenced on an Illumina HiSeq 2500 in the Rapid Run mode using 100 nt single read sequencing.

value: gene disruption (PfPRMT5KO)

tag: Stage

value: schizont

value: no treatment


title: Patient 7 Slide B19 ROI 058


title: Patient 7 Slide B19 ROI 040


title: Patient 7 Slide B19 ROI 039


title: Patient 7 Slide B19 ROI 038


title: Patient 7 Slide B19 ROI 057


title: PfPRMT5KO, 36h

value: late-trophozoite


title: 3D7, 36h

value: wildtype


title: 3D7, 24h

value: early-trophozoite


title: WT_14M_Epi_21

value: colon

value: >12 months

value: colon epithelial


title: Patient 7 Slide B19 ROI 056

value: head and neck carcinoma

value: Male

value: low


title: Patient 7 Slide B19 ROI 055

value: Left parotid

value: med


title: 3D7, 46h


title: Patient 7 Slide B19 ROI 046


title: PfPRMT5KO, 12h

value: Ring


title: 3D7, 12h


title: Patient 7 Slide B19 ROI 044


title: Patient 7 Slide B18 ROI 064

value: Background

value: negative


title: Patient 7 Slide B18 ROI 065


title: PfPRMT5KO, 24h

value: gene disruption (PfPRMT5KO)


title: Liver resident NK donor 5

city: Merelbeke

first: Robert

last: Jansens

address: Salisburylaan 133

department: Department of Translational Physiology, Infectiology and Public Health

country: Belgium

institute: Ghent University

data_processing:
Aligment was performed using Hisat2. The resulting read count tables were used as input for all downstream RNA-seq analysis.
Assembly: Ss11
Supplementary files format and content: csv file containing raw counts for all samples

organism: Sus scrofa

source_name: PBMC

extract_protocol:
RNA was extracted using the RNeasy mini kit (QIAgen)
RNA libraries for RNA-seq were prepared using  the QuantSeq 3' mRNA library prep FWD kit (Lexogen) following manufacturer's protocols.

value: Liver resident NK

tag: individual

value: donor 5


title: Conventional liver NK donor 4

value: Conventional liver NK

value: donor 4


title: Patient 7 Slide B18 ROI 063


title: Blood NK donor 4

value: Blood NK


title: Conventional liver NK donor 5


title: Blood NK donor 5


title: Patient 7 Slide B18 ROI 062


title: Liver resident NK donor 4


title: Liver resident NK donor 3

value: donor 3


title: Patient 7 Slide B18 ROI 058


title: Blood NK donor 3


title: Liver resident NK donor 2

value: donor 2


title: Patient 7 Slide B18 ROI 055

value: high


title: Patient 7 Slide B18 ROI 054

value: head and neck carcinoma


title: Patient 7 Slide B18 ROI 057

value: Male


title: Patient 7 Slide B18 ROI 056


title: Conventional liver NK donor 2


title: Liver resident NK donor 1

value: donor 1


title: Blood NK donor 2


title: Patient 7 Slide B18 ROI 049

value: Left parotid


title: Patient 7 Slide B18 ROI 048

value: low


title: Patient 7 Slide B18 ROI 047


title: Patient 7 Slide B18 ROI 030


title: Conventional liver NK donor 3


title: Conventional liver NK donor 1


title: Patient 7 Slide B18 ROI 029


title: Blood NK donor 1


title: Act_CTRL_Rep4

city: Msida

first: Ruben

last: Cauchi

address: Biomedical Sciences Building

department: Physiology & Biochemistry

country: Malta

institute: University of Malta

data_processing:
Reads mapped to rRNAs were removed. SOAPnuke performed filtering as follows to produce clean reads: removal of reads with adapters, removal of reads in which unknown bases (N) were more than 10%, and removal of low quality reads (where the percentage of bases whose quality is less than 20 is greater than 40% in the read).
Reads were then mapped using HISAT2 to the reference genome (GCF_000001215.4_Release_6_plus_ISO1_MT_NCBI).
StringTie was used to reconstruct transcripts and Cufflinks was used to compare reconstructed transcripts to the reference. CPC was used to predict the coding potential of novel transcripts. Coding novel transcripts and refernce transcripts were then merged to get a complete reference, and downstream analysis was based on this reference.
GATK was used to call SNPs and Indels for each sample.
Differentialy expressed genes were determined using DESeq2. Differentially spliced genes were determined using rMATS.
Assembly: Drosophila melanogaster (GCF_000001215.4_Release_6_plus_ISO1_MT_NCBI)
Supplementary files format and content: GeneExpressionFPKM.txt: tab-delimited text file includes FPKM values by gene (rows) and sample (columns).

organism: Drosophila melanogaster

source_name: Whole body (larvae)

growth_protocol: Drosophila melanogaster stocks were cultured on standard molasses/maize meal in plastic vials at 25 °C. The w1118 stock was utilised as the wild-type fly strain. The expression of UAS-Dctn1-RNAI (VDRC ID: 3785) was driven by Act5C-GAL4.

extract_protocol:
350 µl of Buffer RLT Plus premixed with 3.5 µl of β-mercaptoethanol were added to the tube with the larvae. The larvae were then lysed and homogenised using a rotator until all the larvae had been blended appropriately. The lysate was centrifuged for 5 min at maximum speed (14,500 rpm). The supernatant was then carefully removed by pipetting and transferred to a gDNA eliminator spin column placed in a 2 ml collection tube. The column and tube were centrifuged for 30 s at 10,500 rpm after which the spin column, carrying the genomic DNA, was discarded. 350 µl of 70% ethanol were added to the flow-through and mixed well by pipetting. 700 µl of the sample was then transferred to an RNeasy spin column placed in a 2 ml collection tube. The column and tube were centrifuged for 15 s at 10,000 rpm, binding the total RNA to the spin column. The flow-through was discarded and 700 µl Buffer RW1 was added to the column to initiate the washing steps. The column and tube were centrifuged again for 15 s at 10,000 rpm. The flow-through was discarded and 500 µl Buffer RPE was added to the spin column, followed by another centrifugation step (15 s at 10,000 rpm). The flow-through was discarded again and another 500 µl Buffer RPE was added to the column. The column and tube were then centrifuged again for 2 min at 10,000 rpm. After this final washing step, the RNeasy spin column was placed in a 2 ml collection tube, discarding the old collection tube with the flow-through. The spin column and tube were centrifuged at maximum speed (14,500 rpm) for 1 min to eliminate any carryover of Buffer RPE. The RNeasy spin column was then placed in a new 1.5 ml collection tube and 30-50 µl of RNase-free water were directly added to the spin column membrane. The spin column and tube were centrifuged for 1 min at 10,000 rpm to elute the RNA. The quality and quantity of RNA was assessed with a NanoDrop ND-1000 spectrophotometer (NanoDrop Technologies). Samples were stored at -20 °C until used.
RNA libraries were prepared by BGI for non-stranded mRNA sequencing (PE100) using standard DNBSEQ protocols.

treatment_protocol: Female fruit flies laid their eggs on agar medium. Around 12-15 larvae (ca. 10 mg), which made up one biological replicate, were removed from the agar plate and cleaned by placing them in a watch glass with distilled water. The larvae were subsequently transferred to an Eppendorf tube where the procedure for total RNA extraction from control and RNAi-expressing third instar larvae was begun using an RNeasy Plus Mini Kit (Qiagen).

value: Whole body (larvae)

tag: Sex

value: female

value: Actin control

value: Feeding on grape agar + yeast


title: Patient 7 Slide B18 ROI 028


title: Act_CTRL_Rep2


title: Act_ME18_Rep3

value: DCTN1 knockdown whole body


title: Act_CTRL_Rep3


title: Act_ME18_Rep1


title: Act_ME18_Rep2


title: Patient 7 Slide B18 ROI 027


title: Patient 7 Slide B18 ROI 019


title: Patient 7 Slide B18 ROI 021


title: Patient 7 Slide B18 ROI 020


title: Patient 8 Slide B349 ROI 041

value: Right parotid


title: Patient 7 Slide B18 ROI 022

value: med


title: MCF7_GQC05_2

city: Perth

first: Nicholas

last: Lawler

state: Western Australia

address: 35 Stirling Hwy

country: Australia

institute: University of Western Australia

data_processing:
The reads were mapped to the human reference genome hg38 via STAR (v2.5.3a) (Dobin et al., 2013), with annotations from GENECODE version 25. Counts were summarised at gene level using featureCounts v1.5.3.
Differential expression analysis of the normalised reads was conducted in R using the edgeR package (Robinson et al. 2010)
Assembly: hg38
Supplementary files format and content: Matrix table with raw gene counts for every gene and sample

growth_protocol: MCF-7 human epithelial breast adenocarcinoma cells were cultured in Minimum Essential Medium α supplemented with 10% v/v foetal bovine serum, 1% v/v sodium bicarbonate 7.5% w/v solution, and 1x GlutaMAX. No antibiotic/antimycotic agents were used. Cells were maintained in a humidified incubator at 37 °C, 5% CO2, and passaged at 80% confluency.

extract_protocol:
RNA was extracted using RNeasy Mini Kit (Qiagen).
RNA-seq libraries were then prepared using the TruSeq stranded total RNA with Ribo-Zero Human/Mouse/Rat library prep kit (Illumina).

treatment_protocol: Cells were treated with either 0.3 μM GQC-05 or 20 μM GTC365 for 72 h at 37 °C and 5% CO2.


