title: Liquid_CD-Glc_r3_BS-seq

description: Bisulfite-seq for hyphae from liquid culture with CD-Glc replicate 3

data_processing:
Base-calling and de-multiplexing were performed by HCS version 2.2.58, RTA version 1.18.64, and bcl2fastq2 version 2.17.
Reads were mapped to the reference genome and methylation levels were calculated by Bisulfighter software based on LAST version 572.
Cytosine sites covered by at least 10 reads in all samples were used for the analyses.
The read mapping statistics and the detail setting of program options were provided in Supplementary Material.
Genome_build: The reference genome sequence of the A. oryzae RIB40 strain (revision s01-m09-r05) was downloaded from AspGD.
Supplementary_files_format_and_content: bigWig files that contain methylation levels at cytosine sites covered by at least 10 reads in all samples.

extract_protocol:
DNA was extracted by NucleoSpin® Microbial DNA kit (MACHEREY-NAGEL, Düren, Germany). Briefly, hyphae were harvested after liquid culture, washed by 100 mL of autoclaved Milli-Q water, and ground using a mortar and a pestle in the presence of liquid N2. Hyphae after solid culture were ground similarly, however together with solid medium due to difficulty in the separation. About 40 mg of the frozen powder after grinding hyphae was used for DNA extraction. DNA extraction was performed using the kit based on the manufacturer’s protocol. DNA was finally eluted by 100 µL of 5 mM Tris-HCl (pH 8.5) and stored at -20°C.
Sequencing experiments were conducted by the outsourcing company (Takara, Japan). Briefly, DNA quality was checked by NanoDrop (Thermo Fisher Scientific, USA), Quant-iT Broad-Range dsDNA Assay Kit (Thermo Fisher Scientific, USA), and agarose gel electrophoresis. For each sample, 100 ng of DNA was used for bisulfite conversion with TruSeq DNA Methylation Kit (Illumina, USA) where 0.1 ng of unmethylated lambda DNA (Promega, USA) was added as spike-in control. Sequence libraries were constructed following the manufacturer's protocol, and the library quality was checked by BioAnalyzer 2100 (Agilent Technologies, USA). Paired-end 100 bp reads were obtained by HiSeq 2500 (Illumina, USA).


title: Solid_WB_r2_BS-seq

status: Public on Apr 01 2025

type: SRA

city: Koto-ku

first: Yutaka

last: Saito

state: Tokyo

country: Japan

institute: National Institute of Advanced Industrial Science and Technology (AIST)

description: Bisulfite-seq for hyphae from solid culture with WB replicate 2

library_source: genomic

molecule: genomic DNA

organism: Aspergillus oryzae RIB40

source_name: Solid culture with WB replicate 2

growth_protocol: The Aspergillus oryzae wild-type strain RIB40 was distributed by the National Research Institute of Brewing (NRIB, Hiroshima, Japan). The strain was maintained at 30°C on Czapek–Dox (CD) agar containing 2% glucose for spore formation (Tamano et al. 2007). Liquid culture (CD-Glc) was performed by inoculating 2.5 × 107 spores of RIB40 to 50 mL of CD liquid medium in a 250-mL flask, followed by incubation at 30°C with shaking at 200 rpm for 48 h. Solid medium was prepared by mixing 2.8 g of wheat bran with Milli-Q water (2.2 mL) in a 150 mL flask, followed by autoclaving at 121°C for 30 min as previously described (Tamano et al. 2008). Solid culture (WB) was performed by inoculating 1 × 107 spores of RIB40 per flask, followed by stationary incubation at 30°C for 20 h. Then, the medium with hyphae was mixed by shaking the flask, and incubated similarly for another 28 h.

tag: strain

tag: tissue

value: Hyphae


title: hiPSC>SMC differentiation #1, total RNA, day00, biological replicate #4

city: Munich

first: Bernd

middle: Henrik

last: Northoff

address: Marchioninistr. 15

department: Institute of Laboratory Medicine

country: Germany

institute: Ludwig-Maximilians-University Munich

description:
counts_raw_genes_SMC.txt
counts_raw_transcripts_SMC.txt
counts_raw_circRNAs_SMC.txt

library_source: transcriptomic

data_processing:
Fastq-files were generated using Illumina bcl2fastq and demultiplexed.
Sequenced reads were trimmed for adaptor sequence/low-quality sequence using FastQC software.
Sequenced reads were mapped to the reference genome GRch37 using HISAT2 for quantification of genes and transcripts and segemehl for quantification of circular RNAs.
Aligned reads were quantified using StringTie for genes and transcripts and featureCounts for circular RNAs.
Assembly: GRCh37
Supplementary files format and content: Genes: Tab-delimited text files include raw counts for each sample.
Supplementary files format and content: Transcripts: Tab-delimited text files include raw counts for each sample.
Supplementary files format and content: Circular RNAs: Tab-delimited text files include raw counts for each sample.

molecule: total RNA

organism: Homo sapiens

growth_protocol: The human iPS cell line ISFi001-A was maintained on hESC-qualified Matrigel (BD Biosciences)-coated dishes in mTeSR1 medium (StemCell Technologies).

extract_protocol:
Isolation of RNA was performed using TRIzol reagent (Thermo Fisher Scientific).
RNA libraries for RNA-seq were prepared using Ovation Universal RNA-Seq System Kit (Nugen) following manufacturer's protocols.

treatment_protocol: The human iPS cells were differentiated according to Patsch et al. 2015 (PMID: 26214132).

tag: cell line

tag: cell type

value: Differentiated human pluripotent stem cells

tag: treatment

tag: time

tag: differentiation

tag: biological replicate


title: Solid_WB_r3_BS-seq

description: Bisulfite-seq for hyphae from solid culture with WB replicate 3

source_name: Solid culture with WB replicate 3


title: CON_10h_E

city: Shanghai

first: Xiaowei

last: Chai

address: Siping Road

country: China

institute: Tongji University

description: Library name: Untreated_10h rep 1

data_processing:
Fastp (0.20.1), HISAT2(2.1.0), DESeq2(1.22.2)
Raw reads of fastq format were firstly processed using fastp software and the low quality reads were removed to obtain the clean reads
The clean reads were mapped to the reference genome using HISAT2
Differential expression analysis was performed using the DESeq2
Assembly: C_albicans_SC5314_A22_current_chromosomes
Supplementary files format and content: xls files includes FPKM values for each Sample

organism: Candida albicans SC5314

source_name: Candida albicans SC5314

growth_protocol: Candida albicans was cultured in RPMI1640 medium at a constant temperature of 30°C for 6 hours and 10 hours.

extract_protocol:
Total RNA was extracted using the TRIzol reagent (Invitrogen, CA, USA) according to the manufacturer’s protocol.
Then the libraries were constructed using VAHTS Universal V6 RNA-seq Library Prep Kit according to the manufacturer’s instructions.

treatment_protocol: Candida albicans was cultured  in RPMI1640 medium at 30°C for 6 hours and 10 hours in the presence of the compound at concentrations of 0.5 μg/mL and 2 μg/mL.

value: Candida albicans SC5314

value: Control


title: VEXAS syndrome 1 [1]

city: Paris

first: Chloé

last: Grolleau

address: 1 avenue Claude Vellefaux

department: Hopital saint Louis

country: France

institute: INSERM U1342, eq 16

description:
1
10x Genomics

data_processing:
Quality of raw data has been evaluated with FastQC
Poor quality sequences has been trimmed or removed with Trimmomatic software to retain only good quality paired reads
Illumina DRAGEN bio-IT Plateform (v3.10.11) was used for mapping on hg38 reference genome and quantification with gencode v42 annotation gtf file.
Library orientation, library composition and coverage along transcripts were checked with Picard tools.
Assembly: hg38
Supplementary files format and content: tab-delimited text files including expecting counts and TPM

source_name: skin

extract_protocol:
We included patients with skin lesions of VEXAS syndrome (n=6), myelodysplasia-cutis (n=4), idiopathic sweet syndrome (n=5) and leukemia cutis (n=5). Five healthy controls (HC) were recruited for skin biopsy from plastic breast surgery waste. The study was approved by the by our institutional ethic committee, and all patients were consented. Total RNA was automatically extracted from one lesional formaldehyde-fixed and paraffin-embedded skin biopsy for each patient and control using the Maxwell RSC RNA FFPE kit according to the manufacturer’s protocol.
SMARTer® Stranded Total RNA-Seq Kit v3-Pico Input Mammalian Kit from Takara

value: skin

tag: Sex

value: male

tag: disease

value: VEXAS syndrome


title: hiPSC>SMC differentiation #1, total RNA, day00, biological replicate #3


title: Solid_WB_r1_BS-seq

description: Bisulfite-seq for hyphae from solid culture with WB replicate 1

source_name: Solid culture with WB replicate 1


title: Ileal Surgical tissue, Crohns Disease [ST11]

city: Atlanta

first: Subra

last: Kugathasan

state: GA

address: 1760 Haygood Dr

department: Pediatrics

country: USA

institute: Emory University

data_processing:
library strategy: Spatial Transcriptomics
Sequencing reads obtained were converted to fastq files and aligned to human reference genome GRCh38 to generate count matrices using 10x Cell Ranger and Space Ranger
Assembly: Human reference GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

molecule: polyA RNA

source_name: Ileal Surgical tissue

extract_protocol:
Ileal biopsies obtained were protease digested, the recobered singel cells were processed for 10X Genomics 3’ Single cell RNA sequencing with target of 10000 cells which are later sequnced at a read depth of 50,000 reads per cell
Ileal surgical resections collected are cut into 10μm tissue sections that were processed using 10x Visium spatial transcriptomics for both H&E stain and Immunofluroscence using epithelial marker (E-Cadherin), immune cell marker from Cell Signaling (CD45/ PTPRC) and stromal marker α-Smooth muscle actin (α-SMA).

tag: inflammation status

value: Non-Inflamed

value: Ileal Surgical tissue

tag: gender

value: Female

tag: age

tag: race

value: African American


title: hiPSC>SMC differentiation #1, total RNA, day00, biological replicate #2


title: Liquid_CD-Glc_r2_BS-seq

description: Bisulfite-seq for hyphae from liquid culture with CD-Glc replicate 2

source_name: Liquid culture with CD-Glc replicate 2


title: CAS_2_6h_G

description: Library name: Treated_6h_2 rep 3

value: 2 μg/mL compound


title: CAS_2_6h_E

description: Library name: Treated_6h_2 rep 1


title: CAS_2_6h_F

description: Library name: Treated_6h_2 rep 2


title: Ileal Surgical tissue, Crohns Disease [ST12]


title: Liquid_CD-Glc_r1_BS-seq

description: Bisulfite-seq for hyphae from liquid culture with CD-Glc replicate 1

source_name: Liquid culture with CD-Glc replicate 1


title: Ileal Surgical tissue, Crohns Disease [ST9]

value: Inflamed


title: hiPSC>SMC differentiation #1, total RNA, day00, biological replicate #1


title: hiPSC>EC differentiation #1, total RNA, day12, biological replicate #4

description:
counts_raw_genes_EC.txt
counts_raw_transcripts_EC.txt
counts_raw_circRNAs_EC.txt


title: hiPSC>EC differentiation #1, total RNA, day12, biological replicate #3


title: male, 28 degrees, biorep3

city: Birmingham

first: Alexander

middle: Tate

last: Lasher

state: AL

address: 1300 University Blvd.

department: Biology

institute: University of Alabama at Birmingham

description:
X169
w1118 RNAseq expected counts.csv

data_processing:
Low quality reads were removed with BGI internal software SOAPnuke (version：v1.5.2 parameters: -l 15 -q 0.5 -n 0.1)
Reads were maped to the Drosophila genome using HISAT (Version: v2.0.4 Parameters: --phred64 --sensitive --no-discordant --no-mixed -I 1 -X 1000)
Transcripts were compared to known annotated genes on the Drosophila genome using StringTie (Version: v1.0.4 Parameters: -f 0.3 -j 3 -c 5 -g 100 -s 10000 -p 8) and Cuffcompare (Cufflinks Version: v2.2.1 Parameters: -p 12)
Novel transcripts were predicted with CPC (Version: v0.9-r2 Parameters: Default)
Differently spliced genes were determined with rMATS (Version: v3.2.5 Parameters: -analysis U -t paired -a 8)
reads were mapped to reference using Bowtie2 (Version: v2.2.5 Parameters: -q --phred64 --sensitive --dpad 0 --gbar 99999999 --mp 1,1 --np 1 --score-min L,0,-0.1 -I 1 -X 1000 --nomixed --no-discordant -p 1 -k 200) and expression level calculated with RSEM (Version: v1.2.12 Parameters: default)
Differently expressed genes were detected with DEseq2 (Parameters: Fold Change >= 2.00 and Adjusted Pvalue <= 0.05)
Assembly: dm6
Supplementary files format and content: Comma separated value file with expected counts calculated with RSEM for all samples

organism: Drosophila melanogaster

source_name: whole body

extract_protocol:
RNA was wxtracted with TRIzol following manufacturer protocol.
1.mRNA enrichment and purification. Oligo dT Selection (mRNA enrichment): Use oligo dT beads toenrich mRNA with poly A tail.   2.RNA fragment and reverse transcription.RNA fragmentation and first-strand cDNAs were generated using random N6-primed reverse transcription, followed by the second-strand cDNA synthesis.   3.End repair, add A and adaptor ligation.The synthesized cDNA was subjected to end-repair and then was 3’ adenylated. Adaptors were ligated to the ends of these 3’ adenylated cDNAfragments.   4.PCR amplification. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer.   5.Cyclization. Denature the PCR product by heat and the DNA iscyclized by splint oligo and DNA ligase.   6.DNA nanoball synthesis.

