title: CoCult-Luva-I (miRNA-seq)

value: human mast cell line LUVA

value: CoCult-Luva


title: Pandemic Chilblain 099

status: Public on Feb 13 2025

type: RNA

city: Lausanne

first: JEREMY

last: DI DOMIZIO

state: Vaud

address: Av Boveresses 155, 1066 Epalinges

country: Switzerland

institute: CHUV

description:
internal positive and negative controls were used
PC099

hyb_protocol: standard protocol

scan_protocol: standard protocol

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

label: NanoString indexing

molecule: total RNA

organism: Homo sapiens

source_name: skin biopsy

label_protocol: NanoString indexing

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

treatment_protocol: samples were snap-frozen without any treatment

tag: disease state

value: chillblain


title: shGFP control, replicate1

type: SRA

city: St Petersburg

first: Rui

last: Zhou

state: FL

address: REB 4130, 501 6th Ave S

country: USA

institute: Johns Hopkins University

library_source: transcriptomic

data_processing:
Adaptor sequences and low-quality reads (those with an average quality score < 20) were removed from the paired-end raw data using Trim-galore (version 0.4.4).
The resulting cleaned reads were aligned to the Drosophila melanogaster (dm6) reference genome using the STAR splice-aware aligner (version 2.6.0c) with default parameters.
Ambiguous reads mapping to multiple regions in the genome and reads with a MAPQ score less than 10 were discarded.
Subread featureCounts (version 2.0.1) was then utilized for gene quantification, employing the FlyBase r6.40 gene annotation.
Genes without read counts in all samples were excluded from subsequent analysis.
Assembly: dm6
Supplementary files format and content: matrix table with raw gene counts for every gene and every sample
Supplementary files format and content: tab-delimited text file include RPKM values for every gene and every sample

organism: Drosophila melanogaster

source_name: fat body

growth_protocol: Flies were maintained at room temperature with standard fly food (molasses formula).

extract_protocol:
Total RNA was extracted using TRIzol reagent (Invitrogen).
Total RNA samples were subjected to cDNA library construction using illumine kit.

treatment_protocol: Fat bodies of wandering 3rd instar larvae of appropriate genotypes were dissected in PBS prior to RNA extraction.

tag: tissue

value: fat body

tag: developmental stage

value: wandering 3rd instar larvae

tag: cell type

tag: genotype

value: cg>shGFP


title: FNV, PNA79, 30min, rep C

city: Würzburg

first: Jakob

middle: Jeremias

last: Jung

state: Bayern

address: Josef-Schneider-Str. 2/Bau D15

department: Institute of Molecular Infection Biology (IMIB)

country: Germany

institute: University of Würzburg

description: Library name: Fnv_PNA79_30m_C

data_processing:
RNA-seq raw reads were trimmed, filtered and mapped using the F. nucleatum ssp. nucleatum ATCC 23726 (NZ_CP028109.1) annotation file with costume annotation or the F. nucleatum ssp. vincentii 3_1_36A2 (NZ_ CP003700.1) file.
To remove adapter sequences and trim nucleobases BBduk was used before mapping the reads with BBMap (v38.84).
Differential gene expression was investigated using the featureCounts methods of the Subread (2.0.1) package. For further downstream analysis R/Bioconductor packages were used.
Assembly: NZ_CP028109.1, NZ_ CP003700.1
Supplementary files format and content: raw_counts_FNN.csv is csv table with genes as rownames and samples as colnames for FNN samples
Supplementary files format and content: raw_counts_FNV.csv is csv table with genes as rownames and samples as colnames for FNV samples

organism: Fusobacterium nucleatum

source_name: subspecies vincentii 3_1_36A2

growth_protocol: Three biological replicates for each sample were grown overnight in ColB, diluted the following morning 1:50 in fresh ColB, and after the culture reached OD600 0.5, it was diluted 1:250 to 1x106 cfu ml-1 in MHB.