title: MCF7_GTC365_2

value: 20 uM GTC365


title: MCF7_GQC05_1


title: Patient 7 Slide B18 ROI 06

value: Vehicle

value: negative


title: Patient 7 Slide B18 ROI 04


title: Patient 7 Slide B19 ROI 029


title: Patient 7 Slide B18 ROI 05


title: MCF7_UnT_2

value: Untreated


title: Patient 7 Slide B19 ROI 028


title: MCF7_UnT_1


title: human macrophages infected with wt bacteria, rep 3

city: Wuerzburg

middle: J

last: Fraunholz

address: Theodor-Boveri-Weg

department: Chair of Microbiolgy

institute: University of Wuerzburg

description:
hMDM_Donor11_Sa_WT_10h_3
RAW_COUNT_TABLE_human_ds.csv
RAW_COUNT_TABLE_SA_ds.csv

data_processing:
To assure high sequence quality, Illumina reads were quality and adapter-trimmed via Cutadapt v2.5
Reads were first filtered with FastQScreen and then subsequently mapped to the human and bacterial genomes
Differential Expression analysis with DESeq2 v1.24.0
Assembly: GRCh38.p13 for human and GCF_000013465.1_ASM1346v1 for bacteria
Supplementary files format and content: DESeq2_intracell_Mut_vs_RPMI_Mut_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (brnQ1 mutant in infected macrophages vs growth in RPMI1640)
Supplementary files format and content: DESeq2_intracell_Mut_vs_intracell_WT_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (brnQ1 mutant in infected macrophages vs JE2 WT in infected macrophages)
Supplementary files format and content: DESeq2_intracell_Mut_vs_intracell_WT_HUMAN.xlsx - DESeq2 Comparison of human transcripts (brnQ1 mutant in infected macrophages vs JE2 WT in infected macrophages)
Supplementary files format and content: DESeq2_intracell_WT_vs_RPMI_WT_BACTERIA.xlsx - DESeq2 Comparison of S. aureus transcripts (JE2 WT in infected macrophages vs growth in RPMI1640)

organism:
Staphylococcus aureus
Homo sapiens

source_name: Macrophages

extract_protocol:
RNAprotect Cell Reagent was added immediately to the infected samples. RNA of bacteria or infected macrophages was prepared using RNeasy Mini Kit (Qiagen).
DNA libraries suitable for sequencing were prepared using CORALL Total RNA-Seq Library Prep protocol according to manufacturer’s recommendation.
libraries were sequenced on an Illumina NextSeq platform (1*75 bp single-end run)

value: Macrophages


title: Patient 7 Slide B19 ROI 035

value: head and neck carcinoma


title: MCF7_GTC365_1


title: Patient 7 Slide B19 ROI 027

value: Male


title: human macrophages infected with wt bacteria, rep 2

description:
hMDM_Donor11_Sa_WT_10h_2
RAW_COUNT_TABLE_human_ds.csv
RAW_COUNT_TABLE_SA_ds.csv


title: Patient 7 Slide B19 ROI 030


title: Patient 7 Slide B18 ROI 07


title: human macrophages infected with wt bacteria, rep 1

description:
hMDM_Donor11_Sa_WT_10h_1
RAW_COUNT_TABLE_human_ds.csv
RAW_COUNT_TABLE_SA_ds.csv


title: human macrophages infected with brnQ1 mutant bacteria, rep 3

description:
hMDM_Donor11_Sa_Mut_10h_3
RAW_COUNT_TABLE_human_ds.csv
RAW_COUNT_TABLE_SA_ds.csv


title: Patient 7 Slide B19 ROI 036


title: MCF7_GQC05_2a

data_processing:
Adapters were removed via Cutadapt and reads aligned to the hg19 reference genome using BWA (Burrows-Wheeler Alignment, version 0.7.5) (Li and Durbin, 2009) then sorted using samtools.
Duplicate reads were removed using Picard tools and peak calling was conducted on each individual sample using MACS2.
Peaks were intersected via bedtools (Quinlan and Hall, 2010) and differential peak analysis was conducted in R using the edgeR package (Robinson et al. 2010)
Assembly: hg19
Supplementary files format and content: narrowPeaks

extract_protocol:
Sample preparation was conducted as previously described by Buenrostro et al. (2015)
ATAC-seq libraries were prepared as previously described by Buenrostro et al. (2015)


title: Patient 5 Slide H410 ROI 015

value: Left neck


title: MCF7_GQC05_2b


title: Patient 5 Slide H410 ROI 020


title: Patient 5 Slide H410 ROI 019


title: human macrophages infected with brnQ1 mutant bacteria, rep 2

description:
hMDM_Donor11_Sa_Mut_10h_2
RAW_COUNT_TABLE_human_ds.csv
RAW_COUNT_TABLE_SA_ds.csv


title: human macrophages infected with brnQ1 mutant bacteria, rep 1

description:
hMDM_Donor11_Sa_Mut_10h_1
RAW_COUNT_TABLE_human_ds.csv
RAW_COUNT_TABLE_SA_ds.csv


title: Patient 5 Slide H410 ROI 021

value: Background


title: MCF7_GTC365_1b


title: MCF7_GTC365_2b


title: MCF7_GQC05_1a


title: Patient 5 Slide H410 ROI 017


title: MCF7_GQC05_1b


title: Patient 5 Slide H410 ROI 018

value: low


title: Patient 5 Slide H410 ROI 016


title: Hudep-2 MBD2 KO, replicate 2

city: Richmond

first: Mikhail

last: Dozmorov

state: VA

address: 830 E Main St

department: Biostatistics

institute: Virginia Commonwealth University

data_processing:
Briefly, samples for HUDEP-2 WT and MBD2KO groups were sequenced in triplicates using 75 bp single read sequencing and NextSeq 75HO kit. The data was quality controlled using FastQC v0.11.9. Adapters were trimmed using TrimGalore v0.6.6. Trimmed ATAC-seq reads were aligned to the human reference genome GRCh38/hg38 (http://hgdownload.cse.ucsc.edu/goldenpath /hg38/bigZips/analysisSet/hg38.analysisSet .chroms.tar.gz, accessed on 12/21/2016) using bowtie v.2.4.2.
The resulting alignment files were sorted, indexed, and marked for duplicates using samtools v1.15.1. Reads with mapping quality less than 10 were discarded. Peak calling for nucleosome-free regions was performed using MACS2 v2.2.7.1. The bigWig signal files were produced from MACS2 bedGraph files using bedGraphToBigWig v.4.
Assembly: GRCh38/hg38
Supplementary files format and content: bigWig, narrowPeak

extract_protocol:
50,000 cells of expansion phase HUDEP-2 or derived cell lines were collected, and permeabilized with 50 μL ice cold lysis buffer (10 mM Tris-HCL pH 7.5, 10 mM NaCl, 3 mM MgCl2, 0.1% NP-40, 0.1% Tween-20, 0.01% Digitonin) for 3 min. The transposition reaction was carried out at 37°C for 30 minutes in 50 μL volume containing 25 μL 2× TD buffer and 2.5 μL Tn5 Transpose enzyme (Illumina). DNA was purified with Qiagen MinElute PCR purification kit (Qiagen).
Library amplification was performed with NEBNext Ultra II Q5® Master Mix (contained in NEBNext® Ultra™ II DNA Library Prep Kit). PCR amplification was carried out as follow: 72°C 5 min, 98°C 30 s, 98°C 10 s, 63°C 30 s, 72°C 1 min, repeat steps 3-5 for another 4-6 cycles, hold at 4°C. The resulting libraries were purified using AMPure XP beads (Beckman Coulter) and quantified with Qubit fluorometer and bioanalyzer, and then sequenced in NextSeq 500 platform 76 bp single read sequencing.

value: MBD2 KO


title: Hudep-2 MBD2 KO, replicate 3


title: Patient 5 Slide F18 ROI 023


title: Patient 5 Slide H410 ROI 022


title: Hudep-2 MBD2 KO, replicate 1


title: Patient 5 Slide F18 ROI 022


title: MCF7_GTC365_1a


title: Patient 5 Slide H410 ROI 023


title: MCF7_untreated_2b


title: Hudep-2 MBD2 WT, replicate 2

value: MBD2 WT


title: Patient 5 Slide F18 ROI 020


title: Hudep-2 MBD2 WT, replicate 1


title: Patient 5 Slide F18 ROI 014


title: MCF7_untreated_1b


title: MCF7_untreated_2a


title: Patient 5 Slide F18 ROI 015


title: Patient 5 Slide F18 ROI 011

value: high


title: Patient 5 Slide F18 ROI 019


title: MCF7_GTC365_2a


title: Patient 5 Slide F18 ROI 013


title: Patient 5 Slide F18 ROI 012


title: Patient 5 Slide F18 ROI 010


title: HCb9_Healthy Control_3 months_None

city: Cambridge

first: Scott

last: Jelinsky

state: MA

address: 610 Main Street

department: Inflammation and Immunology

institute: Pfizer

data_processing:
sequencing reads were trimmed using Trim Galore
mapped to the GRCh38 human reference genome and subsequently gene counts were generated using Star v.2.5.3a
Assembly: GRCh38
Supplementary files format and content: individual sample data were normalized using edgeR - limma workflow for analysing RNA-seq data that takes gene-level counts as its input.  Since our individual level data has not been consented to be released we have reported the average normalized expression value of 3-8 subjects