value: whole body

value: M

value: 35 days

tag: genotype

value: 28 degrees


title: female, 28 degrees, biorep4

description:
X170
w1118 RNAseq expected counts.csv

value: F


title: CAS_05_6h_G

description: Library name: Treated_6h_05 rep 3

value: 0.5 μg/mL compound


title: Ileal Surgical tissue, Crohns Disease [ST7]

value: Male


title: hiPSC>EC differentiation #1, total RNA, day11, biological replicate #4

value: Differentiated human pluripotent stem cells


title: male, 28 degrees, biorep2

description:
X168
w1118 RNAseq expected counts.csv


title: female, 28 degrees, biorep3

description:
X162
w1118 RNAseq expected counts.csv


title: CON_6h_G

description: Library name: Untreated_6h rep 3

value: Candida albicans SC5314

value: Control


title: hiPSC>EC differentiation #1, total RNA, day12, biological replicate #2


title: Ileal Surgical tissue, Crohns Disease [ST8]


title: CAS_05_6h_E

description: Library name: Treated_6h_05 rep 1


title: Ileal Surgical tissue, Crohns Disease [ST4]


title: hiPSC>EC differentiation #1, total RNA, day11, biological replicate #3


title: Ileal Surgical tissue, Crohns Disease [ST5]


title: CON_6h_F

description: Library name: Untreated_6h rep 2


title: female, 28 degrees, biorep1

description:
X160
w1118 RNAseq expected counts.csv


title: CON_6h_E

description: Library name: Untreated_6h rep 1


title: hiPSC>EC differentiation #1, total RNA, day11, biological replicate #2


title: Ileal Surgical tissue, Crohns Disease [ST3]


title: hiPSC>EC differentiation #1, total RNA, day11, biological replicate #1


title: male, 28 degrees, biorep1

description:
X155
w1118 RNAseq expected counts.csv


title: male, 24 degrees, biorep4

description:
X110
w1118 RNAseq expected counts.csv

value: 45 days

value: 24 degrees


title: Ileal Surgical tissue, Crohns Disease [ST2]

value: Ileal Surgical tissue


title: hiPSC>EC differentiation #1, total RNA, day10, biological replicate #4


title: hiPSC>EC differentiation #1, total RNA, day12, biological replicate #1


title: female, 24 degrees, biorep4

description:
X78
w1118 RNAseq expected counts.csv


title: Ileal Surgical tissue, Crohns Disease [ST6]


title: female, 28 degrees, biorep2

description:
X161
w1118 RNAseq expected counts.csv


title: Ileal mucosal cells, Crohns Disease [Sc12]

library_source: transcriptomic single cell

data_processing:
Sequencing reads obtained were converted to fastq files and aligned to human reference genome GRCh38 to generate count matrices using 10x Cell Ranger and Space Ranger
Assembly: Human reference GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Ileal mucosal cells

value: Non-Inflamed

value: Ileal mucosal cells

value: European


title: hiPSC>EC differentiation #1, total RNA, day10, biological replicate #3


title: female, 24 degrees, biorep3

description:
X77
w1118 RNAseq expected counts.csv


title: CAS_05_6h_F

description: Library name: Treated_6h_05 rep 2


title: hiPSC>EC differentiation #1, total RNA, day10, biological replicate #2


title: Ileal mucosal cells, Crohns Disease [Sc11]

value: Female


title: female, 24 degrees, biorep2

description:
X76
w1118 RNAseq expected counts.csv

value: whole body


title: female, 24 degrees, biorep1

description:
X75
w1118 RNAseq expected counts.csv


title: hiPSC>EC differentiation #1, total RNA, day10, biological replicate #1


title: Ileal mucosal cells, Crohns Disease [Sc10]


title: Ileal Surgical tissue, Crohns Disease [ST10]

value: African American


title: Ileal mucosal cells, Crohns Disease [Sc8]


title: male, 24 degrees, biorep3

description:
X70
w1118 RNAseq expected counts.csv

value: M


title: hiPSC>EC differentiation #1, total RNA, day09, biological replicate #4


title: Ileal mucosal cells, Crohns Disease [Sc9]


title: Ileal Surgical tissue, Crohns Disease [ST1]

value: Inflamed


title: hiPSC>EC differentiation #1, total RNA, day09, biological replicate #3


title: hiPSC>EC differentiation #1, total RNA, day09, biological replicate #2


title: male, 24 degrees, biorep1

description:
X68
w1118 RNAseq expected counts.csv


title: Ileal mucosal cells, Crohns Disease [Sc7]


title: Ileal mucosal cells, Crohns Disease [Sc6]


title: hiPSC>EC differentiation #1, total RNA, day09, biological replicate #1


title: Ileal mucosal cells, Crohns Disease [Sc5]


title: hiPSC>EC differentiation #1, total RNA, day08, biological replicate #4


title: Water control for batch 8 (Replicate 4).

type: RNA

city: Mason

first: Bastian

middle: Gregory

last: Selman

state: Ohio

address: 8700 Mason Montgomery Rd

institute: Procter & Gamble

hyb_protocol: 7.5 micrograms of labeled cRNA was fragmented manually and hybridized to Affymetrix Human Genome U219-96 arrays for 16 hr, washed, stained and scanned using an Affymetrix GeneTitan (Santa Clara, CA).

scan_protocol: Arrays were scanned using an Affymetrix GeneTitan (Santa Clara, CA).

data_processing: The data were analyzed using the rma function in the affy package for R. This function uses RMA for background correction, performs probe specific correction, normalizes using quantile normalization and finally applies a median polish. Package citation: Gautier L, Cope L, Bolstad BM, Irizarry RA (2004). “affy—analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics, 20(3), 307–315. ISSN 1367-4803, doi:10.1093/bioinformatics/btg405.

label: biotin

source_name: TK6 Human lymphoblastoid cells

label_protocol: Labeled cRNA was synthesized from 250 ng of total RNA using the Affymetrix (Santa Clara, CA) IVT-Express labeling kit according to manufacturer's instructions. Seven and a half micrograms of labeled cRNA was fragmented manually and hybridized to Affymetrix Human Genome U219-96 arrays for 16 hr, washed, stained and scanned using an Affymetrix GeneTitan (Santa Clara, CA).

growth_protocol: TK6 cells were purchased from American Type Culture Collection (ATCC, Manassas, VA, CRL-8015). Cells were cultured at 37C with 5% CO2 and 95% humidity in RPMI 1640 with 10% heat-inactivated FBS and 1% pen-strep. Cells were maintained at or below 1E6 cells/ml.

extract_protocol: Total RNA was extracted using Agencourt RNAdvance Tissue XP beads (Beckman Coulter Inc., Danvers, MA) according to the manufacturer's protocol on the cell lysates. RNA integrity was validated using a NanoDrop 8000 Spectrophotometer (Wilmington, DE).

treatment_protocol: All chemicals were tested in triplicate to a top concentration of 10 mM, or the limit of solubility or cytotoxicity. The final concentration of the solvent in these studies was limited to 0.5% (vol/vol) DMSO or water, although in a few isolated cases 1% DMSO or 10% water was used at a top concentration, in accordance with the OECD guidelines.

value: Water

value: control


title: male, 18 degrees, biorep3

description:
X42
w1118 RNAseq expected counts.csv

value: 18 degrees


title: Water control for batch 7 (Replicate 12).


title: Ileal mucosal cells, Crohns Disease [Sc4]

value: Asian


title: Water control for batch 8 (Replicate 2).


title: Water control for batch 8 (Replicate 1).


title: hiPSC>EC differentiation #1, total RNA, day08, biological replicate #3

value: Differentiated human pluripotent stem cells


title: Water control for batch 7 (Replicate 11).


title: male, 18 degrees, biorep2

description:
X41
w1118 RNAseq expected counts.csv


title: Water control for batch 8 (Replicate 5).


title: Water control for batch 8 (Replicate 3).


title: Ileal mucosal cells, Crohns Disease [Sc2]

value: Male


title: male, 24 degrees, biorep2

description:
X69
w1118 RNAseq expected counts.csv

value: 45 days


title: hiPSC>EC differentiation #1, total RNA, day08, biological replicate #1


title: Water control for batch 7 (Replicate 9).


title: female, 18 degrees, biorep4

description:
X31
w1118 RNAseq expected counts.csv

value: F


title: male, 18 degrees, biorep4

description:
X44
w1118 RNAseq expected counts.csv


title: male, 18 degrees, biorep1

description:
X40
w1118 RNAseq expected counts.csv


title: hiPSC>EC differentiation #1, total RNA, day07, biological replicate #4


title: Ileal mucosal cells, Crohns Disease [Sc1]


title: Water control for batch 8 (Replicate 6).


title: female, 18 degrees, biorep3

description:
X30
w1118 RNAseq expected counts.csv


title: PC3_RCAN3_overexpression plasmid

city: Wuhan

first: Gang

last: Luo

state: Hubei

address: 26 Shengli Street

institute: Huazhong University of Science and Technology

data_processing:
Raw sequencing data was first filtered by Trimmomatic (version 0.36), low-quality reads were discarded and the reads contaminated with adaptor sequences were trimmed. Clean Reads were further treated with in-house scripts to eliminate duplication bias introduced in library preparation and sequencing. In brief, clean reads were first clustered according to the UMI sequences, in which reads with the same UMI sequence were grouped into the same cluster. Reads in the same cluster were compared to each other by pairwise alignment, and then reads with sequence identity over 95% were extracted to a new sub-cluster. After all sub-clusters were generated, multiple sequence alignment was performed to get one consensus sequence for each sub-clusters. After these steps, any errors and biases introduced by PCR amplification or sequencing were eliminated.
Deduplicated Reads were mapped to the reference genome of human using STRA software (version 2.5.3a) with default parameters.
Reads mapped to the exon regions of each gene were counted by featureCounts (Subread-1.5.1; Bioconductor) and then RPKM was calculated.
Genes differentially expressed between groups were identified using the edgeR package (version 3.12.1). p-value cutoff of 0.05 and Fold-change cutoff of 2 were used to judge the statistical significance of gene expression differences.
Gene ontology (GO) analysis and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis for differentially expressed genes were both implemented by KOBAS software (version: 2.1.1) with a P-value cutoff of 0.05 to judge statistically significant enrichment. Alternative splicing events were detected by using rMATS (version 3.2.5) with an FDR value cutoff of 0.05 and an absolute value of Δψ of 0.05.
Assembly: hg38
Supplementary files format and content: reads count
Supplementary files format and content: rpkm value

source_name: prostate cancer cells

extract_protocol:
Total RNAs were extracted from samples using TRIzol reagent(Invitrogen, cat. NO 15596026) following the methods by Chomczynski et al (DOI:10.1006/abio.1987.9999). DNA digestion was carried out after RNA extraction by DNaseI. RNA quality was determined by examining A260/A280 with NanodropTM OneCspectrophotometer (Thermo Fisher Scientific Inc). RNA Integrity was confirmed by 1.5% agarose gel electrophoresis. Qualified RNAs were finally quantified by Qubit3.0 with QubitTM RNA Broad Range Assay kit (Life Technologies，Q10210).
2 μg total RNAs were used for stranded RNA sequencing library preparation using Ribo-off rRNA Depletion Kit (Human/Mouse/Rat) (Catalog NO. MRZG12324, Illumina) and KC-DigitalTM Stranded mRNA Library Prep Kit for Illumina® (Catalog NO. DR08502, Wuhan Seqhealth Co., Ltd. China) following the manufacturer’s instruction. The kit eliminates duplication bias in PCR and sequencing steps, by using unique molecular identifier (UMI) of 8 random bases to label the pre-amplified cDNA molecules. The library products corresponding to 200-500 bps were enriched, quantified and finally sequenced on NovaSeq 6000 sequencer (Illumina) with PE150 model.

value: PC3 prostate cancer cell

value: transfected with circ0003553 overexpression plasmid


title: Water control for batch 7 (Replicate 7).


title: Ileal mucosal cells, Crohns Disease [Sc3]

value: Ileal mucosal cells

value: Hispanic


title: Water control for batch 7 (Replicate 8).


title: hiPSC>EC differentiation #1, total RNA, day07, biological replicate #2


title: hiPSC>EC differentiation #1, total RNA, day07, biological replicate #3


title: hiPSC>EC differentiation #1, total RNA, day08, biological replicate #2


title: PC3_RCAN3_negative control plasmid

value: transfected with negative control plasmid


title: female, 18 degrees, biorep1

description:
X28
w1118 RNAseq expected counts.csv

value: whole body


title: DU145_RCAN3_overexpression plasmid

value: DU145 prostate cancer cell


title: Water control for batch 7 (Replicate 10).