extract_protocol:
To isolate fusobacterial RNA, samples were incubated 1:1 (v:v) with RNAprotect Bacteria (Qiagen) for five minutes at RT, snap frozen in liquid nitrogen and stored at -80°C until further processing. To purify RNA the miRNeasy Micro kit (Qiagen) was used. Briefly, cell dilutions were thawed on ice, centrifuged at 4°C with 13,000 g for 20 minutes, the pellets resuspended in 100 μl 0.5 mg ml-1 lysozyme (Roth) in TE buffer pH 8.0 and incubated for two minutes at RT. The samples were then incubated with 700 μl Qiazol (Qiagen) for five minutes at RT and after addition of 160 μl chloroform shaken vigorously for 15 seconds to obtain phase separation. The upper aqueous phase was mixed 1:1.5 with 100% ethanol and loaded onto the Qiagen columns. Columns washes, DNase I digest and elution were performed according to the manual instructions. RNA concentrations were determined via NanoDrop measurements and samples were stored at -80°C until sequencing.
RNA quality was investigated using the 2100 Bioanalyzer together with the RNA 6000 Pico kit (Agilent Technologies). Risbosomal RNA (rRNA) depletion was performing using the RiboCop META rRNA depletion kit (Lexogen) according to the manufacturer’s instructions. Depleted RNA was further fragmented via ultrasound for 30 s at 4°C. After adapter ligation to the 3’ end, the first-strand cDNA was synthetized using the M-MLV reverse transcriptase. Following purification, 5’ Illumina TruSeq adapters were ligated to the cDNA, the cDNA amplified by PCR and the resulting product purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics). After performing library quality control using the 2100 Bioanalyzer with the DNA High Sensitivity kit (Agilent Technologies), the cDNA was pooled, purified and sequenced using an Illlumina NextSeq 500 system with 10 million reads/sample in single end mode with 75 nt read length.

treatment_protocol: 5 ml of the solution were transferred into 5 ml low-binding tubes (LABsolute) and incubated with 10 μM PNA or the respective volume of water for 30 minutes and 16 hours at 37°C in the anaerobic chamber. The reaction was stopped at the mentioned time points by adding RNAprotect Bacteria (Qiagen).

tag: time

value: 30 minutes

tag: strain

value: subspecies vincentii 3_1_36A2

tag: treatment

tag: replicate

value: C


title: FNV, H20, 16h, rep B

description: Library name: Fnv_H2O_16h_B

value: 16 hours

value: Control

value: B


title: Pandemic Chilblain 156

description:
internal positive and negative controls were used
PC156


title: FNV, PNAscr, 30min, rep A

description: Library name: Fnv_PNAscr_30m_A

value: PNA scrambled

value: A


title: FNV, PNA79, 30min, rep B

description: Library name: Fnv_PNA79_30m_B


title: Bottom position, R3 growth stage, biological replicate 3

city: Urbana

first: Lauriebeth

last: Leonelli

state: Illinois

address: 1206 W Gregory Dr.

department: Department of Agricultural and Biological Engineering

institute: University of Illinois Urbana-Champaign

description:
VuCanopy_014
B-R3-Rep3

data_processing:
Sequence reads were trimmed using the JGI BBDuk shellscript.
Trimmed reads were mapped to the cowpea reference genome using HISAT2.
Reads mapping to exons were counted using the featureCounts program.
Assembly: Vigna unguiculata v1.2, Phytozome genome ID: 540, NCBI taxonomy ID: 3917.
Supplementary files format and content: raw read counts for each sample.
Supplementary files format and content: DESeq2 normalized read counts for each sample.

molecule: polyA RNA

organism: Vigna unguiculata

source_name: Leaf

growth_protocol: Cowpea were planted in-ground in a Plant Care Facility greenhouse at the University of Illinois Urbana-Champaign. Seeds were planted with 3 inches between plants and 30 inches between rows. Plant maintenance involved irrigation, weekly fertilizer application, and supplemental lighting (14h/10h photoperiod, 1000 umol/m^2*s).

extract_protocol:
RNA was purified using the MagMAX kit for RNA extraction (Thermo Fisher Scientific, cat# AM1830).
Libraries were constructed using the Kapa HyperPrep mRNA kit (Roche, cat# KK8581).