source_name: peripheral blood

extract_protocol:
The RNA was extracted from PBMCs, freshly isolated using CPT tubes (BD Biosciences) using isopropanol extraction
RNA was sequenced using an Illumina HiSeq 2000, the TruSeq RNA sample preparation kit with 2 × 100 base pair (bp) paired end reads to a mean read depth of 15.7 million read pairs per sample

tag: subject status

value: Healthy Control

value: 3 months

value: peripheral blood


title: HCb8_Healthy Control_3 months_None

tag: tissue


title: Patient 5 Slide F18 ROI 09

tag: gender

value: med


title: Patient 5 Slide F18 ROI 021

tag: anatomical location


title: Patient 5 Slide F18 ROI 08

tag: age


title: Patient 5 Slide F18 ROI 07

tag: tumor level


title: RD_Bcat_cutrun

city: Beijing

first: wang

last: jiawen

address: 7 Science Park Road ZGC Life Science Park

institute: National institute of biological sciences

data_processing:
library strategy: CUT&RUN
Basecalls performed using CASAVA version 1.9
CUT&RUN-seq reads were aligned to the mm10 genome assembly using bowtie version 2.4.1 with parameters --very-sensitive-local --no-unal --no-mixed --no-discordant --phred33 –I 10 –X 700
peaks were called using MACS2 version 2.1.1 with parameters callpeak -g mm -B --SPMR
Assembly: mm10
Supplementary files format and content: bigWig files were converted from bdg files generated by MACS2 version 2.2.7.1; Scores were calculated by comparing treatment value and control value.

source_name: prostate organoid cell

growth_protocol: Mouse prostate basal cells were flow-sorted and cultured as organoids using standard protocol (Drost et al, Nature Protocols 2016).

extract_protocol:
Organoid cells were enzymatically dissociated into single cells by incubation in prewarmed TrypLE at 37°C for 20min with pipetting disruption. CUT&RUN was performed based on published protocol (Skene et al, Nature Protocols 2018).
Libraries were prepared using the NEBNext Ultra II DNA Library Prep Kit.

treatment_protocol: Organoids were treated with organoid medium containing either R-spondin1 (500 ng/ml) or R-spondin1 plus DHT (10-7M).

value: prostate organoid cell

tag: chip-grade antibody

value: Cell Signaling #8814 (D13A1)

tag: antibody dilution

tag: treatment

value: R-spondin and DHT


title: HCb6_Healthy Control_3 months_None


title: Hudep-2 MBD2 WT, replicate 3

tag: genotype


title: Ctrl

city: Jinan

first: Qinglu

last: Wang

state: Shandong

address: 10600 Century Avenue

institute: Shandong Sport University

description: 10x Genomics

data_processing: none provided

molecule: nuclear RNA

source_name: Adipose tissue of the epididymis

extract_protocol: none provided

value: Adipose tissue of the epididymis

value: full diet


title: Mid_Ob

description: 10x Genomics

value: high fat diet


title: HCb7_Healthy Control_3 months_None


title: RD_AR_cutrun

tag: cell type

value: Abcam #ab108341


title: Ob

description: 10x Genomics


title: Patient 5 Slide F18 ROI 03

data_processing: Raw probe level counts from the NanoString DSP machine were subjected to QC and normalization as follows. ROIs with deduplicated read counts of <10,000 were excluded. Count data was then normalized using TMM normalization(26) prior to performing limma analysis

extract_protocol: Tissue sections were baked, deparaffinized, washed in PBS, and targets were retrieved for 20 minutes in 1x Tris-EDTA pH 9.0 buffer (Invitrogen #00-4956-58) at 100 °C. Next, tissues were washed in PBS, incubated in 0.1 μg/ml proteinase K (Thermo Fisher Scientific, #AM2546) in PBS for 15 minutes at 37 °C and washed again in PBS. Protein targets were post-fixed in 10% neutral-buffered formalin for 5 minutes, followed by two 5-minute incubations in 12.25 mg/ml Tris base, 7.5 mg/ml Glycine stop buffer diluted in DEPC-treated water. Tissues were incubated overnight at 37 °C with hybridization solution (Human Cancer Transcriptome Atlas probe mix (NanoString #121400101), Buffer R (NanoString #121300313), and DEPC-treated water). During incubation, slides were covered with HybriSlip hybridization covers (Grace BioLabs #714022). After incubation, HybriSlip covers were gently removed by soaking in 2x SSC buffer. Two 25 minute stringent washes were performed using 50% formamide in 2x SSC at 37 °C. Tissues were washed for 5 minutes in 2× SSC and incubated in blocking buffer W (NanoString #121300313) for 30 minutes at room temperature in a humidity chamber. Primary antibody targeted against MIL113 was diluted in buffer W and incubated with the tissues for 1 hour followed by a 1 hour incubation with fluorescently-labeled secondary antibody diluted in buffer W. After the slides were washed twice for 5 minutes in 5x SSC buffer they were incubated for 1 hour in SYTO13 (50 nM) and fluorescently conjugated antibody targeting PanCK in blocking  8  buffer. Following staining the sections were washed for 5 minutes in fresh 2x SSC. Following whole slide imaging, multiple geometric ROIs of 400 μm2 were placed in regions of subasumstat drug exposure according to MIL113 signal intensity and regions of vehicle or background. Indexing oligonucleotides were then cleaved and quantified via next gen sequencing on a NovaSeq 6000 Illumina sequencer as previously described(25)

value: head and neck carcinoma

value: Male

value: Left neck

value: Vehicle


title: R_Bcat_cutrun

value: R-spondin


title: Patient 5 Slide F18 ROI 02


title: Patient 5 Slide E18 ROI 027

value: Background

value: negative


title: Patient 5 Slide F18 ROI 01


title: Patient 5 Slide E18 ROI 026


title: R_AR_cutrun


title: Patient 7 Slide B19 ROI 037

value: Left parotid


title: Patient 5 Slide E18 ROI 025


title: Patient 5 Slide E18 ROI 024

value: low


title: HCb3_Healthy Control_3 months_None

value: Healthy Control

value: 3 months

value: peripheral blood


title: Patient 5 Slide E18 ROI 023


title: MCF7_untreated_1a

value: Untreated


title: HCb4_Healthy Control_3 months_None


title: Patient 5 Slide E18 ROI 022


title: Patient 5 Slide E18 ROI 021


title: HCb2_Healthy Control_3 months_None


title: HCb10_Healthy Control_3 months_None


title: HCb1_Healthy Control_3 months_None


title: hTSC-H4K20me3-1

city: Xiamen

first: Jinhua

last: Lu

address: No. 4221, Xiangan Road, Xiangan District, Xiamen city

institute: Xiamen University

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 hg38 whole genome using HISAT2 with default parameters
MACS2 was used to call the peaks of these antibodies binding using default parameters.
Genome_build: hg38
Supplementary_files_format_and_content: pileup peaks

source_name: human TSC

growth_protocol: Advanced DMEM/F12 supplemented with 0.1mM 2-mercaptoethanol, 0.2% FBS, 1% ITS-X supplement, 0.3% BSA, 0.5% Penicillin -Streptomycin, 1.5 μg/ml L-ascorbic acid, 0.5 μM A83-01, 50 ng/ml EGF, 1μM SB431542, 2 μM CHIR99021, 5 μM Y27632 and 0.8 mM VPA

extract_protocol:
ChIP was performed according to the reported previousl with slight modification. Briefly, about 2x10^6 TS cells were cross-linked with 1/15 volume of 16% formaldehyde (CST) at room temperature for 10 minutes and quenched with 1/10 volume of 1.25 M glycine for 15 minutes on ice. Cell lysate in lysis buffer III were sonicated using Bioruptor pico (Diagenode) and then incubated with 4 µg antibody overnight at 4℃ with rotation. Immunoprecipitated complexes were collected with 15 µl Protein A Dynabeads (Invitrogen, 10002D) for 1 hour at 4℃ with rotation. Subsequently, beads were washed sequentially once with low-salt buffer, twice with high-salt buffer, once with LiCl buffer, twice with TE, and then eluted in 400 µl of elution buffer for 30 min at 65℃. The eluates were incubation at 65℃ for 8 h to reverse the cross-linking. Next, eluates were treated with proteinase K for 1 h at 55℃ and then RNase A for 30 min at 37℃ before DNA was extracted and purified. The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150.
The ChIP libraries were prepared using KAPA HyperPrep Kits (Roche, 07962347001) and then run on the Illumina sequencer Hiseq-Xten PE150 using standard Illumina protocols

value: Human trophoblast stem cells

tag: chip antibody

value: Anti-Histone H4 (tri methyl K20), Abcam, catalog number:ab9053


title: Patient 5 Slide E18 ROI 020

city: Seattle

last: Klinghoffer

address: 530 Fairview Ave N

institute: Presage Biosciences


title: Patient 5 Slide E18 ROI 015


title: hTSC-H4K20me3-2


title: Liver_TAA_8W_rep2

city: chengdu

first: shuaijie

last: qian

address: NO. 1, 4th Keyuan Road, Chengdu,

institute: West China Hospital, Sichuan University

description: A total of 896 spot data on the Arraystar Mouse circRNA Array.

hyb_protocol: Array hybridization was performed according to the manufacturer’s protocol (Arraystar Inc.). 1 μg of each labeled cRNA was fragmented by adding 5 μl 10 × Blocking Agent and 1 μl of 25 × Fragmentation Buffer, then heated the mixture at 60 °C for 30 min, finally 25 μl 2 × Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the circRNA expression microarray slide. The slides were incubated for 17 hours at 65°C in an Agilent Hybridization Oven.