title: hiPSC>EC differentiation #1, total RNA, day07, biological replicate #1


title: hiPSC>EC differentiation #1, total RNA, day06, biological replicate #4


title: Placenta_fetus#8

city: Columbia

first: SUSANTA

last: BEHURA

state: MO

address: 920 East Campus Dr

institute: University of Missouri

data_processing:
The quality of raw sequences was checked using FastQC.
Adaptor trimming was performed using cutadapt. The fastp tool was used to perform base quality trimming (Phred score >30) by sliding window scan (4 nucleotides).
Then the reads were mapped to the pig reference genome Sscrofa11.1 using the STAR aligner
Differential gene expression analysis was performed using edgeR
Assembly: Sscrofa11.1
Supplementary files format and content: Read counts in tab separated text file

organism: Sus scrofa

source_name: Plaenta

growth_protocol: Large White x Landrace gilts from the University of Missouri Swine Research Farm were used. The gilts were bred by artificial insemination (AI). The day of AI was considered as gestation day (GD) 1. On GD 45, pregnant pigs (n=6) were euthanized. The uterine horns were opened on the antimesometrial side and all the fetuses and corresponding placentae were removed. Placenta of male and female fetuses from three dams (thus 3 male placentae and 3 female placentae) were used for RNA-seq.

extract_protocol:
Total RNA was isolated from the male and female placenta (in triplicates) using an AllPrep DNA/RNA Mini Kit (Qiagen, Cat No./ID: 80204). A Nanodrop 1000 spectrophotometer (Thermo Fisher Scientific) was used to measure RNA concentration of RNA. The RNA Integrating Number (RIN) was determined using Agilent 2100 bioanalyzer. RNA was supplied to the Novogene Cooperation Inc (Sacramento, CA, USA) for preparation of sequencing libraries and sequencing (RNA-seq).
Each library was sequenced to 20 million paired end reads of 150 bases using a NovaSeq 6000 sequencer.

treatment_protocol: No treatment.

value: Plaenta

tag: fetal sex

tag: gestation day

value: day 45


title: Water control for batch 7 (Replicate 6).

value: Water


title: DU145_RCAN3_negative control plasmid


title: hiPSC>EC differentiation #1, total RNA, day06, biological replicate #3


title: Ara-C resistant KG-1a repeat 1

type: genomic

city: Guangzhou

first: Xinghua

last: Pan

state: Guangdong

address: Shatai South Road

department: Department of Biochemistry and Molecular Biology

institute: Southern Medical University

description:
N1
Ara-C resistant KG-1a repeat 1

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

scan_protocol: Arrays were imaged using BeadArray Reader ( HiScan ) and standard recommended Illumina scanner setting.

data_processing:
Raw EPIC array data were preprocessed using the RnBeads R/Bioconductor package.
Average Beta

label: Cy3 and Cy5

source_name: bone marrow

label_protocol: Standard Illumina Protocal

extract_protocol: DNA was extracted from cell lines according to the service provider (Novogene Co., Ltd).

value: bone marrow

value: leukemia cells


title: hiPSC>EC differentiation #1, total RNA, day06, biological replicate #2


title: Ara-C resistant KG-1a repeat 2

description:
N2
Ara-C resistant KG-1a repeat 2


title: Water control for batch 7 (Replicate 4).

value: control


title: Placenta_fetus#7

value: Female


title: Placenta_fetus#12

value: Male


title: naive KG-1a repeat 2

description:
K2
naive KG-1a repeat 2


title: hiPSC>EC differentiation #1, total RNA, day06, biological replicate #1

value: Differentiated human pluripotent stem cells


title: naive KG-1a repeat 1

description:
K1
naive KG-1a repeat 1


title: Placenta_fetus#11


title: female, 18 degrees, biorep2

description:
X29
w1118 RNAseq expected counts.csv

value: F

value: 45 days

value: 18 degrees


title: Water control for batch 7 (Replicate 3).


title: hiPSC>EC differentiation #1, total RNA, day05, biological replicate #4


title: Water control for batch 6 (Replicate 7).

tag: solvent


title: Placenta_fetus#9

tag: tissue


title: hiPSC>EC differentiation #1, total RNA, day05, biological replicate #3

tag: cell line


title: Water control for batch 7 (Replicate 1).


title: Water control for batch 6 (Replicate 8).


title: Placenta_fetus#10


title: Water control for batch 7 (Replicate 2).


title: hiPSC>EC differentiation #1, total RNA, day05, biological replicate #2

tag: cell type


title: BMA41 mub1delta, CFW20, rep2

city: Zagreb

first: Bojan

last: Zunar

address: Pierottijeva 6

country: Croatia

institute: University of Zagreb Faculty of Food Technology and Biotechnology

data_processing:
The obtained reads were quality-controlled with FASTQC 0.12.1. S. cerevisiae W303 assembly (GenBank GCA_002163515.1) was annotated through liftover with flo, using S288c R64-3-1 assembly as the source, and RNA-seq reads were mapped to it with HISAT2 2.2.1, using default parameters. Count matrices were produced with featureCounts 2.0.3.
Assembly: S. cerevisiae W303 assembly (GenBank GCA_002163515.1)
Supplementary files format and content: csv file containing count matrices

organism: Saccharomyces cerevisiae

source_name: BMA41 mub1Δ

growth_protocol: Exponential phase S. cerevisiae wild type (BMA41) and its mub1Δ derivative were grown for 5 hours in either standard chemically defined yeast medium or standard chemically defined yeast medium supplemented with 20 µg/ml Calcofluor white.

extract_protocol:
Total RNA was isolated by the hot phenol method, as in https://doi.org/10.1093/nar/18.10.3091, precipitated by ethanol, digested by the RNase-free DNase I, and purified by the phenol-chloroform treatment.
RNA was used to prepare stranded, polyA-enriched True-seq libraries and sequenced them with NovaSeq 6000 (2x 150 bp) following the manufacturer's instructions.

value: deleted mub1

tag: treatment

value: 20 ug/ml Calcofluor white


title: Water control for batch 7 (Replicate 5).


title: BMA41 mub1delta, CFW20, rep1


title: hiPSC>EC differentiation #1, total RNA, day05, biological replicate #1

tag: time


title: hiPSC>EC differentiation #1, total RNA, day04, biological replicate #4

tag: differentiation


title: BMA41 mub1delta, CFW0, rep1

value: 0 ug/ml Calcofluor white


title: BMA41, CFW20, rep2

value: WT


title: hiPSC>EC differentiation #1, total RNA, day04, biological replicate #3

tag: biological replicate


title: BMA41, CFW20, rep1


title: SRNA61D_TOP3B_NOSGAL4

city: Baltimore

first: Weidong

last: Wang

state: Maryland

address: 251 Bayview Blvd

institute: National Institute on Aging/NIH

data_processing:
RNA SEQ fastq files are first passed fastqc to remove potentially low quality bases
After cleaning, the fastq files are mapped to fly dm6 genome
The bam files are sorted by samtools.v1.9 sort and index, and then converted to bed format files by bamtools.v1.8 with convert function
The bam files are used to do further gene expression differential analysis by Tuxedo Suite  v2.2.1 pipleline to do genome structrte mapping, merging and gei siginificant defferential gene lists for each comparison.
The bed files are used to get gene raw counts data and fpkm normalized data for further analyses.
Assembly: dm6
Supplementary files format and content: bedGraph

source_name: ovary

growth_protocol: Normal growth condition (standard cornmeal food, 12/12 light cycle, 25'C temp). 4-7 days female matured ovary was dissected in PBS

extract_protocol:
RNA was extracted byTRizol following the product manual. For small RNA, total RNA was run using 15% TBE-urea gel, followed by cutting the 15-35 nt RNA fragments. RNA was extracted by incubating overnight in RNA gel extraction buffer (300 mM sodium acetate ( pH 5.5), 1.0 mM EDTA and 0.25% (wt/vol) SDS)
Library was constructed by standard Illumina protocol. Small RNA-seq library was generated by NEBNext® Multiplex Small RNA Library Prep Set for Illumina (E7300S, New England BioLabs).

value: ovary

tag: Sex

value: female

tag: library type

value: small RNA-seq


title: BMA41, CFW0, rep2


title: hiPSC>EC differentiation #1, total RNA, day04, biological replicate #1


title: Water control for batch 6 (Replicate 5).

value: Water


title: BMA41 mub1delta, CFW0, rep2


title: SRNA61D_TOP3B_NOSAUBKD2


title: Water control for batch 6 (Replicate 6).


title: hiPSC>EC differentiation #1, total RNA, day03, biological replicate #4


title: BMA41, CFW0, rep1


title: SRNA61D_TOP3B_NOSAUBKD1


title: Water control for batch 6 (Replicate 2).


title: hiPSC>EC differentiation #1, total RNA, day03, biological replicate #3


title: Water control for batch 6 (Replicate 4).


title: Water control for batch 6 (Replicate 3).


title: Gastric cancer peritoneal metastasis Tissue3_rep1

first: Sihao

last: Huang

address: Donghu Road 169

description:
Gene expression in gastric cancer peritoneal metastasis tissues from patient3
3PM

hyb_protocol: 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 × GE Hybridization buffer was added to dilute the labeled cRNA. 50 μl of hybridization solution was dispensed into the gasket slide and assembled to the LncRNA 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 with using the Agilent DNA Microarray Scanner (part number G2505C)

data_processing: Agilent Feature Extraction software (version 11.0.1.1) was used to analyze acquired array images. Quantile normalization and subsequent data processing were performed with using the GeneSpring GX v12.1 software package (Agilent Technologies). After quantile normalization of the raw data, LncRNAs and mRNAs that at least 5 out of 10 samples have flags in Present or Marginal (“All Targets Value”) were chosen for further data analysis. Differentially expressed LncRNAs and mRNAs with statistical significance between the two groups were identified through P-value/FDR filtering. Differentially expressed LncRNAs and mRNAs between the two samples were identified through Fold Change filtering. Hierarchical Clustering and combined analysis were performed using homemade scripts.

source_name: Gastric cancer peritoneal metastasis tissues from patient3_rep1

label_protocol: Sample labeling and array hybridization were performed according to the Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technology) with minor modifications. Briefly, mRNA was purified from total RNA after removal of rRNA (mRNA-ONLY™ Eukaryotic mRNA Isolation Kit, Epicentre). Then, each sample was amplified and transcribed into fluorescent cRNA along the entire length of the transcripts without 3' bias utilizing a random priming method (Arraystar Flash 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: Total RNA were extracted using Trizol. The RNA quantity and quality were measured by NanoDrop ND-1000. RNA integrity was assessed by standard denaturing agarose gel electrophoresis.

tag: tnm stage

tag: pathological type

value: adenocarcinoma

tag: grade


title: SRNA61D_NOSAUBKD2


title: hiPSC>EC differentiation #1, total RNA, day03, biological replicate #2


title: hiPSC>EC differentiation #1, total RNA, day04, biological replicate #2


title: Primary Human Gastric Cancer Tissue2_rep1

institute: Gastric cancer peritoneal metastasis Tissue

description:
Gene expression in primary gastric cancer tissues from patient2
2CA

source_name: Primary gastric cancer tissues from patient2_rep1

tag: gender

tag: age


title: Primary Human Gastric Cancer Tissue3_rep1

description:
Gene expression in primary gastric cancer tissues from patient3
3CA

source_name: Primary gastric cancer tissues from patient3_rep1


title: Primary Human Gastric Cancer Tissue1_rep1

description:
Gene expression in primary gastric cancer tissues from patient1
1CA

source_name: Primary gastric cancer tissues from patient1_rep1


title: hiPSC>EC differentiation #1, total RNA, day03, biological replicate #1


title: SRNA61D_NOSAUBKD1

tag: genotype


title: Gastric cancer peritoneal metastasis Tissue1_rep1

description:
Gene expression in gastric cancer peritoneal metastasis tissues  from patient1
1PM

source_name: Gastric cancer peritoneal metastasis tissues from patient1_rep1


title: Water control for batch 2 (Replicate 7).


title: hiPSC>EC differentiation #1, total RNA, day02, biological replicate #4


title: Water control for batch 6 (Replicate 1).


title: SRNA61D_NOAGAL4


title: Water control for batch 2 (Replicate 5).


title: Water control for batch 2 (Replicate 6).


title: hiPSC>EC differentiation #1, total RNA, day02, biological replicate #3


title: fly_sRNA_Top3b


title: fly_sRNA_Top3b_aubKD


title: Water control for batch 2 (Replicate 4).


title: Water control for batch 2 (Replicate 3).


title: LS174T cells treated with CompE (250nM) for 48h, biological replicate 3

city: New York

first: Teresa

last: Palomero

state: New York

address: 1130 St Nicholas Ave Rm 607

institute: Institute for Cancer Genetics -Columbia University

description: Gene expression data from LS174T adenocarcinoma cells treated with CompE for 48h

hyb_protocol: hybridized on Affymetrix Human U133 Plus 2.0 arrays according to the manufacturer’s protocol as previously described (Real PJ et al., 2009)

scan_protocol: Standard Affymetix protocol

data_processing: We normalized interarray intensity differences with dCHIP and averaged the expression across triplicate samples.