value: Leaf

tag: canopy position

value: Bottom position

value: R3 growth stage


title: CoCult-Luva-I-II (miRNA-seq)

city: Goettingen

first: Gabriela

last: Salinas

state: Lower-Saxony

address: Kreuzbergring 57

department: Department of Pathology

institute: Universitaetsmedizin Goettingen

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0
Assembly: GRCh38 version 110
Supplementary files format and content: Tab-delimited miRNA counts

source_name: human mast cell line LUVA

extract_protocol:
RNA isolation was performed using Trizol reagent (Thermo Fisher Scientific, Waltham, MA, USA) according to the manufacturer's instructions. RNA quality was assessed by measuring the RNA integri-ty number (RIN) using a Fragment Analyzer HS Total RNA Kit (Advanced Analytical Technologies, Inc.)
RNA libraries were prepared for sequencing using standard Illumina protocols

tag: cell line

value: human mast cell line LUVA


title: Pandemic Chilblain 093

description:
internal positive and negative controls were used
PC093


title: FNV, PNA79, 30min, rep A

description: Library name: Fnv_PNA79_30m_A


title: Pandemic Chilblain 150

description:
internal positive and negative controls were used
PC150


title: Top position, R3 growth stage, biological replicate 3

description:
VuCanopy_018
T-R3-Rep3

value: Top position


title: PCI-13-I

data_processing:
Sequence images were transformed with Illumina software BaseCaller to BCL files, which was demultiplexed to fastq files with bcl2fastq v2.20.0
STAR version 2.7.8a was used to align the reads to the GRCh38 genome using 2 mismatches within 50 bases
featureCounts version 1.5.0-p1 was used to quantify reads for genes in GRCh38 version 110
Assembly: GRCh38 version 110
Supplementary files format and content: Tab-delimited gene counts

source_name: human OSCC cell line PCI-13

value: human OSCC cell line PCI-13

value: monoculture


title: CoCult-Luva-II (miRNA-seq)