scan_protocol: The hybridized arrays were washed, fixed and scanned using the Axon GenePix 4000B microarray scanner (Molecular Devices, Inc.).

data_processing:
Scanned images were imported into GenePix Pro 6.0 software (Axon) for grid alignment and raw data extraction. Quantile normalization of raw data and subsequent data processing were performed using the R software package. After quantile normalization of the raw data, low intensity filtering was performed, and the circRNAs that at least 5 out of 10 samples have flag expressed(greater than 2 times background standard deviation) were retained for further analyses.
When comparing two groups or samples of profile differences, the “fold change” (i.e. the ratio of the group averages) between the groups or samples for each circRNA is computed. The statistical significance of the difference may be conveniently estimated by t-test.
circRNAs having fold changes >= 2.0 and p-values =< 0.05 are selected as the significantly differentially expressed ones.

source_name: Liver_Wild type mice_8-week thioacetamide i.p.

label_protocol: Sample labeling was performed according to the manufacturer’s protocol (Arraystar Inc.). The circRNA were treated with Rnase R (Epicentre, Inc.) to remove linear RNAs. Then, each sample was amplified and transcribed into fluorescent cRNA utilizing a random priming method (Arraystar Super RNA Labeling Kit; Arraystar). The labeled cRNAs were purified by RNeasy Mini Kit (Qiagen).The concentration and specific activity of the labeled cRNAs (pmol Cy3/μg cRNA) were measured by NanoDrop ND-1000.

extract_protocol: The purity and concentration of total RNA samples were determined with NanoDrop ND-1000. Results were provided in Sample QC report.

treatment_protocol: Liver from liver fibrosis model induced by intraperitoneal injection of thioacetamide (TAA) in C57BL/6J mice for 8 weeks. Control mice received the same volume of normal saline (NS).

value: Liver

value: Wild type mice

tag: agent

value: thioacetamide  i.p.


title: Liver_TAA_8W_rep4


title: Patient 5 Slide H410 ROI 024

first: Rich

value: head and neck carcinoma

value: Male


title: Liver_TAA_8W_rep3


title: HCa9_Healthy Control_0 months_None

tag: time

value: 0 months


title: hTSC-H4K20me1-2

value: Histone H4K20me1 antibody(Active motif),catalog number:#39727


title: Liver_TAA_8W_rep5


title: Patient 5 Slide E18 ROI 014

value: Left neck

value: Vehicle


title: Liver_saline_8W_rep5

source_name: Liver_Wild type mice_8-week saline i.p.

value: saline i.p.


title: Patient 5 Slide E18 ROI 019

value: negative


title: Liver_TAA_8W_rep1


title: HCa8_Healthy Control_0 months_None

value: Healthy Control


title: Liver_saline_8W_rep4


title: hTSC-H4K20me1-1


title: HCa7_Healthy Control_0 months_None


title: Patient 5 Slide E18 ROI 013


title: Liver_saline_8W_rep3


title: HCa6_Healthy Control_0 months_None


title: Humidity_recovery replicate 3

city: Cerdanyola del Vallès

first: ANTONI

last: GARCIA-MOLINA

state: Barcelona

address: Campus UAB - CRAG Building

department: Plant Development and Signal Transduction

country: Spain

institute: Centre for Research in Agrigenomics

description:
Humidity_recovery
replicate 3

data_processing:
RNA-Seq datasets were analysed on Galaxy (https://usegalaxy.org/).
Briefly, reads were cleaned from adapters using Trimmomatic and mapped to the Arabidopsis reference genome (TAIR10) with STAR. Read counts were computed with featureCounts and differentially expressed genes were calculated in groups of pair-wise comparisons between standard conditions and each treatment under the recovery and end-point setup (absolute log2 fold-change ≥ 1, adj-P  ≤ 0.05, Wald test) according to DESeq2.
Assembly: Arabidopsis reference genome (TAIR10)
Supplementary files format and content: csv file containing rlog-normalised counts obtained with featureCounts.

organism: Arabidopsis thaliana

growth_protocol: Arabidopsis thaliana ecotype Col0 was used as wild type. Seeds were stratified at 4 ºC for 2 day and sown on soil jiffy-7 (Jiffy Group International, Zwijndrecht, The Netherlands) under a 12 h light (22 ºC and 120 µmols m-2 s-1) / 12h dark (18 ºC) cycle with relative humidity of 65% in FitoClima 1200 PLH LED cabinets (Aralab, Rio de Mouro, Portugal).

extract_protocol:
Total RNA from 18-day-old rosettes was extracted with the Maxwell® RSC Plant RNA kit (Promega, Wisconsin, USA) according to manufacturer’s indications. RNA quality and integrity was checked in gel.
RNA-Seq libraries were prepared and pair-end sequenced (2x150 bp) at Sistemas Genómicos (València, Spain) with standard Illumina protocols.

treatment_protocol: For the recovery setup, 12-d-old seedlings grown under standard conditions were treated with abiotic stressors for 3 days and recovered under standard conditions for 3 additional days. For the end-point setup, 15-d-old seedling grown under standard conditions were treated with the abiotic stressors. Abiotic stress treatments consisted in raising diurnal light to 350 µmols m-2 s-1 (high light), sealing trays with water excess (humidity), water shortage (drought), increasing temperature cycles to 27 ºC/ 23 ºC (heat), lowering temperature cycles to 12 ºC/ 8 ºC and adjusting light intensity to 80 µmols m-2 s-1 (cold) or to 200 µmols m-2 s-1 (cold-high light) and combinations of conditions. Rosette leaves were flash-frozen in liquid nitrogen and stored at -80 ºC. All samples were harvested 6h after onset of lights.

tag: cell line

value: rosette leaves

value: WT

value: day 18


title: Patient 5 Slide E18 ROI 012

value: med


title: Liver_saline_8W_rep2


title: Humidity_recovery replicate 2

description:
Humidity_recovery
replicate 2


title: Patient 5 Slide E18 ROI 011


title: HCa5_Healthy Control_0 months_None

value: peripheral blood


title: X54_36_3

city: Yunnan Kunming

first: xie

middle: mei

last: hua

state: Yunnan

address: 121 street

institute: Yunnan university

data_processing:
The expression quantification software RSEM was used to quantitatively analyze the expression levels of genes and transcripts, respectively. The quantitative index was TPM
The FUS3 matrix table uses the R language to calculate the Pearson correlation coefficient.

organism: Orbilia oligospora

source_name: Arthrobotrys oligospora and nematode

growth_protocol: WT and ΔAofus3 strains grown on cellophane-overlaid PDA plates at 28°C for 5 days.

extract_protocol: After collecting the samples, RNA was extracted with the AxyPrep Multisource RNA Miniprep Kit (Axygen, Jiangsu, China)

treatment_protocol: Approximately 600 nematodes were then added to each plate for 0, 12, 24, and 36 h of induction, three replicates were used for each sample.

value: Fungal hyphae cells

value: Aofus3 WT

value: nematode induction

tag: timepoint (h)