source_name: LS174T cell line

label_protocol: RNA of each sample was amplified and labeled using the 3’ IVT Express Kit (Affymetrix)

growth_protocol: LS174T cells were grown in EMEM 10% FBS 1% Pen/Strep, 37C, 5% CO2

extract_protocol: total RNA was extracted using RNeasy Plus Mini kit (Qiagen) according to the manufacturer’s protocol.

treatment_protocol: triplicate cultures of LS174T cells were treated for 48 h with vehicle (DMSO) or CompE (250 nM)

tag: cancer type

value: adenocarcinoma cell line


title: hiPSC>EC differentiation #1, total RNA, day02, biological replicate #1


title: fly_sRNA_control


title: fly_sRNA_aubKD


title: Water control for batch 2 (Replicate 1).

value: control

tag: solvent


title: Water control for batch 2 (Replicate 2).


title: LS174T cells treated with CompE (250nM) for 48h, biological replicate 1


title: Water control for batch 1 (Replicate 6).


title: LS174T cells treated with vehicle (DMSO) for 48h, biological replicate 3

description: Gene expression data from LS174T adenocarcinoma cells treated with DMSO for 48h


title: LS174T cells treated with CompE (250nM) for 48h, biological replicate 2


title: Water control for batch 1 (Replicate 4).


title: LS174T cells treated with vehicle (DMSO) for 48h, biological replicate 2


title: zucKD_set61

tag: tissue

value: RNA-seq


title: Gastric cancer peritoneal metastasis Tissue2_rep1

description:
Gene expression in  gastric cancer peritoneal metastasis tissues from patient2
2PM

source_name: Gastric cancer peritoneal metastasis tissues from patient2_rep1

value: Male


title: hiPSC>EC differentiation #1, total RNA, day01, biological replicate #3

tag: cell line

value: Differentiated human pluripotent stem cells


title: zucKD_set60


title: hiPSC>EC differentiation #1, total RNA, day01, biological replicate #2

tag: cell type


title: LS174T cells treated with vehicle (DMSO) for 48h, biological replicate 1


title: hiPSC>EC differentiation #1, total RNA, day01, biological replicate #4

tag: treatment


title: WT_set93


title: hiPSC>EC differentiation #1, total RNA, day02, biological replicate #2

tag: time


title: WT_set92


title: hiPSC>EC differentiation #1, total RNA, day00, biological replicate #3

tag: differentiation


title: hiPSC>EC differentiation #1, total RNA, day00, biological replicate #4

tag: biological replicate


title: hiPSC>EC differentiation #1, total RNA, day00, biological replicate #2


title: WT_set54

tag: Sex


title: WT_set59

tag: library type


title: WT_set53


title: Water control for batch 1 (Replicate 5).


title: hiPSC>EC differentiation #1, total RNA, day00, biological replicate #1


title: Water control for batch 1 (Replicate 3).


title: WT_set47


title: airway basal cells, AR, Der p1, 6

city: Leuven

first: Emma

last: Ruysseveldt

address: UZ herestraat 49, box 811

department: Microbiology, immunology and transplantation

country: Belgium

institute: KU Leuven

description:
Library name: GC153055
Column name in count_matrix.txt: GC153055

data_processing:
Quality control of the raw sequencing data was performed using FastQC. Within Galaxy, Cutadapt was used to remove the poly-A tail, mitochondrial RNA and ribosomal RNA. Trimmomatic was used to filter low quality read (parameters included MINLEN: 20; AVGQUAL: 20 or 25; SLIDINGWINDOW: 4:20; TRAILING: 3) . Mapping to the hg38 human genome was performed using HISAT.
Assembly: hg38
Supplementary files format and content: Processed data files comprise .bam files of the cleaned reads from every sample mapped against the hg38 human genome.

source_name: nasal (inferior turbinate)

growth_protocol: "culture" or "culture + Der p1" control and AR basal cells were seeded on collagen-coated wells from a 24-well plate in PneumaCult Ex Plus medium (05040, StemCell Technologies). At confluence, medium was exchanged for BEGM (CC-3170, Lonza). Medium was refreshed every other day. Cells were cultured for 14 days.

extract_protocol:
Cells were lysed using RLT lysis buffer (79216, Qiagen) and RNA was extracted using the RNeasy Mini Kit (74104, Qiagen), both according to the manufacturer's instructions.
Library prep was done using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD (196, Lexogen).

treatment_protocol: At day 14 in culture, "culture + Der p1" control and AR basal cells were stimulated with 1 µg/mL Der p1 (22A02, Citeq Biologicals) for 6 hours.

value: nasal (inferior turbinate)

value: primary nasal epithelial cells

value: basal cells

value: AR

value: 2 weeks culture + 1 µg/mL Der p1

tag: batch


title: RE757_38_WF006_Tonsil_TFR

city: Cambridge

first: William

last: Foster

state: County (optional)

address: Babraham Research Campus

country: United Kingdom

institute: Babraham Institute

hyb_protocol: Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on Affymetrix Human Genome U133 plus 2.0 Array. GeneChips were washed and stained in an Affymetrix Fluidics Station 450.

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

data_processing: Data was processed and normalized using frma method

source_name: Sorted Tonsil TFR

label_protocol: Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, 2001, Affymetrix).

growth_protocol: in vitro TFH: naïve peripheral blood CD4 T cells were first exposed to anti-CD3 to stimulate the TCR in the presence of CD28 and ICOS-L co-stimulation. After 24 hours the cells were then cultured in the presence of IL-6, IL-12, IL-1β, TGF-β and Activin A,

extract_protocol: RNA was extracted using the Qiagen mini-kit, according to manufacturers instructions.

treatment_protocol: naïve CD4 T cells were isolated from peripheral blood by lymphoprep separation followed by stemcell naïve CD4 human T cell negative selection kit following manufacturers protocols. In vitro TFH were generated from naïve CD4 T cells as detailed in the growth protocol. Tonsil samples were sorted as detailed in the summary from cryopreserved paediatric tonsil samples.

value: ex vivo sorted tonsil


title: vas_set47


title: DMSO control for batch 8 (Replicate 6).

value: DMSO


title: Water control for batch 1 (Replicate 1).


title: Water control for batch 1 (Replicate 2).


title: RE757_41_WF009_Tonsil_TFR


title: RE757_39_WF007_Tonsil_TFR


title: airway basal cells, AR, fresh, 6

description:
Library name: GC153053
Column name in count_matrix.txt: GC153053

value: fresh (no treatment)


title: RE757_36_WF003_Tonsil_TFR


title: RE757_37_WF005_Tonsil_TFR


title: DMSO control for batch 8 (Replicate 5).


title: RE757_34_WF008_Tonsil_TFH

source_name: Sorted Tonsil TFH


title: airway basal cells, AR, culture, 6

description:
Library name: GC153054
Column name in count_matrix.txt: GC153054

value: 2 weeks culture


title: DMSO control for batch 8 (Replicate 4).


title: RE757_40_WF008_Tonsil_TFR


title: RE757_33_WF007_Tonsil_TFH


title: RE757_32_WF006_Tonsil_TFH


title: RE757_31_WF005_Tonsil_TFH


title: top3bzucKD_set60

value: ovary

value: female


title: airway basal cells, AR, Der p1, 5

description:
Library name: GC153052
Column name in count_matrix.txt: GC153052


title: DMSO control for batch 6 (Replicate 7).


title: airway basal cells, AR, culture, 5

description:
Library name: GC153051
Column name in count_matrix.txt: GC153051


title: top3bvas_set47


title: hiPSC>EC differentiation #1, total RNA, day01, biological replicate #1


title: top3bnos2_set60


title: DMSO control for batch 6 (Replicate 6).


title: RE757_35_WF009_Tonsil_TFH


title: DMSO control for batch 8 (Replicate 3).


title: DMSO control for batch 8 (Replicate 2).


title: DMSO control for batch 6 (Replicate 8).


title: top3bzucKD_set61


title: top3bnos_set63


title: airway basal cells, AR, fresh, 5

description:
Library name: GC153050
Column name in count_matrix.txt: GC153050


title: top3bnos_set61


title: RE757_29_H71_Naive_CD4

source_name: Naïve CD4 T cells

value: in vitro cultured peripheral blood CD4


title: airway basal cells, AR, culture, 4

description:
Library name: GC153048
Column name in count_matrix.txt: GC153048


title: top3bnos_set60


title: airway basal cells, AR, fresh, 4

description:
Library name: GC153047
Column name in count_matrix.txt: GC153047


title: RE757_30_WF003_Tonsil_TFH


title: DMSO control for batch 8 (Replicate 1).

source_name: TK6 Human lymphoblastoid cells


title: airway basal cells, AR, culture, 3

description:
Library name: GC153045
Column name in count_matrix.txt: GC153045


title: top3baubKD1_set60


title: top3baubKD_set61


title: airway basal cells, AR, Der p1, 4

description:
Library name: GC153049
Column name in count_matrix.txt: GC153049


title: airway basal cells, AR, fresh, 3

description:
Library name: GC153044
Column name in count_matrix.txt: GC153044


title: DMSO control for batch 6 (Replicate 5).


title: airway basal cells, AR, Der p1, 2

description:
Library name: GC153043
Column name in count_matrix.txt: GC153043


title: top3barmiKD2_set63


title: top3baubKD2_set60


title: airway basal cells, AR, Der p1, 3

description:
Library name: GC153046
Column name in count_matrix.txt: GC153046


title: RE757_26_H70_Naive_CD4


title: DMSO control for batch 6 (Replicate 4).


title: RE757_23_H61_Naive_CD4


title: DMSO control for batch 6 (Replicate 1).


title: top3barmiKD1_set63


title: RE757_25_H69_Naive_CD4


title: RE757_24_H68_Naive_CD4


title: DMSO control for batch 6 (Replicate 2).


title: DMSO control for batch 4 (Replicate 8).


title: top3bago3_set59


title: airway basal cells, AR, fresh, 2

description:
Library name: GC153041
Column name in count_matrix.txt: GC153041


title: DMSO control for batch 4 (Replicate 7).


title: RE757_27_H74_Naive_CD4


title: top3bago3_set54


title: RE757_28_H75_Naive_CD4


title: RE757_7_H75_unstim_TFH

source_name: in vitro TFH


title: DMSO control for batch 4 (Replicate 5).


title: DMSO control for batch 6 (Replicate 3).


title: DMSO control for batch 4 (Replicate 4).


title: DMSO control for batch 4 (Replicate 6).


title: airway basal cells, AR, culture, 2

description:
Library name: GC153042
Column name in count_matrix.txt: GC153042


title: top3b26_set53


title: airway basal cells, AR, culture, 1

description:
Library name: GC153039
Column name in count_matrix.txt: GC153039


title: airway basal cells, AR, Der p1, 1

description:
Library name: GC153040
Column name in count_matrix.txt: GC153040


title: RE757_5_H70_unstim_TFH


title: airway basal cells, AR, fresh, 1

description:
Library name: GC153038
Column name in count_matrix.txt: GC153038


title: airway basal cells, control, Der p1, 6

description:
Library name: GC153037
Column name in count_matrix.txt: GC153037


title: top3b10-2_set93


title: top3b10-2_set92


title: ZSCAN4, without  Dox, ChiP

first: yang

last: song

state: MD

address: HSF-3, 3rd Floor; 670 W Baltimore St.

department: Department: Institute for Genome Sciences

institute: University of Maryland in Baltimore

data_processing:
ChIP-seq reads were trimmed from 3' end until the final base had a quality score >20 using Trimmomatic V0.38.
ChIP-seq reads were aligned to the mm10 genome using Bowtie2 version 2.4.4, the mapped reads are reformatted in the bigWig file format
Assembly: mm10
Supplementary files format and content: bigwig

organism: Mus musculus

source_name: (HNSCC) cell line (TU167)

growth_protocol: Tu167 cell line were cultured in complete DMEM medium (Invitrogen) supplemented with 10% fetal bovine serum (FBS) , 2 mM GlutaMAX, penicillin (100 U/mL) and streptomycin (100 μg/mL).

extract_protocol:
Genomic  paired end DNA libraries were constructed for sequencing on the Illumina platform using the KAPA Library Hyper Preparation Kit (Kapa Biosystems, Woburn, MA).
60 ng of DNA was fragmented with the Covaris E220( Woburn,MA). Then libraries were prepared using a modified version of manufacturer’s protocol. The DNA was purified between enzymatic reactions and the size selection of the library was performed with  SPRIselect beads (Beckman Coulter Genomics, Danvers, MA).  Samples were indexed during a final amplification using primers designed to amplify on an illumina hiseq 4000.

treatment_protocol: tet-FLAG-ZSCAN4-Tu167 cells were grown to 50% confluency and incubated for 48 hours with or without 1 µg/ml doxycycline

value: (HNSCC) cell line (TU167)

value: Head and neck squamous cell carcinoma


title: RE757_22_H60_Naive_CD4


title: ZSCAN4, with Dox, ChiP

value: Dox


title: set92_Y332F

value: RNA-seq


title: airway basal cells, control, culture, 6

description:
Library name: GC153036
Column name in count_matrix.txt: GC153036

value: control


title: airway basal cells, control, fresh, 6

description:
Library name: GC153035
Column name in count_matrix.txt: GC153035

value: nasal (inferior turbinate)


title: top3b26_set47


title: set_93_Y332F


title: RNA-Seq WZB10_P18C

city: Cologne

first: Jens

last: Brüning

address: Gleueler Str. 50

institute: Max Planck Institute for Metabolism Research

description:
Passage NO.18
rnaseq_counts.csv

data_processing:
RNA-Seq: The reads were alligned using the community curated nf-core/rnaseq pipeline version 1.4. bacTRAP: The reads were alligned using the community curated nf-core/rnaseq pipeline version 3.0.
Assembly: GRCm38
Supplementary files format and content: bactrap_counts.csv, rnaseq_counts.csv

source_name: Brain

extract_protocol:
BacTrap-based ribosomal profiling of hypothalamic ECs  Afﬁnity puriﬁcation of translating ribosomes (Trap) was performed as described previously (Heiman et al., 2014; 2008)  with minor modiﬁcations. 12-week-old male and female Slco1c1CreERT2tg/wt::ROSA26lSlL10aGFPtg/wt mice were used for the BacTrap experiment (an equal number of male and female mouse hypothalamic tissue was pooled in each sample). 3 weeks after tamoxifen induction, mice were put either on a CD or an HFD for 3 days. Afterwards, mice were sacrificed and the hypothalamus was rapidly dissected using a stainless steel brain matrix (Agnthos) and immediately frozen in liquid nitrogen. Buffer preparation: Lysis buffer (20mM HEPES [pH 7.4], 5mM MgCl2, 150 mM KCl, 0.5 mM DTT, 100µg/ml cycloheximide, 40U/ml Ribonuclease Inhibitor (Rnasin, Promega) and protease inhibitor [1 tablet of cOmplete mini EDTA-free protease inhibitor cocktail/7 mL and 2 tablets of PhosSTOP/10 ml]) ; 0.15M KCl IP wash buffer (20mM HEPES [pH 7.4], 5mM MgCl2, 150 mM KCl, 1% NP-40, 0.5 mM DTT, 100 µg/ml cycloheximide) ; 0.35 M KCl IP wash buffer (20mM HEPES [pH 7.4], 5mM MgCl2, 350 mM KCl, 1% NP-40, 0.5mM DTT, 100 µg/ml cycloheximide). Bead preparation: Dynabeads Protein A (375 µl, Novex, per IP) were washed in 1mL 0.15M KCl IP wash buffer for three times. Afterward, beads were resuspended in 275µL 0.15M KCl IP wash buffer. 50 µg of antibody 19C8 and 50 µg of antibody 19F7 (Cat# Htz-GFP-19F7, RRID: AB_2716736 and Htz-GFP-19C8, RRID: AB_2716737, Memorial Sloan Kettering Monoclonal Antibody Facility) per IP was added into each bead tube. The beads were incubated with slow end-over-end mixing at 4°C overnight. Afterward, the supernatant was removed and the beads were washed in 1mL 0.15 KCl IP wash buffer for 3 three times. After the wash, beads were resuspended in 200µL 0.15M KCl IP wash buffer. Pooled hypothalamic tissue (4 pooled mice per sample; 4 samples per group) was homogenized on ice with lysis buffer (1mL per sample) at 4 °C. Homogenates were transferred to low binding microcentrifuge tubes (Nonstick, RNase-free microfuge tubes,1.5 ml, Ambion, Invitrogen) and centrifuged 10 minutes, 2000g at 4 °C to obtain the post-nuclear supernatant. The supernatant was transferred to a new tube on ice, and 1/9 sample volume of 10% NP-40 (ﬁnal concentration: 1%) and 1/9 sample volume of 300 mM DHPC (ﬁnal concentration: 30 mM) were added. This solution was mixed, incubated on ice for 2 min and then centrifuged at 17,000 g for 10 min at 4 °C. The resulting supernatant was transferred to a new tube and a 25 µL aliquot was removed, transferred to a new tube, ﬂash frozen in liquid nitrogen and stored at -80°C for puriﬁcation as input RNA. 200 µL of antibody-bound beads were added (800-1000 µL supernatant) and incubated at 4°C for one hour with end-over-end mixing. Beads were collected with a magnet and resuspended in 1 mL 0.35 M KCl IP wash buffer. Beads were washed three more times with 1mL of 0.35 M KCl IP wash buffer. After the ﬁnal wash, the beads were collected with a magnet and the supernatant removed. The RNA was eluted by the addition of buffer RLT (350 µL) to the beads, allowed to incubate at room temperature (RT) for 5 minutes and RNA was subsequently puriﬁed using the RNeasy Micro Kit (#74004, QIAGEN). RNA integrity was assessed using an Agilent 2100 bioanalyzer.     Single nucleus isolation and sorting   Single nucleus sequencing was performed according to Habib et al. (2017) with minor modiﬁcations. Hypothalami were dissected and homogenized in 2ml EZ PREP (#NUC101, Merck) on ice and incubated for 5 min with an additional 2 ml ice-cold EZ PREP. The nuclei were centrifuged at 500g for 5 min at 4 °C. The pellets were washed with 4 ml ice-cold EZ PREP and incubated on ice for 5 min. After centrifugation, the nuclei were washed in 4ml nucleus suspension buffer (NSB, consisting of 1× PBS, 0.04% BSA and 0.1% RNase inhibitor (#2313A, Clontech)). Isolated nuclei were resuspended in nucleus suspension buffer (400µl per hypothalamus) and filtered through a 35μm prewetted cell strainer. The nuclei suspension was stained with DAPI (1:1000, #62248, Thermo Fisher Scientiﬁc). ZsGreen/DAPI double-positive nuclei were collected as brain endothelial cell nuclei. BD FACSAria IIIu was used for gating and sorting nuclei. Single nuclei were identified based on side scatter (SSC-A) and DAPI fluorescence (area versus width). ZsGreen fluorescence was detected with 488 nm excitation and 530 nm emission. Sorting was performed at 4 °C with a 70 µm nozzle. Sorted ZsGreen positive nuclei were collected into 1xPBS buffer with 0.04% BSA for 10x genomics single nucleus sequencing.
RNA Bulk Sequencing   Pre-ampliﬁcation using the Ovation RNASeq System V2 was performed. Total RNA was used for ﬁrst strand cDNA synthesis, using both poly(T) and random primers, followed by second strand synthesis and isothermal strand-displacement ampliﬁcation. For library preparation, the Illumina Nextera XT DNA sample preparation protocol was used, with 1 ng cDNA input. After validation (Agilent 2200 TapeStation) and quantiﬁcation (Invitrogen Qubit System) all 24 transcriptome libraries were pooled. The pool was quantiﬁed using the Peqlab KAPA Library Quantiﬁcation Kit and the Applied Biosystems 7900HT Sequence Detection and sequenced on an Illumina NovaSeq S2 ﬂowcell with a PE100 protocol. The RNA sequencing pipeline utilizes the GRCm38 assembly of the mouse genome as gene sets from Ensembl release 96 (Yates et al., 2015). We quantiﬁed the gene expression of each sample by (1) aligning the RNA-sequencing reads to the mm10 reference genome using hisat 2.1.0 (Kim et al., 2015). (2) computationally depleted rRNA reads using samtools 1.8.0 (Li et al., 2009) and (3) transcript assembly and quantiﬁcation as well as the differential analysis between the experimental conditions using the cufﬂinks 2.2.1 suite (Trapnell et al., 2010).

value: Brain

value: cEND

value: Endothelial cell


title: airway basal cells, control, Der p1, 5

description:
Library name: GC153034
Column name in count_matrix.txt: GC153034

value: primary nasal epithelial cells

value: basal cells

value: 2 weeks culture + 1 µg/mL Der p1


title: nos2_set60


title: airway basal cells, control, culture, 5

description:
Library name: GC153033
Column name in count_matrix.txt: GC153033


title: RNA-Seq WZB10_P12C

description:
Passage NO.12
rnaseq_counts.csv


title: RNA-Seq WZB10_P14C

description:
Passage NO.14
rnaseq_counts.csv


title: RE757_3_H68_unstim_TFH


title: DMSO control for batch 2 (Replicate 6).

value: DMSO


title: DMSO control for batch 2 (Replicate 8).


title: RE757_1_H60_unstim_TFH


title: airway basal cells, control, fresh, 5

description:
Library name: GC153032
Column name in count_matrix.txt: GC153032

value: fresh (no treatment)


title: RE757_4_H69_unstim_TFH


title: nos1_set60

value: ovary


title: DMSO control for batch 4 (Replicate 1).


title: DMSO control for batch 2 (Replicate 5).


title: DMSO control for batch 2 (Replicate 7).


title: RE757_2_H61_unstim_TFH


title: DMSO control for batch 2 (Replicate 3).


title: DMSO control for batch 2 (Replicate 2).


title: DMSO control for batch 2 (Replicate 4).


title: RNA-Seq WZB05_P18B

description:
Passage NO.18
rnaseq_counts.csv


title: nos_set63

value: female


title: airway basal cells, control, Der p1, 4

description:
Library name: GC153031
Column name in count_matrix.txt: GC153031


title: RNA-Seq WZB05_P14B

description:
Passage NO.14
rnaseq_counts.csv


title: airway basal cells, control, culture, 4

description:
Library name: GC153030
Column name in count_matrix.txt: GC153030

value: 2 weeks culture


title: nos_set61


title: RNA-Seq WZB05_P12B

description:
Passage NO.12
rnaseq_counts.csv


title: airway basal cells, control, fresh, 4

description:
Library name: GC153029
Column name in count_matrix.txt: GC153029


title: RNA-Seq DMSO_P18A

description:
Passage NO.18
rnaseq_counts.csv


title: DMSO control for batch 1 (Replicate 9).


title: aubKD1_set60


title: DMSO control for batch 2 (Replicate 1).


title: DMSO control for batch 4 (Replicate 2).


title: RNA-Seq DMSO_P14A

description:
Passage NO.14
rnaseq_counts.csv


title: airway basal cells, control, culture, 3

description:
Library name: GC153027
Column name in count_matrix.txt: GC153027


title: aubKD_set61


title: aubKD2_set60


title: armiKD_set63


title: DMSO control for batch 1 (Replicate 7).


title: airway basal cells, control, fresh, 3

description:
Library name: GC153026
Column name in count_matrix.txt: GC153026


title: airway basal cells, control, Der p1, 2

description:
Library name: GC153025
Column name in count_matrix.txt: GC153025


title: bacTRAP HFD INPUT 4

description:
4pooled per sample, 2male and 2 females
bactrap_counts.csv

source_name: Hypothalamus

value: Hypothalamus

value: high fat diet


title: ago3_set59

source_name: ovary

value: AGO3 t2/t3


title: airway basal cells, control, culture, 2

description:
Library name: GC153024
Column name in count_matrix.txt: GC153024


title: bacTRAP HFD IP_GFP 3


title: DMSO control for batch 1 (Replicate 6).


title: DMSO control for batch 1 (Replicate 8).


title: DMSO control for batch 1 (Replicate 5).


title: airway basal cells, control, fresh, 2

description:
Library name: GC153023
Column name in count_matrix.txt: GC153023


title: DMSO control for batch 1 (Replicate 2).


title: bacTRAP HFD INPUT 3


title: airway basal cells, control, Der p1, 3

description:
Library name: GC153028
Column name in count_matrix.txt: GC153028


title: DMSO control for batch 1 (Replicate 3).


title: RNA-Seq DMSO_P12A

description:
Passage NO.12
rnaseq_counts.csv


title: DMSO control for batch 1 (Replicate 4).


title: bacTRAP HFD IP_GFP 4


title: Exposed to epfr 8

city: Baton Rouge

first: Tammy

middle: R

last: Dugas

state: LA

address: Skip Bertman Drive

department: Comparative Biomedical Sciences

institute: LSU School of Veterinary Medicine

hyb_protocol: An overnight hybridization was performed, followed by a two-step magnetic bead-based purification. The purified target/probes complexes were immobilized on the catridge for data collection in nCounter SPRINT Profiler.

scan_protocol: Digitial images were taken from immobilized target/probes complex and color-coded barcode were counted.

data_processing: Run files in RCC format were analyzed using nSolver software. Raw counts for miRNA were subjected to background substraction, followed by normalization using positive control normalization and CodeSet Content Normalization.

label: Biotin

source_name: plasma

label_protocol: 10 ng of plasma RNA were ligated with unique oligonucleotide tags. Then, tagged miRNA were labeled using oligonucleotide probes with color-coded signal in 5' end and biotin on its 3' end.

extract_protocol: Exosomal RNA were isolated from 200 µL plasma using a Plasma/Serum RNA Purification Kit (Norgen Biotek).