title: HCa4_Healthy Control_0 months_None


title: Humidity_recovery replicate 1

description:
Humidity_recovery
replicate 1


title: HCa3_Healthy Control_0 months_None


title: X54_36_2


title: Humidity_end-point replicate 3

description:
Humidity_end-point
replicate 3


title: Patient 5 Slide E18 ROI 010

source_name: head and neck carcinoma

value: head and neck carcinoma


title: X54_24_3


title: Patient 5 Slide H410 ROI 014

value: Male

value: high


title: X54_36_1


title: Humidity_end-point replicate 1

description:
Humidity_end-point
replicate 1


title: Humidity_end-point replicate 2

description:
Humidity_end-point
replicate 2


title: HCa10_Healthy Control_0 months_None

value: 0 months


title: HCa2_Healthy Control_0 months_None


title: Liver_saline_8W_rep1

value: Liver

value: Wild type mice


title: Patient 5 Slide E18 ROI 08

value: Left neck


title: HL_recovery replicate 3

description:
HL_recovery
replicate 3


title: Patient 5 Slide H410 ROI 013


title: X54_24_1


title: Patient 5 Slide F18 ROI 027

value: Background

value: negative


title: HL_recovery replicate 2

description:
HL_recovery
replicate 2

value: rosette leaves


title: Bb9_Rheumatoid Arthitis_3 months_TNFi

value: Rheumatoid Arthitis

value: 3 months

value: TNFi


title: X54_12_3


title: HL_recovery replicate 1

description:
HL_recovery
replicate 1

value: WT

value: day 18


title: X54_12_2

value: Fungal hyphae cells

value: Aofus3 WT


title: Patient 5 Slide F18 ROI 026

value: head and neck carcinoma


title: Patient 5 Slide F18 ROI 025

value: Male


title: Bb7_Rheumatoid Arthitis_3 months_TNFi

value: peripheral blood


title: Bb8_Rheumatoid Arthitis_3 months_TNFi


title: HCb5_Healthy Control_3 months_None

value: Healthy Control


title: HL_end-point replicate 2

description:
HL_end-point
replicate 2


title: Patient 5 Slide E18 ROI 09

value: med


title: HL_end-point replicate 3

description:
HL_end-point
replicate 3


title: HL_end-point replicate 1

description:
HL_end-point
replicate 1


title: Bb6_Rheumatoid Arthitis_3 months_TNFi


title: X54_24_2

value: nematode induction


title: X54_12_1


title: Bb4_Rheumatoid Arthitis_3 months_TNFi


title: X54_0_3


title: Bb5_Rheumatoid Arthitis_3 months_TNFi


title: X54_0_1


title: Patient 5 Slide F18 ROI 024

value: Left neck


title: Patient 5 Slide E18 ROI 07


title: Patient 5 Slide E18 ROI 03

value: Vehicle

value: low


title: Bb3_Rheumatoid Arthitis_3 months_TNFi


title: Heat-HL_recovery replicate 2

description:
Heat-HL_recovery
replicate 2

value: rosette leaves


title: Heat-HL_recovery replicate 1

description:
Heat-HL_recovery
replicate 1


title: Patient 5 Slide E18 ROI 02


title: Bb2_Rheumatoid Arthitis_3 months_TNFi

value: Rheumatoid Arthitis


title: AO_36_3

value: Aofus3 KO


title: AO_36_2


title: Patient 5 Slide E18 ROI 01


title: Bb10_Rheumatoid Arthitis_3 months_TNFi

value: 3 months

value: TNFi


title: Heat-HL_end-point replicate 3

description:
Heat-HL_end-point
replicate 3

value: WT

value: day 18


title: AO_36_1

value: Fungal hyphae cells


title: Heat-HL_recovery replicate 3

description:
Heat-HL_recovery
replicate 3


title: Patient 4 Slide A27 ROI 016

value: head and neck carcinoma

value: Right neck


title: X54_0_2

value: Aofus3 WT


title: Ba9_Rheumatoid Arthitis_0 months_None

value: 0 months

value: peripheral blood


title: AO_24_3

value: nematode induction


title: Patient 4 Slide A27 ROI 015

value: Male

value: med


title: Heat-drought-HL_recovery replicate 3

description:
Heat-drought-HL_recovery
replicate 3


title: Heat-HL_end-point replicate 1

description:
Heat-HL_end-point
replicate 1


title: Ba8_Rheumatoid Arthitis_0 months_None


title: Heat-drought-HL_recovery replicate 2

description:
Heat-drought-HL_recovery
replicate 2


title: Ba7_Rheumatoid Arthitis_0 months_None


title: AO_24_1


title: Bb1_Rheumatoid Arthitis_3 months_TNFi


title: AO_12_3


title: Patient 4 Slide A27 ROI 014


title: Patient 4 Slide A27 ROI 013

value: high


title: Patient 4 Slide A27 ROI 017


title: Patient 4 Slide A27 ROI 012

value: low


title: AO_12_2


title: Patient 4 Slide A27 ROI 011


title: Heat-HL_end-point replicate 2

description:
Heat-HL_end-point
replicate 2

value: rosette leaves


title: Heat-drought-HL_end-point replicate 3

description:
Heat-drought-HL_end-point
replicate 3


title: Ba5_Rheumatoid Arthitis_0 months_None

value: Rheumatoid Arthitis


title: AO_0_3

value: Aofus3 KO


title: Heat-drought-HL_end-point replicate 2

description:
Heat-drought-HL_end-point
replicate 2


title: AO_24_2


title: Patient 4 Slide A112 ROI 020

value: Background

value: negative


title: Patient 4 Slide A112 ROI 015


title: Ba3_Rheumatoid Arthitis_0 months_None


title: AO_0_2


title: Ba2_Rheumatoid Arthitis_0 months_None


title: AO_0_1


title: Patient 4 Slide A112 ROI 014


title: Heat-drought_recovery replicate 3

description:
Heat-drought_recovery
replicate 3

value: WT

value: day 18


title: Heat-drought_recovery replicate 2

description:
Heat-drought_recovery
replicate 2


title: Patient 4 Slide A112 ROI 013

value: head and neck carcinoma


title: Heat-drought_recovery replicate 1

description:
Heat-drought_recovery
replicate 1


title: Ba10_Rheumatoid Arthitis_0 months_None


title: THP-1 EVs, M2-like GAM, rep3

city: Chongqing

first: Chao

last: Xu

address: 118 Xingguang Boulevard, Liang Jiang New Area

institute: Chongqing General Hospital

description: EVs RNA

data_processing:
The raw tags were processed using the following steps: remove low quality tags; remove tags with 5 primer contaminants; remove tags without 3 primer; remove tags without insertion; remove tags with poly A; remove tags shorter than 18 nt. After filtering, the clean tags were mapped to the reference genome and other sRNA database including miRbase, siRNA, piRNA and snoRNA with Bowtie2 (2 2.2.9). Particularly, cmsearch (1.1.2) was performed for Rfam mapping. The software miRDeep2 (2.0.0.8) was used to predict novel miRNA by exploring the secondary structure. The small RNA expression level is calculated by counting absolute numbers of molecules using unique molecular identifiers. Differential expression analysis was performed using the DEGseq, Q value≤ 0.001 and the absolute value of Log2Ratio ≥ 1 as the default threshold to judge the significance of expression difference.
Assembly: GRCh38
Supplementary files format and content: tab-delimited text files include Read count and expression for each Sample

growth_protocol: THP-1 was cultured in RPMI 1640 medium supplemented with 10% fetal bovine serum (FBS; Gibco), 200 mM glutamine, 50 units/ml penicillin and 50 μg/ml streptomycin.

extract_protocol:
M1- and M2- EVs were extracted by ultracentrifugation.  Total RNA of EVs was extracted with exoRNeasy Maxi Kit (Qiagen, Hilden, Germany)according to the handbook instructment.
miRNA libraries were prepared for sequencing using BGI DNA nanoball sequencing protocols.

treatment_protocol: THP-1 cells were pretreated with 100 ng/ml phorbol myristate acetate (PMA; Sigma‒Aldrich, St. Louis, USA) for 48 h to obtain differentiated macrophage-like cells. GAM activation was conducted in accordance with previously reported procedures with some modifications (21). In brief, to obtain M1-GAMs, PMA-stimulated THP-1 cells were cultured with 50 ng/mL granulocyte-macrophage colony stimulating factor (GM-CSF; PeproTech, Cranbury, USA) for 3 days, while IL-4 and IL-13 (PeproTech) were applied to stimulate the generation of M2-GAMs.

value: monocytes

value: PMA and IL-4/IL-13 stimulated


title: Ba6_Rheumatoid Arthitis_0 months_None

value: 0 months


title: Ba1_Rheumatoid Arthitis_0 months_None

value: peripheral blood


title: Heat-drought-HL_recovery replicate 1

description:
Heat-drought-HL_recovery
replicate 1


title: Patient 4 Slide A112 ROI 012

value: Right neck


title: Ab9_Rheumatoid Arthitis_3 months_MTX

value: 3 months

value: MTX


title: Patient 4 Slide A112 ROI 016

value: Male


title: Ba4_Rheumatoid Arthitis_0 months_None


title: Heat-drought_end-point replicate 3

description:
Heat-drought_end-point
replicate 3


title: Patient 4 Slide A112 ROI 019


title: Heat-drought-HL_end-point replicate 1

description:
Heat-drought-HL_end-point
replicate 1


title: THP-1 EVs, M2-like GAM, rep2

description: EVs RNA


title: THP-1 EVs, M2-like GAM, rep1

description: EVs RNA


title: Heat-drought_end-point replicate 2

description:
Heat-drought_end-point
replicate 2


title: Patient 4 Slide A112 ROI 018


title: Ab8_Rheumatoid Arthitis_3 months_MTX


title: THP-1 EVs, M1-like GAM, rep2

description: EVs RNA

value: PMA and GM-CSF stimulated


title: Heat_recovery replicate 3

description:
Heat_recovery
replicate 3

value: rosette leaves


title: Ab6_Rheumatoid Arthitis_3 months_MTX

value: Rheumatoid Arthitis


title: Patient 4 Slide A112 ROI 017

value: high


title: Ab5_Rheumatoid Arthitis_3 months_MTX


title: Ab4_Rheumatoid Arthitis_3 months_MTX


title: Heat-drought_end-point replicate 1

description:
Heat-drought_end-point
replicate 1


title: HCa1_Healthy Control_0 months_None

value: Healthy Control


title: Patient 4 Slide A27 ROI 019

value: Background

value: negative


title: Heat_recovery replicate 1

description:
Heat_recovery
replicate 1

value: WT

value: day 18


title: Patient 3 Slide A141 ROI 019

value: head and neck carcinoma

value: Female

value: Right lateral tongue


title: 3D7, WT, Schizont, IgG, rep2

description: CUT&Tag-seq

data_processing:
Illumina adapter sequence removal and quality trimming of reads were performed using Trimmomatic. Only reads that had a minimum length of 50 base pairs were retained.
The reads of CUT&Tag-seq from three biological replicates were mapped to the P. falciparum genome (PlasmoDB Release 39.0 by using BWA (Li and Durbin 2009) after FastQC quality control
The peak calling was finished by MACS2 version 2.2.7.1 with parameters ‘callpeak -f BAMPE’ and a q-value cutoff of 0.05.
To further strengthen the reproducibility, we only kept the peaks presenting at least 50% overlapping between two biological replicates for downstream analysis.
Assembly: pf3D7_V3.0.fasta
Supplementary files format and content: Overlapped peaks.xlsx, Peak calling.xlsx
Library strategy: CUT&Tag-seq

extract_protocol:
Parasites of designated developmental stages were harvested after lysis of the RBC membrane with 0.1% (v/v) saponin in PBS.
PCR with appropriate barcoded primers was performed using the CUTANA High Fidelity 2x PCR Master Mix (EpiCypher #15-1018) according to the manufacturer's recommendations. Amplified DNA libraries were captured by incubating with 1.3 × Kapa pure beads (Roche #KK8001) according to the manufacturer's recommendations.

tag: strain

tag: antibody

value: IgG control antibodies

tag: developmental stage

value: schizont stage

value: no treatment

value: whole parasite


title: 3D7, WT, Schizont, IgG, rep3

description: CUT&Tag-seq

tag: tissue


title: Ab3_Rheumatoid Arthitis_3 months_MTX

tag: subject status

value: 3 months

value: MTX

value: peripheral blood


title: Ab2_Rheumatoid Arthitis_3 months_MTX

value: Rheumatoid Arthitis


title: Heat_recovery replicate 2

description:
Heat_recovery
replicate 2

value: rosette leaves


title: Heat_end-point replicate 2

description:
Heat_end-point
replicate 2


title: Heat_end-point replicate 1

description:
Heat_end-point
replicate 1


title: Ab7_Rheumatoid Arthitis_3 months_MTX


title: Patient 3 Slide A141 ROI 015

tag: gender

tag: anatomical location

tag: age

value: med


title: Patient 3 Slide A141 ROI 016

tag: tumor level

value: low


title: THP-1 EVs, M1-like GAM, rep1

description: EVs RNA

value: monocytes

tag: treatment

value: PMA and GM-CSF stimulated


title: Ab10_Rheumatoid Arthitis_3 months_MTX


title: Patient 3 Slide A141 ROI 018

value: Background

value: negative


title: Ab1_Rheumatoid Arthitis_3 months_MTX


title: Aa9_Rheumatoid Arthitis_0 months_None

value: 0 months


title: Patient 4 Slide A27 ROI 018

value: head and neck carcinoma

value: Male

value: Right neck


title: Heat_end-point replicate 3

description:
Heat_end-point
replicate 3

tag: genotype

value: WT

value: day 18


title: Pool4_FB

city: Erlangen

first: Hashem

last: Mohammadian

address: Ulmenweg 18

department: Department of Medicine 3 - Rheumatology and Immunology

institute: University of Erlangen-Nürnberg

description: healthy and EAE microglia HTO library

library_source: transcriptomic single cell

data_processing:
The barcoded processing, gene counting and HTO processing were made using the Cell Ranger software v6.0.6
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: brain

extract_protocol:
Mice were perfused with ice-cold PBS by cardiac puncture and brains were collected in RPMI medium on ice. Tissue was homogenised using a tissue dounce grinding set. Homogenates were subjected to density centrifugation (37% Percoll, 550g, 18 min) to remove myelin debris. Surface staining was performed in PBS containing BioLegend CD45 (I3/2.3), CD11b (M1/70), CX3CR1 (SA011F11) and P2RY12 (S16007D) antibodies for 30 min at 4°C. The antibody cocktail for cell sorting was supplemented with hashtag antibodies (TotalSeq-B0301/B0302/B0303/B0304 anti-mouse hashtag 1/2/3/4, Biolegend) to label individual animals. Microglia were isolated by fluorescence-activated cell sorting (FACS) for the presence of CD45 (intermediate), CD11b, CX3CR1 and P2RY12 signals. Cells were sorted from individual animals, washed, counted and concentrated to 1,000 cells/µl before pooling. Three independent pools were generated, each containing equal numbers of cells from healthy wild-type, healthy CD83 knock-out, EAE wild-type and EAE CD83 knock-out animals (12 animals in total, 3 biological replicates per condition in 3 pools, 1 pool containing all 4 conditions).
Up to 25,000 cells (hyper-loading) pooled from 4 animals were loaded into a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev D). Libraries were sequenced as PE150 by Illumina sequencing to 65-80% saturation by the external provider Novogene.

treatment_protocol: To induce EAE, mice were immunized subcutaneously with 100 µl of emulsified complete Freund’s adjuvant (CFA) supplemented with 10 µg/µl Mycobacterium tuberculosis and 100 µg MOG35-55 peptide and received intraperitoneal injections of 200 ng pertussis toxin at the time of immunization and 48 h later.

tag: cell type

value: microglia

value: brain

value: CX3CR1-CreERT2 x CD83-flox

tag: genotype 1

value: #1 - #4 CX3CR1-CreERT2 +

tag: genotype 2

tag: treatment 1

value: Tamoxifen

tag: treatment 2

value: #1 control #2 control; #3 EAE; #4 EAE

tag: library type

value: HTO

tag: antibodies/tags

value: #1="mouse 1"=ACCCACCAGTAAGAC; #2="mouse 2"=GGTCGAGAGCATTCA; #3= "mouse 3"=CTTGCCGCATGTCAT; #4="mouse 4"=AAAGCATTCTTCACG


title: Drought_recovery replicate 2

description:
Drought_recovery
replicate 2

tag: cell line

value: rosette leaves

tag: time


title: 3D7, WT, Schizont, H3T2me2s, rep1

description: CUT&Tag-seq

tag: strain

tag: antibody

value: anti-H3R2me2s antibodies

tag: developmental stage

value: schizont stage

value: no treatment

tag: tissue

value: whole parasite


title: Patient 3 Slide A141 ROI 017

value: head and neck carcinoma

tag: gender

value: Female

tag: anatomical location

value: Right lateral tongue

tag: age

value: Background

value: negative


title: Aa8_Rheumatoid Arthitis_0 months_None

tag: subject status

value: Rheumatoid Arthitis

value: 0 months

tag: treatment

value: peripheral blood


title: Drought_recovery replicate 1

description:
Drought_recovery
replicate 1

tag: cell type

tag: genotype

value: WT

value: day 18


title: Patient 3 Slide A141 ROI 012

tag: tumor level

value: low


title: 3D7, WT, Schizont, IgG, rep1

description: CUT&Tag-seq

value: IgG control antibodies


title: Pool4_GEX

description: healthy and EAE microglia gene expression library

value: microglia

value: brain

value: CX3CR1-CreERT2 x CD83-flox

tag: genotype 1

value: #1 - #4 CX3CR1-CreERT2 +

tag: genotype 2

tag: treatment 1

value: Tamoxifen

tag: treatment 2

value: #1 control #2 control; #3 EAE; #4 EAE

value: mRNA

value: 15-27 weeks


title: Aa7_Rheumatoid Arthitis_0 months_None

tag: time


title: 3D7, WT, Schizont, H3T2me2s, rep3

description: CUT&Tag-seq

tag: strain

value: anti-H3R2me2s antibodies

value: schizont stage

value: no treatment

value: whole parasite


title: Pool3_FB

description: healthy and EAE microglia HTO library

tag: library type

value: HTO

tag: antibodies/tags

value: #1="mouse 1"=ACCCACCAGTAAGAC; #2="mouse 2"=GGTCGAGAGCATTCA; #3= "mouse 3"=CTTGCCGCATGTCAT; #4="mouse 4"=AAAGCATTCTTCACG


title: Aa6_Rheumatoid Arthitis_0 months_None

value: Rheumatoid Arthitis

value: 0 months

tag: tissue

value: peripheral blood


title: AO_12_1

value: Fungal hyphae cells

value: Aofus3 KO

value: nematode induction

tag: timepoint (h)


title: Patient 3 Slide A141 ROI 011

value: head and neck carcinoma

tag: gender

value: Female

tag: anatomical location

value: Right lateral tongue

value: high


title: Drought_end-point replicate 2

description:
Drought_end-point
replicate 2

tag: cell line

value: rosette leaves

value: WT

value: day 18


title: Drought_end-point replicate 3

description:
Drought_end-point
replicate 3

tag: treatment


title: 3D7, WT, Schizont, H3T2me2s, rep2

description: CUT&Tag-seq

tag: antibody

value: anti-H3R2me2s antibodies

tag: developmental stage

value: schizont stage

value: no treatment


title: Drought_recovery replicate 3

description:
Drought_recovery
replicate 3

tag: cell type

tag: genotype


title: Patient 2 Slide A410 ROI 016

value: Male

value: Right neck

tag: age

tag: tumor level

value: low


title: Aa5_Rheumatoid Arthitis_0 months_None

tag: subject status

value: Rheumatoid Arthitis

value: 0 months

value: peripheral blood


title: Pool3_GEX

value: microglia

value: brain

value: CX3CR1-CreERT2 x CD83-flox

tag: genotype 1

value: #1 - #4 CX3CR1-CreERT2 +

tag: genotype 2

tag: treatment 1

value: Tamoxifen

tag: treatment 2

value: #1 control #2 control; #3 EAE; #4 EAE

value: mRNA

value: 15-27 weeks


title: Drought_end-point replicate 1

description:
Drought_end-point
replicate 1

value: rosette leaves

value: WT

tag: time

value: day 18


title: Pool2_FB

description: healthy and EAE microglia HTO library

tag: tissue

tag: strain

tag: library type

value: HTO

tag: antibodies/tags

value: #1="mouse 1"=ACCCACCAGTAAGAC; #2="mouse 2"=GGTCGAGAGCATTCA; #3= "mouse 3"=CTTGCCGCATGTCAT; #4="mouse 4"=AAAGCATTCTTCACG