tag: strain

value: Male

value: 20 weeks

value: plasma


title: airway basal cells, control, Der p1, 1

description:
Library name: GC153022
Column name in count_matrix.txt: GC153022

value: nasal (inferior turbinate)

value: control


title: bacTRAP HFD INPUT 2

value: Endothelial cell


title: DMSO control for batch 1 (Replicate 1).


title: Exposed to epfr 7


title: bacTRAP HFD IP_GFP 2


title: Exposed to epfr 6


title: bacTRAP HFD IP_GFP 1


title: ago3_set54

value: RNA-seq


title: bacTRAP HFD INPUT 1


title: Exposed to epfr 5


title: 232-HBO (Control hindbrain organoid)

city: Belval

first: Gemma

last: Gomez Giro

address: 6, Avenue du Swing

country: Luxembourg

institute: Luxembourg Centre for Systems Biomedicine

description: 10x Genomics

data_processing:
Data was demultiplexed and converted into fastq files using bcl2fastq2 v2.20 and subsequently single cell demultiplexed andconverted intocount matrixes using cellranger5.0.1.
Assembly: GRCh38-2020-A-2.0.0
Supplementary files format and content: Tab-separated values files and matrix files

molecule: nuclear RNA

source_name: Hindbrain organoid

growth_protocol: For the nuclei extraction, the samples from the 3 batches were pooled.

extract_protocol:
Tissues were lysed by adding 1 mL chilled Lysis Buffer, andsuspension was filtered using a 30μm MACS® SmartStrainer to remove cell debris and large clumps and nuclei were pelleted by centrifugation at 500 rcf for 5 min and at 4°C. The supernatant was removed without disrupting the nuclei pellet and pellets were washed in 0.7ml nuclei wash and resuspension buffer  incubated on ice for 15-30 min whilst being physically disrupted by pipetting up and down gently. Then, the suspension was filtered using a 30μm MACS® SmartStrainer to remove cell debris and large clumps and nuclei were pelleted by centrifugation at 500 rcf for 5 min and at 4°C. The supernatant was removed without disrupting the nuclei pellet and pellets were washed in 0.7ml nuclei wash and resuspension buffer. Nuclei-pellets were suspended in the DAPI solution (5µl DAPI (300µM) in 1000µl 1× PBS) and incubated for 5 min prior to FACS sorting. In the subsequent FACS sorting, single DAPI-positive nuclei were filtered by size and granularity using a calibrated FACS ARIA III Cell Sorter (BD Biosciences) to minimize the amount of cell debris in the suspension, using 4-way purity sort with 32 purity mask. Based on the number of intact nuclei obtained, we adjusted the amount of nuclei suspension buffer to yield a single nuclei solution of ~1000 nuclei/μl and proceeded immediately with 10X Chromium.
After nuclei extraction an individual lane per sample ofChromium Next GEM Single Cell 3' Kit v3.1 chemistry was run on a Chromium Controller device(10X Genomics). Libraries were generated following manufacturer's recommendations.

value: Hindbrain organoid

tag: disease state

value: Healthy control

value: No treatment


title: bacTRAP CD IP_GFP 4

value: control diet


title: bacTRAP CD INPUT 4


title: 232-232 (Control midbrain co-cultured with control hindbrain)

description: 10x Genomics

source_name: Midbrain organoid

value: Midbrain organoid


title: Exposed to epfr 4


title: Exposed to epfr 3


title: airway basal cells, control, culture, 1

description:
Library name: GC153021
Column name in count_matrix.txt: GC153021

value: primary nasal epithelial cells

value: basal cells


title: Tertiary-butylhydroquinone sample tested at 90.91 uM (Replicate: 3, Control Batch Id: 4).

value: Tertiary-butylhydroquinone

value: sample

value: DMSO


title: airway basal cells, control, fresh, 1

description:
Library name: GC153020
Column name in count_matrix.txt: GC153020

value: fresh (no treatment)


title: Exposed to epfr 2

value: Male

value: 20 weeks


title: 336-MO (PD midbrain organoid)

description: 10x Genomics

value: Parkinson Disease


title: bacTRAP CD IP_GFP 3

value: Hypothalamus


title: 232-336 (Control midbrain co-cultured with PD hindbrain)

description: 10x Genomics


title: 786-O cells, 8 hours post infection [786-O_08_RPF_CopWT_8h_2_AIYL-403]

city: Ottawa

first: Adrian

last: Pelin

state: Ontario

address: 501 Smyth Rd.

country: Canada

institute: Ottawa Hospital Research Institute

description:
polysome mRNA
786-O_08_RPF_CopWT_8h_2_AIYL-403

data_processing:
Illumina Casava1.7 software used for basecalling.
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomatic.
Trimmed sequence reads were mapped to Vaccinia Copenhagen (GenBank M35027) genome using HISAT.
Read count extraction and normalization were using StringTie. Processed data is shown as TPM (tags per million)
Assembly: GenBank M35027
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

organism: Orthopoxvirus vaccinia

growth_protocol: 786-O cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen). Total RNA was used for polysome enrichment and subsequenty for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using smRNA-Seq Library Prep Kit following manufacturer's protocols.

treatment_protocol: Confluent cells were infected at an MOI of 3 with Vaccinia virus

value: Human adenocarcinoma

value: WT

value: Vaccinia Copenhagen


title: 786-O cells, 8 hours post infection [786-O_07_RPF_CopWT_8h_3_AIYL-407]

description:
polysome mRNA
786-O_07_RPF_CopWT_8h_3_AIYL-407


title: Exposed to epfr lo 8

value: plasma


title: Tertiary-butylhydroquinone sample tested at 150 uM (Replicate: 2, Control Batch Id: 4).


title: Tertiary-butylhydroquinone sample tested at 55.1 uM (Replicate: 2, Control Batch Id: 4).


title: Tertiary-butylhydroquinone sample tested at 55.1 uM (Replicate: 3, Control Batch Id: 4).


title: Tertiary-butylhydroquinone sample tested at 90.91 uM (Replicate: 1, Control Batch Id: 4).


title: 786-O cells, 4 hours post infection [786-O_06_RPF_CopWT_4h_2_AIYL-400]

description:
polysome mRNA
786-O_06_RPF_CopWT_4h_2_AIYL-400


title: bacTRAP CD INPUT 2

value: Endothelial cell


title: Tertiary-butylhydroquinone sample tested at 90.91 uM (Replicate: 2, Control Batch Id: 4).


title: 786-O cells, 2 hours post infection [786-O_04_RPF_CopWT_2h_2_AIYL-397]

description:
polysome mRNA
786-O_04_RPF_CopWT_2h_2_AIYL-397


title: Exposed to epfr lo 7


title: bacTRAP CD INPUT 3

value: control diet


title: Exposed to epfr lo 6


title: bacTRAP CD IP_GFP 1


title: 786-O cells, 4 hours post infection [786-O_05_RPF_CopWT_4h_1_AIYL-354]

description:
polysome mRNA
786-O_05_RPF_CopWT_4h_1_AIYL-354


title: Exposed to epfr lo 5


title: 786-O cells, 2 hours post infection [786-O_03_RPF_CopWT_2h_1_AIYL-351]

description:
polysome mRNA
786-O_03_RPF_CopWT_2h_1_AIYL-351


title: bacTRAP CD IP_GFP 2


title: Exposed to epfr 1


title: TLR2.8

city: Shanghai

first: yunjie

last: shi

address: No 800，Xiangyin Road

institute: Naval Medical University

description: microbiome

data_processing:
Using FLASH v1.2.7 software, the reads of each sample are spliced by overlap, and the spliced sequence is the raw Tags.Using Trimmomatic v0.33 software, the Raw Tags obtained by splicing were filtered to obtain high-quality Tags data (Clean Tags)
Using UCLUST in QIIME(version 1.8.0) software to cluster Tags at the similarity level in ninety-seven percent, OTU was obtained, and the OTU was taxonomically annotated based on Silva (bacteria) and UNITE (fungi) taxonomic databases.
Comparing the representative sequence of the OTUs with a microbial reference database to obtain species classification information corresponding to each OTU, and counting the composition of each sample community at each level,
The Alpha diversity index of samples was evaluated using the Mothur (version v.1.30) software. In general, the index of diversity was compared among samples, and the number of sequences contained in samples was standardized for analysis.
The PICRUSt software was used to deduce the functional gene composition in samples by comparing the species composition information obtained from 16S sequencing data, so as to analyze the functional differences between different samples or subgroups.
Library strategy: 16s-rDNA sequencing

organism: mouse gut metagenome

source_name: fecal samples of mice

extract_protocol:
Extraction of total genomic DNA through the DNA Extraction Kit (Tiangen Biotechnology Company, Beijing, China) was conducted following the instructions of the kit.
DNA libraries for 16s-rDNA sequencing were prepared using SMARTER DNA-Seq Library Prep Kit following manufacturer's protocols.

value: fecal samples of mice


title: KOPT-K1, replicate 3

city: London

first: Stephen

last: Henderson

address: Paul O'Gorman Building

department: Cancer Institute

institute: University College London

description:
Library name: KOPTK1_REP3
mRp = "merged replicate"
KOPTK1.mRp.clN.bigWig
KOPTK1.mRp.clN_peaks.broadPeak

data_processing:
Demultiplexed reads were aligned and processed using nf-core/atacseq pipeline version 2.1.2
Adapters were trimmed using Trim Galore! v0.6.7 with default setting
Alignment was done using bwa in MEM mode v0.7.17-r1188
bigWig files were generated using bedtools v2.30.0 and ucsc-bedgraphtobigwig v445, scaled to 1 million mapped reads
macs2 v2.2.7.1 was used to call peaks in broad peak calling mode
Assembly: GRCh38
Supplementary files format and content: bigWig (normalised read)
Supplementary files format and content: broadPeak (contains annotation of called peaks)

growth_protocol: Cells were grown with RPMI1640 supplemented with 10% FBS and antibiotics in humidified incubators at 5% CO2 and 37 degree Celsius

extract_protocol:
Nuclei were collected from 50000 cells by lysing them with lysis buffer according to Omni-ATAC protocol (https://doi.org/10.1038/nmeth.4396)
Libraries were constructed using Tagment DNA TDE1 Enzyme and Buffer Kits (Illumina), followed by indexing and amplification using Ultra II Q5 Master Mix (NEB) for 8 to 9 cycles on a thermal cycler. Primer dimers and large DNA fragment (> ~1kbp) were removed using Ampure XP beads (Beckman). Library quality was examined with High Sensitivity D1000 Tape on TapeStation (Agilent) and quantify using NEBNext Library Quant Kit for Illumina (NEB)

value: T-ALL

value: Wildtype


title: armiKD2_set63

value: ovary

value: female

value: RNA-seq


title: Tertiary-butylhydroquinone sample tested at 55.1 uM (Replicate: 1, Control Batch Id: 4).

first: Bastian

last: Selman

address: 8700 Mason Montgomery Rd

institute: Procter & Gamble

data_processing: The data were analyzed using the rma function in the affy package for R. This function uses RMA for background correction, performs probe specific correction, normalizes using quantile normalization and finally applies a median polish. Package citation: Gautier L, Cope L, Bolstad BM, Irizarry RA (2004). “affy—analysis of Affymetrix GeneChip data at the probe level.” Bioinformatics, 20(3), 307–315. ISSN 1367-4803, doi:10.1093/bioinformatics/btg405.

extract_protocol: Total RNA was extracted using Agencourt RNAdvance Tissue XP beads (Beckman Coulter Inc., Danvers, MA) according to the manufacturer's protocol on the cell lysates. RNA integrity was validated using a NanoDrop 8000 Spectrophotometer (Wilmington, DE).

value: Tertiary-butylhydroquinone

value: sample

value: DMSO


title: KOPT-K1, replicate 2

description:
Library name: KOPTK1_REP2
mRp = "merged replicate"
KOPTK1.mRp.clN.bigWig
KOPTK1.mRp.clN_peaks.broadPeak


title: TLR2.7

description: microbiome


title: Exposed to epfr lo 4

value: Male

value: 20 weeks


title: Exposed to epfr lo 2


title: Tertiary-butylhydroquinone sample tested at 150 uM (Replicate: 3, Control Batch Id: 4).


title: TLR2.6

description: microbiome


title: KOPT-K1, replicate 1

description:
Library name: KOPTK1_REP1
mRp = "merged replicate"
KOPTK1.mRp.clN.bigWig
KOPTK1.mRp.clN_peaks.broadPeak


title: RE757_6_H74_unstim_TFH

value: in vitro cultured peripheral blood CD4


title: bacTRAP CD INPUT 1

value: Hypothalamus


title: TLR2.5

description: microbiome


title: Tertiary-butylhydroquinone sample tested at 150 uM (Replicate: 1, Control Batch Id: 4).