title: Patient 3 Slide A141 ROI 014

value: head and neck carcinoma

tag: gender

value: Female

tag: anatomical location

value: Right lateral tongue

tag: treatment

value: med


title: Cont_recovery replicate 3

description:
Cont_recovery
replicate 3

tag: cell line

tag: cell type


title: Aa4_Rheumatoid Arthitis_0 months_None

value: Rheumatoid Arthitis

value: 0 months

value: peripheral blood


title: Cont_recovery replicate 2

description:
Cont_recovery
replicate 2

tag: genotype


title: Pool2_GEX

value: microglia

value: brain

value: CX3CR1-CreERT2 x CD83-flox

value: #1 - #4 CX3CR1-CreERT2 +

tag: age


title: Aa3_Rheumatoid Arthitis_0 months_None

tag: subject status


title: Aa2_Rheumatoid Arthitis_0 months_None


title: Cont_recovery replicate 1

description:
Cont_recovery
replicate 1


title: Patient 2 Slide A410 ROI 012

value: Male

value: Right neck

tag: tumor level

value: high


title: Patient 2 Slide A410 ROI 017

value: Background

value: negative


title: Cold-HL_recovery replicate 3

description:
Cold-HL_recovery
replicate 3

value: rosette leaves

value: WT

value: day 18


title: Aa10_Rheumatoid Arthitis_0 months_None


title: Pool1_GEX

extract_protocol:
Mice were perfused with ice-cold PBS by cardiac puncture and brains were collected in RPMI medium on ice. Tissue was homogenised using a tissue dounce grinding set. Homogenates were subjected to density centrifugation (37% Percoll, 550g, 18 min) to remove myelin debris. Surface staining was performed in PBS containing BioLegend CD45 (I3/2.3), CD11b (M1/70), CX3CR1 (SA011F11) and P2RY12 (S16007D) antibodies for 30 min at 4°C. The antibody cocktail for cell sorting was supplemented with hashtag antibodies (TotalSeq-B0301/B0302/B0303/B0304 anti-mouse hashtag 1/2/3/4, Biolegend) to label individual animals. Microglia were isolated by fluorescence-activated cell sorting (FACS) for the presence of CD45 (intermediate), CD11b, CX3CR1 and P2RY12 signals. Cells were sorted from individual animals, washed, counted and concentrated to 1,000 cells/µl before pooling. Four independent pools were generated, each containing equal numbers of cells from healthy wild-type, healthy CD83 knock-out, EAE wild-type and EAE CD83 knock-out animals (16 animals in total, 4 biological replicates per condition in 4 pools, 1 pool containing all 4 conditions).
Up to 25,000 cells (hyper-loading) pooled from 4 animals were loaded into a single well of a Chromium chip G (10x Genomics). 3’ gene expression libraries were generated using Chromium Next GEM Single Cell 3' Kit 3.1 with 3' Feature Barcode Kit and dual indexing (10x Genomics protocol CG000316 Rev D). Libraries were sequenced as PE150 by Illumina sequencing to 65-80% saturation by the external provider Novogene.

tag: genotype 1

tag: genotype 2

value: Tamoxifen

value: #1 control #2 control; #3 EAE; #4 EAE

value: mRNA

value: 15-27 weeks


title: Cold-HL_recovery replicate 1

description:
Cold-HL_recovery
replicate 1


title: Aa1_Rheumatoid Arthitis_0 months_None

value: Rheumatoid Arthitis

value: 0 months

value: peripheral blood


title: Patient 2 Slide A410 ROI 018

value: head and neck carcinoma

value: low


title: Patient 2 Slide A410 ROI 015

value: Male

value: med


title: EGR2 CUT&Tag of Egr2ΔT Mouse 2D2 TH17 Cells

city: Bethesda

first: Behdad (Ben)

last: Afzali Khoshkbijari

state: MD

address: 10 Center Drive, 10/8D03

department: Kidney Diseases Branch

institute: National Institutes of Diabetes, Digestive, and Kidney Diseases

data_processing:
EGR2 peaks were called by SEACR v1.3 (Sparse Enrichment Analysis for CUT&RUN) with options ‘0.01 non stringent’, all fragment sizes included. EGR2 and Rat IgG CUT&Tag bigwig files for WT and Egr2ΔT nuclei were generated using deepTools v3.5.1 bamCoverage with options ‘extendReads and normalizeUsing RPKM’. To further filter peaks, RPKM normalized signal +/- 200bp from peak summits was calculated by deepTools computeMatrix via sum. Bona fide EGR2 peaks were established as those with EGR2 signal at least 4-fold higher than IgG in WT nuclei and at least 4-fold higher than EGR2 signal in Egr2ΔT nuclei and excluded from the blacklist (mm10). RPKM normalized EGR2 and IgG CUT&Tag signals +/-5kb from filtered EGR2 peaks were visualized with deepTools. EGR2 peaks and signal files were visualized in IGV v2.4.14. Filtered peaks were ranked by SEACR calculated total signal within peaks. EGR2 known motif scoring was evaluated by HOMER v4.11.1 findMotifsGenome.pl with option -size 200 and EGR2 peaks were annotated to genes and features with annotatePeaks.pl.
Assembly: mm10/GRCm38
Supplementary files format and content: bigWig
Library strategy: CUT&Tag

source_name: In Vitro Polarized TH17 Cells

extract_protocol: CUT&Tag was performed using the established bench top CUT&Tag V.3 protocol (https://www.protocols.io/view/bench-top-cut-amp-tag-kqdg34qdpl25/v3) with the following specifications. Briefly, natively isolated nuclei from in vitro polarized mouse 2D2 WT or Egr2ΔT TH17 cells were prepared after cell sorting of live (propidium iodide negative) cells. 6 x 10^5 ConA-bound nuclei per genotype were resuspended in antibody buffer and distributed equally into four conventional 1.5 ml tubes. Antibodies were diluted at 1:50 for anti-EGR2 (Clone: erongr2, CUST06000, Invitrogen, Custom Stock Dilution: 0.5 µg/ml) and 1:100 for Rat IgG (16-4321-82, Invitrogen, Custom Stock Dilution: 1 µg/mL) and incubated with nuclei for 1 hr at RT. Rabbit anti-rat (ab102248, Abcam) secondary antibody was used at 1:100 dilution. pA-Tn5 was sourced pre-loaded (C01070001, Diagenode). Prepared libraries were normalized and prepared for sequencing via NovaSeq SP (Illumina) at the NHLBI Genomics Core. Raw reads were processed using CutRunTools/2020062990 with the mm10 mouse genome as reference.

value: In Vitro Polarized TH17 Cells

tag: chip antibody

value: CD4+ T Cells

value: Live cell sorting and nuclei extraction, followed by CUT&Tag


title: IgG CUT&Tag of Wild Type Mouse 2D2 TH17 Cells

value: anti-IgG

value: Wild Type


title: IgG CUT&Tag of Egr2ΔT Mouse 2D2 TH17 Cells

value: IgG


title: Patient 2 Slide A410 ROI 014

value: Right neck

value: high


title: Patient 2 Slide A410 ROI 013


title: Cold-HL_end-point replicate 3

description:
Cold-HL_end-point
replicate 3

value: rosette leaves

value: WT

tag: time

value: day 18


title: Patient 2 Slide A410 ROI 021

tag: tissue


title: T3 10nM+Irisin 2

city: Botucatu

first: Miriane

last: Oliveira

address: District of Rubião Jr

country: Brazil

institute: Botucatu Medical School, São Paulo State University (UNESP), Botucatu, São Paulo, Brazil.

data_processing:
Steps for adapter removal and low quality read filtering were performed using Cutadapt and Trimmomatic software.
The reads were aligned and quantified in Kallisto (version 0.43.0) using the Gh38 human genome index (GRCh38.p12 release-92) as a reference.
The abundance data (Counts) generated were imported using the Bioconductor Tximport package from R  and used for the analysis of differential gene expression with the Deseq2 package. Multifactor design analysis was used to control the effect of biological variation between samples from the same condition.
Assembly: GRCh38.p12 release-92
Supplementary files format and content: Matrix table with raw gene counts for every gene and every sample

source_name: human subcutaneous adipocytes

growth_protocol: Human subcutaneous preadipocytes (HPAd - 802S-05A; Cell Applications, Inc., San Diego, CA, USA) were purchased from Sigma-Aldrich (St. Louis, MO, USA). Cultured HPAd were differentiated into mature adipocytes according to the manufacturer's instructions. In brief, preadipocytes were cultured in preadipocyte basal medium (Cat No. 811-500; Sigma-Aldrich). After reaching approximately 70%–80% confluence, preadipocytes were transferred to 6-well plates (approximately 1.7 × 105 cells/well) and maintained in the basal medium for 48 h. After 48 h (day 0), cells differentiation was initiated using a human adipocyte differentiation medium (Cat No. 811D-250; Sigma-Aldrich). The differentiation medium was renewed every 3 days for 16 days, according to protocol . Differentiated adipocytes were deprived of pre-existing hormones using a human adipocyte starvation medium (Cat No. 811S-250; Sigma-Aldrich) one day before application of treatments.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, Carlsbad, CA, USA). RNA samples were quantified in Qubit and the integrity of the RNA was analyzed using a  Bioanalyzer 2100® (Agilent, Santa Clara, CA, USA). Three RNA samples from each group were used to build each of the libraries.
The libraries were constructed using the TruSeq1 RNA Sample Prep kit v2 (Illumina, San Diego, CA, USA) following the protocol suggested by the manufacturer. Runs were performed on the Illumina HiSeq2500 platform with 100 bp paired end reads.