title: JURKAT, GFP-TAL1, GATA3 binding sites 2 and 3 disrupted, replicate 3

description:
Library name: J_GT_2m3m_REP3
mRp = "merged replicate"
J_GT_2m3m.mRp.clN.bigWig
J_GT_2m3m.mRp.clN_peaks.broadPeak

source_name: JURKAT

value: JURKAT

value: GFP-TAL1, 2m3m


title: Exposed to epfr lo 3

value: plasma


title: Exposed to epfr lo 1


title: Tertiary-butylhydroquinone sample tested at 33.39 uM (Replicate: 1, Control Batch Id: 4).


title: DMSO control for batch 4 (Replicate 3).

value: control


title: TLR2.4

description: microbiome

value: fecal samples of mice


title: Tertiary-butylhydroquinone sample tested at 20.24 uM (Replicate: 3, Control Batch Id: 4).


title: Tertiary-butylhydroquinone sample tested at 33.39 uM (Replicate: 2, Control Batch Id: 4).


title: Tertiary-butylhydroquinone sample tested at 20.24 uM (Replicate: 2, Control Batch Id: 4).


title: Exposed to filtered air 8


title: Sodium Diclofenac sample tested at 280 uM (Replicate: 3, Control Batch Id: 6).

value: Sodium Diclofenac


title: JURKAT, GFP-TAL1, GATA3 binding sites 2 and 3 disrupted, replicate 2

description:
Library name: J_GT_2m3m_REP2
mRp = "merged replicate"
J_GT_2m3m.mRp.clN.bigWig
J_GT_2m3m.mRp.clN_peaks.broadPeak

value: T-ALL


title: TLR2.3

description: microbiome


title: Tertiary-butylhydroquinone sample tested at 20.24 uM (Replicate: 1, Control Batch Id: 4).


title: Exposed to filtered air 7


title: JURKAT, GFP-TAL1, GATA3 binding sites 2 and 3 disrupted, replicate 1

description:
Library name: J_GT_2m3m_REP1
mRp = "merged replicate"
J_GT_2m3m.mRp.clN.bigWig
J_GT_2m3m.mRp.clN_peaks.broadPeak


title: Sodium Diclofenac sample tested at 280 uM (Replicate: 2, Control Batch Id: 6).


title: Exposed to filtered air 6


title: JURKAT, GFP-TAL1, Mutation of the TAL1 enhancer-repaired, replicate 3

description:
Library name: J_GT_MuTER_REP3
mRp = "merged replicate"
J_GT_MuTER.mRp.clN.bigWig
J_GT_MuTER.mRp.clN_peaks.broadPeak

value: GFP-TAL1, MuTER


title: TLR2.1

description: microbiome


title: TLR2.2

description: microbiome


title: Exposed to filtered air 5


title: JURKAT, GFP-TAL1, Mutation of the TAL1 enhancer-repaired, replicate 2

description:
Library name: J_GT_MuTER_REP2
mRp = "merged replicate"
J_GT_MuTER.mRp.clN.bigWig
J_GT_MuTER.mRp.clN_peaks.broadPeak


title: WT. 7

description: microbiome

value: WT


title: WT. 8

description: microbiome


title: WT. 6

description: microbiome


title: Exposed to filtered air 3


title: JURKAT, GFP-TAL1, Mutation of the TAL1 enhancer-repaired, replicate 1

description:
Library name: J_GT_MuTER_REP1
mRp = "merged replicate"
J_GT_MuTER.mRp.clN.bigWig
J_GT_MuTER.mRp.clN_peaks.broadPeak


title: JURKAT, GFP-TAL1, Wildtype, replicate 3

description:
Library name: J_GT_WT_REP3
mRp = "merged replicate"
J_GT_WT.mRp.clN.bigWig
J_GT_WT.mRp.clN_peaks.broadPeak

value: GFP-TAL1, Wildtype Enhancer


title: JURKAT, GFP-TAL1, Wildtype, replicate 2

description:
Library name: J_GT_WT_REP2
mRp = "merged replicate"
J_GT_WT.mRp.clN.bigWig
J_GT_WT.mRp.clN_peaks.broadPeak


title: JURKAT, GFP-TAL1, Wildtype, replicate 1

description:
Library name: J_GT_WT_REP1
mRp = "merged replicate"
J_GT_WT.mRp.clN.bigWig
J_GT_WT.mRp.clN_peaks.broadPeak


title: WT. 5

description: microbiome


title: Exposed to filtered air 1


title: WT. 4

description: microbiome


title: Sodium Diclofenac sample tested at 160 uM (Replicate: 2, Control Batch Id: 6).


title: Sodium Diclofenac sample tested at 280 uM (Replicate: 1, Control Batch Id: 6).


title: Exposed to epfr ko 7

value: 129/Sv × 129S6/SvEvTac


title: MDA-MB-231, without treatment, 24 hrs, rep3

city: Tainan

first: Li-Chan

last: Chang

address: 7F., No. 35, Xiaodong Rd., North Dist., Tainan City 704017, Taiwan (R.O.C.)

department: Institute of Clinical Medicine

country: Taiwan

institute: National Cheng Kung University

description: Library name: M_C_3

data_processing:
mRNA (1 μg) was isolated from total RNA using oligo(dT)-coupled magnetic beads and subsequently fragmented at an elevated temperature. The firststrand cDNA was synthesized using reverse transcriptase and random primers. After the generation of double-strand cDNA and adenylation at the 3' ends of DNA fragments, adaptors were ligated and purified using the AMPure XP system from Beckman Coulter, Beverly, USA. The library quality was assessed using the Agilent Bioanalyzer 2100 and Real-Time PCR systems. Subsequently, the qualified libraries were sequenced on an Illumina Novaseq X plus platform, generating 150 bp paired-end reads, by Genomics, BioSci & Tech Co., New Taipei City, Taiwan.
Assembly: GRCh38
Supplementary files format and content: The fastp program (version 0.20.0) was employed to eliminate low-quality bases and sequences originating from adapters in the raw data. The processed reads were aligned to the reference genomes using HISAT2 (version 2.1.0). The FeatureCounts software (v2.0.1) within the Subread package was utilized for gene abundance quantification.

growth_protocol: Cells are cultured in DMEM medium (#11965092, Thermo Fisher Scientific) containing 10% FBS (#10437028, Thermo Fisher Scientific) and 100 U/mL Penicillin-Streptomycin (#15140122, Thermo Fisher Scientific) at 37 °C with 5% CO2.

extract_protocol:
Total RNA was extracted from experimental cells using Trizol Reagent (#15596026, Thermo Fisher Scientific)
For RNA library preparation, the refined RNA was processed with the TruSeq Stranded mRNA Library Prep Kit (Illumina, San Diego, CA, USA) according to the manufacturer's guidelines.

treatment_protocol: Cells are treated with 300 ppm Au@MIL nanoparticles or without treatment for 24 hrs.


title: Sodium Diclofenac sample tested at 90 uM (Replicate: 3, Control Batch Id: 6).

value: sample


title: Exposed to epfr ko 6


title: Sodium Diclofenac sample tested at 160 uM (Replicate: 1, Control Batch Id: 6).

value: DMSO


title: Sodium Diclofenac sample tested at 90 uM (Replicate: 2, Control Batch Id: 6).


title: Exposed to filtered air 4

value: Male


title: Sodium Diclofenac sample tested at 160 uM (Replicate: 3, Control Batch Id: 6).


title: WT. 3

description: microbiome


title: Sodium Diclofenac sample tested at 50 uM (Replicate: 3, Control Batch Id: 6).


title: WT. 2

description: microbiome


title: Exposed to epfr ko 5

value: 20 weeks


title: MDA-MB-231, without treatment, 24 hrs, rep1

description: Library name: M_C_1


title: Tertiary-butylhydroquinone sample tested at 33.39 uM (Replicate: 3, Control Batch Id: 4).

value: Tertiary-butylhydroquinone


title: WT. 1

description: microbiome


title: Hep G2, without treatment, 24 hrs, rep3

description: Library name: H_C_3

source_name: Hep G2

value: Hep G2


title: MDA-MB-231, without treatment, 24 hrs, rep2

description: Library name: M_C_2


title: Exposed to epfr ko 4

value: Female


title: Sodium Diclofenac sample tested at 90 uM (Replicate: 1, Control Batch Id: 6).


title: Hep G2, without treatment, 24 hrs, rep2

description: Library name: H_C_2


title: Sodium Diclofenac sample tested at 50 uM (Replicate: 2, Control Batch Id: 6).


title: Exposed to epfr ko 3


title: Hi-C_A7r5 cells, siRNALemd3, replicate 2

city: Beijing

first: Yunxi

last: Liao

state: Beijing

address: 38 Xueyuan Rd, Haidian District

institute: School of Basic Medical Sciences, Peking University

description: LEMD3 knockdown

data_processing:
We pooled 2 Hi-C sample from the same group. For all Hi-C data sets, we used the HiCExplorer (v3.7.2)78 analysis pipeline. Reads pairs were aligned to the rn7 genomes using bwa-mem2 algorithm. Aligned read pairs were assigned to DpnII restriction fragments. Invalid pairs like dangling end were filtered out. The genome was divided into specific size bins, and valid pairs were counted per bins. We used 100, 40, 20, 10 kb bin sizes to generate raw and ICE (iterative correction and eigenvector decomposition) normalized matrix. 100 kb matrix was used to identify compartments by juicer_tools (v1.6)79 eigenvector, and 40kb matrix was used to define TAD boundaries through calculating insulation score by “hicexplorer hicFindTADs”. As for TAD-TAD contact, we classified genome-wide interactions into intra-TAD interactions, interactions between neighboring TADs and interactions between non-neighboring TADs (long-distant interactions), and counted the contat values within each region. Differences in TAD-TAD contats between control and Lemd3 KD were compared by edgR, respectively.
Assembly: rn7
Supplementary files format and content: We pooled 2 Hi-C sample from the same group. There are hic format files of the siLEMD3 and siNC groups, eigenvector information, TAD position, lammps data for molecular dynamics simulation and Rdata file for analysis of different TADs.

organism: Rattus norvegicus

extract_protocol:
Cells were centrifuged at 500 ×g for 5 min. Following one wash with ice-cold PBS cells were resuspended in 50 μl ice-cold Hi-C lysis Buffer. 50 μl of Transposome Mix was added to each sample and incubated at 37 °C for 30 min. This was followed by DNA extraction and purification.
Libraries for Hi-C were prepared using Chromatin Profile Kit for Illumina following manufacturers's protocols.

value: aortic thoracic smooth muscle cells

value: LEMD3 knockdown


title: Sodium Diclofenac sample tested at 50 uM (Replicate: 1, Control Batch Id: 6).

city: Mason


title: Sodium Diclofenac sample tested at 30 uM (Replicate: 3, Control Batch Id: 6).


title: Hi-C_A7r5 cells, siRNALemd3, replicate 1

description: LEMD3 knockdown


title: Exposed to epfr ko 2

value: plasma


title: Exposed to epfr ko 1


title: Sodium Diclofenac sample tested at 30 uM (Replicate: 2, Control Batch Id: 6).


title: MDA-MB-231, 300 ppm Au@MIL, 24 hrs, rep2

description: Library name: M_N_2


title: Exposed to filtered air 2


title: MDA-MB-231, 300 ppm Au@MIL, 24 hrs, rep3

description: Library name: M_N_3


title: ATAC-seq_A7r5 cells, siRNALemd3, replicate 3

data_processing:
Paired ChIP-seq and ATAC-seq raw reads were trimmed with Trim galore (v0.32) and then aligned to rn7 genome using bwa-mem2 (v2.0pre2), and produce to sam files. Sam files were then sorted and converted to bam format using samtools (v1.15.1). PCR duplicates were removed using gatk (v4.2.6.1) MarkDuplicates. Finally, bam files were filtered using samtools view with ‘-f 2 -q 24’ parameters. As for ATAC-seq, we merge three biological replicates using “samtools merge”. We use danpos (v2.4)75 to call peak and genarate nomalized wig files with the parameters “danpos.py dregion --smooth_width 0 -c 25000000 -u 1 --frsz 200 --extend 200 --region_dis 3000 --pheight 1e-10” for ChIP-seq data, and “danpos.py dpeak -c 25000000 -u 1 --frsz 200 -m 1 --smooth_width 0 --pheight 1e-20” for ATAC-seq. We use wigToBigWig (v4) tool form UCSC to convert wig files to bigwig files.
Assembly: rn7
Supplementary files format and content: There are bigwig files of separate samples and pooled two groups.

extract_protocol:
Cells were centrifuged at 500 ×g for 5 min. Following one wash with ice-cold PBS cells were resuspended in 50 μl ice-cold ATAC lysis Buffer. 50 μl of Transposome Mix was added to each sample and incubated at 37 °C for 30 min. This was followed by DNA extraction and purification.
Libraries for ATAC-seq were prepared using Chromatin Profile Kit for Illumina following manufacturers's protocols.


title: Exposed to epfr control 7


title: MDA-MB-231, 300 ppm Au@MIL, 24 hrs, rep1

description: Library name: M_N_1


title: Hi-C_A7r5 cells, siRNAscramble, replicate 1

description: WT


title: Sodium Arsenite sample tested at 7.7 uM (Replicate: 2, Control Batch Id: 6).

value: Sodium Arsenite

value: Water


title: ATAC-seq_A7r5 cells, siRNALemd3, replicate 2


title: Hep G2, without treatment, 24 hrs, rep1

description: Library name: H_C_1


title: ATAC-seq_A7r5 cells, siRNALemd3, replicate 1


title: Exposed to epfr control 5


title: Hi-C_A7r5 cells, siRNAscramble, replicate 2

description: WT


title: Exposed to epfr control 6


title: Hep G2, 300 ppm Au@MIL, 24 hrs, rep2

description: Library name: H_N_2


title: Hep G2, 300 ppm Au@MIL, 24 hrs, rep1

description: Library name: H_N_1


title: Exposed to epfr control 4


title: ATAC-seq_A7r5 cells, siRNAscramble, replicate 3


title: ATAC-seq_A7r5 cells, siRNAscramble, replicate 1


title: RIP_WT_R2

city: Buffalo

first: Laurie

last: Read

state: NY

address: 955 Main Street

department: Department of Microbiology and Immunology

institute: University at Buffalo

data_processing:
Illumina adaptors were trimmed using Cutadapt (v3.5), reads were mapped using Bowtie2 (v2.4.4) again the T. brucei genome version TriTrypDB-66_TbruceiTREU927 from TryTrypDB.org. After indexing and sorting the BAM files, featureCounts was used to count the reads for each gene_id. featureCounts output was utilized for DESeq2 for differential expression analysis.
Assembly: Trypanosoma brucei brucei TREU927
Supplementary files format and content: 2913_WT_RF_RK_PRMT1_RIPseq_counts.csv
Supplementary files format and content: featureCounts output from RIP-seq experiments

organism: Trypanosoma brucei

source_name: 29-13-derived PF

growth_protocol: The 29-13-derived PF cell line containing a doxycycline-inducible RNAi construct that targets the 3′ UTR of DRBD18 was used in this study, harbouring the doxycycline-inducible N-terminal MYC tagged DRBD18 over-expression and over-expression of its methyl mutants (Triple R to F and triple R to K mutant) generated by site-directed mutagenesis. Cells were grown in standard conditions at 27ºC in SDM-79 medium supplemented with 10% fetal bovine serum and 10U/ml of penicillin/streptomycin. Drug concentrations used in this work were 15 µg/ml of hygromycin (Sigma), 15 µg/ml of neomycin (Sigma), 2.5 µg/mL of phleomycin, 50 µg/ml of puromycin (Invivogen) and 1 µg/ml of doxycycline (Sigma). The 29-13-derived PF cell line containing a doxycycline-inducible PRMT1 RNAi construct. Cells were grown in standard conditions at 27ºC in SDM-79 medium supplemented with 10% fetal bovine serum and 10U/ml of penicillin/streptomycin. Drug concentrations used in this work were 15 µg/ml of hygromycin (Sigma), 15 µg/ml of neomycin (Sigma), 2.5 µg/mL of phleomycin and 2.5 µg/ml of doxycycline (Sigma).

extract_protocol:
UV crosslinked DRBD18-RNA, DRBD18(R→F)-RNA and DRBD18(R→K)-RNA complexes were immunopurified from the lysate using anti-MYC antibodies attached to MYC beads (GE Healthcare). The unbound fraction was also collected; 10% was used for RNA extraction and 2% for western blotting. Beads were washed three times with IP buffer (lysis buffer plus 150 mM NaCl) and treated with DNase 1 (Sigma) followed by proteinase K (Roche) after confirmation by western blot. RNA was extracted from beads with phenol/chloroform 16 and ethanol precipitated. RNA was isolated from the input fractions using Trizol and ethanol precipitation.
Takara ThruPlex DNAseq kit (R400675) for Illumina. Samples were sequenced on a NovaSeq 6000, PE50, XP flow cell.

treatment_protocol: Three biological replicates of the DRBD18 RNAi cells harbouring either N2MYC-DRBD18(WT), N2MYC-DRBD18(R→F), or N2MYC-DRBD18(R→K) were grown in the presence of 1 µg/ml doxycycline for 36 hrs. Three biological replicates of the PRMT1 RNAi cells  were grown in the presence and absence of 2.5 µg/ml doxycycline for 48 hrs.

value: 29-13-derived PF

value: procyclic form

value: siDRBD18 + N2MYC-DRBD18-induced

value: 1 ug/ml doxycylcine


title: RIP_WT_R3


title: Exposed to epfr control 2

value: 129/Sv × 129S6/SvEvTac


title: Hep G2, 300 ppm Au@MIL, 24 hrs, rep3

description: Library name: H_N_3


title: A7r5 cells, siRNALemd3, H3K9me3, Input, replicate 2

extract_protocol:
Cells were crosslinked with 1% formaldehyde for 10 min at room temperature and quenched by the addition of glycine to a final concentration of 125 mM for 5 min. The fixed cells were resuspended in lysis buffer containing protease inhibitors, then subjected to 30 cycles (30 s on and off) of sonication (Bioruptor, Diagenode) to generate chromatin fragments of ~300 bp in length. Lysates were diluted in buffer (1% Triton X-100, 2 mM EDTA, 150 mM NaCl, and 20 mM Tris-HCl, pH 8.1) containing protease inhibitors. For immunoprecipitation, the diluted chromatin was incubated with normal IgG (control) or indicated antibodies at 4℃ overnight with constant rotation, followed by incubation with 50 μl of 50% (v/v) protein A/G Sepharose beads for 2 h. Beads were successively washed. The pulled-down chromatin complex eluted by TE (1 mM EDTA and 10 mM Tris-HCl, pH 8.0) and input were de-crosslinked at 55℃ for 16 h in elution buffer (1% SDS and 0.1 M NaHCO3). The DNA was purified with the QIAquick PCR Purification Kit (QIAGEN).
Libraries for ChIP-seq were prepared using VAHTS Universal Pro DNA Library Prep Kit for Illumina following manufacturers's protocols.

tag: chip antibody


title: RIP_WT_R1


title: Exposed to filtered air ko 5

tag: age


title: Exposed to epfr control 3


title: Exposed to filtered air ko 4


title: Sodium Arsenite sample tested at 5.13 uM (Replicate: 1, Control Batch Id: 6).

value: sample


title: RIP_RK1_R3

tag: genotype

value: siDRBD18 +  N2MYC-DRBD18(R->K) -induced


title: Sodium Arsenite sample tested at 5.13 uM (Replicate: 3, Control Batch Id: 6).


title: ATAC-seq_A7r5 cells, siRNAscramble, replicate 2

value: WT


title: A7r5 cells, siRNAscramble,H3K9me3, Input, replicate 2


title: Exposed to filtered air ko 3

value: 20 weeks


title: Sodium Arsenite sample tested at 7.7 uM (Replicate: 3, Control Batch Id: 6).


title: Sodium Arsenite sample tested at 7.7 uM (Replicate: 1, Control Batch Id: 6).


title: Sodium Diclofenac sample tested at 30 uM (Replicate: 1, Control Batch Id: 6).

value: Sodium Diclofenac

value: DMSO


title: Sodium Arsenite sample tested at 5.13 uM (Replicate: 2, Control Batch Id: 6).


title: Sodium Arsenite sample tested at 3.42 uM (Replicate: 1, Control Batch Id: 6).


title: A7r5 cells, siRNAscramble,H3K9me3, Input, replicate 1


title: RIP_RK1_R1


title: Exposed to epfr control 1

value: Female


title: RIP_RF1_R3

value: siDRBD18 +  N2MYC-DRBD18(R->F)-induced


title: A7r5 cells, siRNALemd3, H3K9me3, Input, replicate 1

value: aortic thoracic smooth muscle cells

value: LEMD3 knockdown


title: A7r5 cells, siRNALemd3, H3K9me3, ChIP, replicate 2


title: Sodium Arsenite sample tested at 2.28 uM (Replicate: 3, Control Batch Id: 6).

value: Sodium Arsenite


title: Sodium Arsenite sample tested at 2.28 uM (Replicate: 2, Control Batch Id: 6).

value: Water


title: Exposed to filtered air control 6

value: Male

value: plasma


title: A7r5 cells, siRNALemd3, H3K9me3, ChIP, replicate 1


title: Exposed to filtered air ko 1


title: Sodium Arsenite sample tested at 3.42 uM (Replicate: 2, Control Batch Id: 6).


title: Sodium Arsenite sample tested at 3.42 uM (Replicate: 3, Control Batch Id: 6).


title: RIP_RF1_R2

value: 29-13-derived PF

value: procyclic form


title: A7r5 cells, siRNAscramble, H3K9me3, ChIP, replicate 2


title: RIP_RF1_R1

value: 1 ug/ml doxycylcine


title: Exposed to filtered air ko 2

value: 129/Sv × 129S6/SvEvTac


title: A7r5 cells, siRNAscramble, H3K9me3, ChIP, replicate 1


title: Sodium Arsenite sample tested at 2.28 uM (Replicate: 1, Control Batch Id: 6).

value: sample


title: Sodium Arsenite sample tested at 1.52 uM (Replicate: 2, Control Batch Id: 6).


title: Exposed to filtered air control 5


title: Exposed to filtered air control 3


title: Exposed to filtered air control 4


title: Sodium Arsenite sample tested at 1.52 uM (Replicate: 1, Control Batch Id: 6).


title: RIP_PRMT1_KD_R3_MinusDox

value: PRMT1 KD

value: No Dox


title: RIP_PRMT1_KD_R2_PlusDox


title: A7r5 cells, siRNALemd3, H3K27ac, Input, replicate 1


title: RIP_RK1_R2

value: siDRBD18 +  N2MYC-DRBD18(R->K) -induced


title: Exposed to filtered air control 2

value: 20 weeks


title: Quercetin sample tested at 33.09 uM (Replicate: 3, Control Batch Id: 1).

value: Quercetin

value: DMSO


title: Exposed to filtered air control 1

value: Female


title: A7r5 cells, siRNAscramble,H3K27ac, Input, replicate 2

value: aortic thoracic smooth muscle cells

value: WT


title: 6514_D, snRNA+snATAC

city: Toronto

first: Federico

last: Gaiti

address: 101 college street

institute: Princess Margaret Cancer Centre

description: Library name: 6514_D_multiome

library_source: other

data_processing:
Sample demultiplexing, cell barcode demultiplexing, read alignment, gene count aggregation were conducted using CellRanger v2.0.0 or v2.0.2
Assembly: hg38
Supplementary files format and content: Matrix files and tab-separated value file
Library strategy: Multiome

molecule: other

source_name: GBM patient brain tissue

extract_protocol:
Single-nuclei suspension was prepared following the nuclei isolation protocol Single Cell Multiome ATAC + Gene Expression Sequencing protocol using Chromium Nuclei Isolation Kit (10x Genomics). Tissue was dissociated by mechanical grinding and lysed with NP40 lysis buffer. The isolated pellet was repeatedly washed with PBS + 1% BSA + 1U/µl RNase Inhibitor and concentrated by centrifugation and stained with 7-AAD. Approximately 500,000 nuclei were collected and sorted based on cell size and granularity as well as 7-AAD-postive cells to separate out debris. The sorted nuclei were permeabilized in 0.1x lysis buffer, resuspended in Tris-based diluted nuclei buffer, and countered using a cell counter to achieve the corresponding nuclei stock concentration targeting recovery of 10,000 nuclei.
Following 10x Genomics Chromium Next GEM Single Cell Multiome ATAC + Gene Expression protocol (10x Genomics; CG000338), nuclei suspension was incubated in transposition mix at 37°C for 60 minutes to digest DNA into fragments at open chromatin regions. The transposed nuclei were then loaded onto a Chromium Next GEM Chip J (10x Genomics; PN-1000234) through a Chromium controller (10x Genomics) to generate Gel Bead-In Emulsions (GEM), which partition nuclei with barcoded gel-beads to enable single-nuclei barcoding. Dissolving the gel bead allows to produce barcoded transposed DNA (Illumina® P5 sequence and a 16 nt 10x ATAC barcode added) and cDNA from poly-adenylated capture of mRNA (Illumina® TruSeq Read 1 sequencing primer and a 16 nt RNA 10x barcode added), followed by Dynabeads cleanup and SPRIselect for size selection. The material was pre-amplified with 7 cycles of PCR for separated ATAC and gene expression library construction.  ATAC library was prepared by PT and sample index addition through PCR amplification. Gene expression library was prepared by obtaining cDNA amplicon though PCR amplification, followed by enzymatic fragmentation, end repair, A-tailing, adaptor ligation and PCR for adding P5, P7, i7 and i5 sample indexes, and TruSeq Read 2 primer sequence.

value: GBM patient brain tissue


title: Quercetin sample tested at 33.09 uM (Replicate: 2, Control Batch Id: 1).


title: RIP_PRMT1_KD_R2_MinusDox


title: A7r5 cells, siRNAscramble,H3K27ac, Input, replicate 1


title: 6514_C, snRNA+snATAC

description: Library name: 6514_C_multiome


title: RIP_PRMT1_KD_R3_PlusDox


title: A7r5 cells, siRNALemd3, H3K27ac, ChIP, replicate 2

value: LEMD3 knockdown