treatment_protocol: After 16d of growth in differentiation medium, adipocytes were treated with 10 nM triiodothyronine (T3 group; Sigma- Aldrich St. Louis, MO, USA) or 1 μg/ml (20 nM) irisin (I group; Sigma- Aldrich St. Louis, MO, USA); control cells were allowed to grow in the same culture conditions, but in the absence of test hormones.

value: Subcutaneous adipocytes cell

value: treated with T3 10nM+Irisin 20nM


title: Patient 2 Slide A410 ROI 020

value: head and neck carcinoma

value: Background

value: negative


title: T3 10nM+Irisin 1


title: Irisin 20nM 3

value: treated with Irisin 20nM


title: Cold-HL_recovery replicate 2

description:
Cold-HL_recovery
replicate 2


title: Cold_recovery replicate 3

description:
Cold_recovery
replicate 3


title: Patient 12 Slide D18 ROI 052

value: Male

value: Left lateral tongue


title: Patient 2 Slide A410 ROI 019


title: Irisin 20nM 2


title: pituitaries of hpg mice, Male, GnRH, 23

city: New York

first: Stuart

last: Sealfon

state: NY

address: One Gustave L. Levy Place

department: Department of Neurology

institute: Icahn School of Medicine at Mount Sinai

data_processing:
Raw data were processed using bcl2fastq Conversion Software (Illumina) to obtain FASTQ files, and the FASTQ files were aligned to the mm10 genome using STAR (Dobin et al., 2013).
Gene expression was quantified with featureCounts (Liao et al., 2014).
Assembly: mm10
Supplementary files format and content: tab delimited file including the counts of reads for all genes and for all samples

source_name: pituitaries of hpg mice

extract_protocol:
Mouse pituitary tissues were homogenized in a Bead Ruptor Elite bead mill homogenizer (Omni International, Kennesaw, GA) cooled by liquid nitrogen and homogenized for 2 x 20 seconds at 4.2 m/s. Pituitary tissue homogenates were processed for RNA extraction using the Agencourt RNAdvance Tissue Kit (Beckman Coulter, Indianapolis, IN) on a BioMek FXP Laboratory Automation Workstation (Beckman Coulter, Indianapolis, IN) according to the manufacturer’s instructions. The purity and concentration of the RNA samples were evaluated on a NanoDrop One/One spectrophotometer (ThermoFisher Scientific) and quantified using Quant-iT RiboGreen RNA Assay Kit (ThermoFisher Scientific). The RNA integrity was assessed with an RNA Nano 6000 Assay Kit of the Agilent Bioanalyzer 2100 system (Agilent Technologies, Palo Alto, CA, United States). RNA integrity numbers (RINs) for all samples were above 8.2 with a median RIN of 9.1. A total of 250 ng total RNA per sample was used as input material for the cDNA library preparation.
cDNA libraries were constructed from total RNA using the Universal Plus mRNA-Seq kit (Tecan Genomics, San Carlos, CA, United States) in a Biomek i7 Automated Workstation (Beckman Coulter). Briefly, mRNA was isolated from purified 300 ng total RNA using oligo-dT beads and used to synthesize cDNA following the manufacturer’s instructions. The transcripts for ribosomal RNA (rRNA) and globin were further depleted using the AnyDeplete kit (Tecan Genomics) prior to the amplification of libraries. Library concentration was assessed fluorometrically using the Qubit dsDNA HS Kit (Thermo Fisher), and quality was assessed with the Genomic DNA 50Kb Analysis Kit (DNF-467, Agilent Technologies). Following library preparation, samples were pooled, preliminary sequencing of cDNA libraries (average read depth of 90,000 reads) was performed using a MiSeq system (Illumina) to confirm library quality and concentration. Deep sequencing was subsequently performed using an S4 flow cell in a NovaSeq sequencing system (Illumina) (average read depth ~30 million pairs of 2×100 bp reads). In addition to the 8-base i5 and i7 barcodes, the i7 adaptor contains 8 random bases immediately following the library index. The additional 8 bases are used for duplicate read determination using the Duplicate Marking Tool. To take advantage of this feature, the libraries were sequenced using 16 cycles for the i7 index read.

treatment_protocol: Hypogonadal mice (hpg/hpg) were injected once daily i.p. with GnRH (1 µg) or saline for a total of 10 days. One hour after the last injection, animals were sacrificed, and pituitaries were snap frozen for bulk RNA-seq and qPCR analyses.

value: pituitaries

value: hpg

tag: Sex

tag: group

value: GnRH


title: Irisin 20nM 1


title: Cold_recovery replicate 1

description:
Cold_recovery
replicate 1


title: Cold_recovery replicate 2

description:
Cold_recovery
replicate 2


title: pituitaries of hpg mice, Male, GnRH, 22


title: Cold-HL_end-point replicate 2

description:
Cold-HL_end-point
replicate 2


title: EGR2 CUT&Tag of Wild Type Mouse 2D2 TH17 Cells

value: In Vitro Polarized TH17 Cells

value: CD4+ T Cells

value: Wild Type

value: Live cell sorting and nuclei extraction, followed by CUT&Tag


title: Patient 12 Slide D18 ROI 051

value: med


title: pituitaries of hpg mice, Male, GnRH, 21


title: pituitaries of hpg mice, Male, GnRH, 25


title: T3 10nM 3

value: treated with T3 10nM


title: Patient 12 Slide D18 ROI 048

value: high


title: pituitaries of hpg mice, Male, GnRH, 20


title: Patient 12 Slide D18 ROI 049


title: Cold-HL_end-point replicate 1

description:
Cold-HL_end-point
replicate 1

value: rosette leaves

value: WT

value: day 18


title: T3 10nM 2

value: Subcutaneous adipocytes cell


title: pituitaries of hpg mice, Male, GnRH, 24


title: Patient 12 Slide D18 ROI 047

value: head and neck carcinoma


title: T3 10nM 1


title: Patient 12 Slide D18 ROI 046

value: Male


title: Cold_end-point replicate 1

description:
Cold_end-point
replicate 1


title: Cold_end-point replicate 3

description:
Cold_end-point
replicate 3


title: pituitaries of hpg mice, Male, GnRH, 19


title: pituitaries of hpg mice, Male, GnRH, 18


title: CTRL 3

value: untreated


title: Patient 12 Slide D18 ROI 045

value: Left lateral tongue

value: negative


title: Cold_end-point replicate 2

description:
Cold_end-point
replicate 2


title: EOMA _circRNA-007371-pLC5-ciR_rep3 [ncRNA-Seq]

data_processing:
Raw data (raw reads) of fastq format were firstly processed through custom perl and python scripts. In this step, clean datas(clean reads) were obtained by removing reads containing ploy-N, with 5’ adapter contaminants, without 3’adapter or the insert tag, containing ploy A or T or G or C and low quality reads from raw data. At the same time, Q20, Q30, and GC-content of the raw dataswere calculated.
For known miRNA alignment, the acquired clean data were mapped to miRBase20.0 using modified software mirdeep2 and srna-tools-cli to obtain the potential miRNA and draw the secondary structures.
For novel miRNA prediction,  miREvo  and mirdeep2 were used to predict novel miRNA through exploring the secondary structure.
MiRNA expression levels were estimated by TPM (transcript per million) through the following criteria (Zhou et al., 2010):Normalization formula: Normalized expression = mapped readcount/Total reads*1000000
Differential expression analysis of two groups was performed using the DESeq R package (3.0.3). The resulting P-values were adjusted using the Benjamini and Hochberg’s approach.
Assembly: miRBase20.0
Supplementary files format and content: Matrix table with miRNA TPM (transcript per million) for each sample

source_name: EOMA

extract_protocol:
Total RNA was extracted from EOMA cells using TRIzol reagent (Thermo Fisher Scientific, USA).
Sequencing libraries were generated using NEBNext®Multiplex Small RNA Library Prep Set for Illumina®(NEB, USA.) following manufacturer’s recommendations

value: EOMA


title: CTRL 2


title: EOMA _circRNA-007371-pLC5-ciR_rep2 [ncRNA-Seq]


title: Pool1_FB

description: healthy and EAE microglia HTO library

value: microglia

value: brain

tag: strain

value: CX3CR1-CreERT2 x CD83-flox

value: #1 - #4 CX3CR1-CreERT2 +

tag: treatment 1

value: Tamoxifen

tag: treatment 2

value: #1 control #2 control; #3 EAE; #4 EAE

tag: library type

value: HTO

tag: antibodies/tags

value: #1="mouse 1"=ACCCACCAGTAAGAC; #2="mouse 2"=GGTCGAGAGCATTCA; #3= "mouse 3"=CTTGCCGCATGTCAT; #4="mouse 4"=AAAGCATTCTTCACG


title: Patient 12 Slide D18 ROI 043

tag: gender

tag: anatomical location

tag: treatment


title: EOMA _circRNA-007371-pLC5-ciR_rep1 [ncRNA-Seq]

tag: cell line


title: Patient 12 Slide D18 ROI 044

tag: age

tag: tumor level


title: CTRL 1

tag: cell type


title: EOMA _Empty- pLC5-ciR_rep3 [ncRNA-Seq]

value: Empty- pLC5-ciR


title: pituitaries of hpg mice, Male, placebo, 17

value: pituitaries

tag: genotype

value: hpg

value: placebo


title: pituitaries of hpg mice, Male, placebo, 14

value: Male


title: pituitaries of hpg mice, Male, placebo, 15


title: Patient 12 Slide D18 ROI 042

value: head and neck carcinoma