value: CoCult-Luva


title: FNV, H20, 30min, rep C

description: Library name: Fnv_H2O_30m_C


title: Bottom position, R1 growth stage, biological replicate 3

description:
VuCanopy_013
B-R1-Rep3

value: R1 growth stage


title: Top position, R3 growth stage, biological replicate 2

description:
VuCanopy_012
T-R3-Rep2


title: PCI-13-II


title: Middle position, R1 growth stage, biological replicate 3

description:
VuCanopy_015
M-R1-Rep3

value: Middle position


title: Pandemic Chilblain 148

description:
internal positive and negative controls were used
PC148

value: chillblain


title: Top position, R1 growth stage, biological replicate 2

description:
VuCanopy_011
T-R1-Rep2


title: FNV, H20, 30min, rep B

description: Library name: Fnv_H2O_30m_B

value: 30 minutes

value: subspecies vincentii 3_1_36A2


title: FNV, H20, 30min, rep A

description: Library name: Fnv_H2O_30m_A

value: Control


title: Middle position, R3 growth stage, biological replicate 2

description:
VuCanopy_010
M-R3-Rep2


title: PCI-13-I-II


title: Pandemic Chilblain 146

description:
internal positive and negative controls were used
PC146


title: Pandemic Chilblain 147

description:
internal positive and negative controls were used
PC147


title: Luva-I


title: FNN, PNAscr, 16h, rep C

description: Library name: Fnn23_PNAscr_16h_C

source_name: subspecies nucleatum ATCC 25586

value: 16 hours

value: subspecies nucleatum ATCC 25586

value: C


title: Middle position, R1 growth stage, biological replicate 2

description:
VuCanopy_009
M-R1-Rep2

value: Leaf


title: Pandemic Chilblain 010

description:
internal positive and negative controls were used
PC010


title: Luva-I-II


title: CoCult-PCI-13-I

value: coculture


title: Bottom position, R3 growth stage, biological replicate 2

description:
VuCanopy_008
B-R3-Rep2

value: Bottom position

value: R3 growth stage


title: FNN, PNAscr, 16h, rep B

description: Library name: Fnn23_PNAscr_16h_B

value: PNA scrambled

value: B


title: FNN, PNA79, 16h, rep B

description: Library name: Fnn23_PNA79_16h_B


title: Bottom position, R1 growth stage, biological replicate 2

description:
VuCanopy_007
B-R1-Rep2


title: Pandemic Chilblain 259

description:
internal positive and negative controls were used
PC259


title: Luva-II

value: human mast cell line LUVA

value: monoculture


title: Pandemic Chilblain 001

description:
internal positive and negative controls were used
PC001


title: Top position, R3 growth stage, biological replicate 1

description:
VuCanopy_006
T-R3-Rep1

value: Top position


title: FNN, PNA79, 16h, rep C

description: Library name: Fnn23_PNA79_16h_C


title: Pandemic Chilblain 149

description:
internal positive and negative controls were used
PC149


title: CoCult-PCI-13-II

value: human OSCC cell line PCI-13


title: Pandemic Chilblain 082

description:
internal positive and negative controls were used
PC082

value: chillblain


title: Top position, R1 growth stage, biological replicate 1

description:
VuCanopy_005
T-R1-Rep1

value: R1 growth stage


title: FNN, PNA79, 16h, rep A

description: Library name: Fnn23_PNA79_16h_A

value: A


title: CoCult-PCI-13-I-II


title: Pandemic Chilblain 058

description:
internal positive and negative controls were used
PC058


title: Middle position, R3 growth stage, biological replicate 1

description:
VuCanopy_004
M-R3-Rep1

value: Middle position


title: CoCult-Luva-I


title: FNN, H20, 16h, rep C

description: Library name: Fnn23_H2O_16h_C

value: 16 hours

value: Control


title: Middle position, R1 growth stage, biological replicate 1

description:
VuCanopy_003
M-R1-Rep1


title: CoCult-Luva-II


title: FNN, PNAscr, 16h, rep A

description: Library name: Fnn23_PNAscr_16h_A

value: subspecies nucleatum ATCC 25586


title: Bottom position, R3 growth stage, biological replicate 1

description:
VuCanopy_002
B-R3-Rep1

value: Leaf


title: FNN, H20, 16h, rep B

description: Library name: Fnn23_H2O_16h_B


title: R_DMSO1

city: Xiamen

first: aicun

last: li

address: South Xiang'an Road 4221-120, Xiang'an Campus, Xiamen University, Xiang'an District

country: China

institute: Xiamen University

description: PR_DMSO_DT_processed data.xls

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the human reference genome (hg38) using HISAT2 (v2.1.0)
Cufflinks (v2.2.1) was used to calculate the expression of RefSeq annotated genes
Assembly: hg38
Supplementary files format and content: xls files include FPKM values for each Sample

growth_protocol: A375 cells were cultured in DMEM supplemented with 10% FBS, in humidified atmosphere with 5% CO2 at 37C.

extract_protocol:
Cells were lyzed by trizol.
RNA library preparation was performed by using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq 3000 at RiboBio Co., Ltd Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano Lab Chip Kit (Agilent, CA, USA) with RIN number >7.0. Approximately 1 ug of total RNA was used to deplete ribosomal RNA according to the manuscript of NEBNext rRNA Depletion Kit (NEB E6310). Following purification, the poly(A)- or poly(A)+ RNA fractions is fragmented into small pieces using divalent cations under elevated temperature. Then the cleaved RNA fragments were reverse-transcribed to create the final cDNA library in accordance with the protocol for the mRNA-Seq sample preparation kit (NEB, E7760), the average insert size for the paired-end libraries was 300 bp (±50 bp). And then we performed the paired-end sequencing on an Illumina Hiseq X-Ten at Amogene (Xiamen, China) Biotech Co., Ltd following the vendor's recommended protocol.

treatment_protocol: Cells were infected with indicated lentivirus and/or treated with indicated drugs.

value: melanoma

value: WT

value: DMSO


title: FNN, PNAscr, 30min, rep C

description: Library name: Fnn23_PNAscr_30m_C

value: 30 minutes

value: PNA scrambled

value: C


title: ChIP_FosL1_K116Q

library_source: genomic

data_processing:
Basecalling was performed using CASAVA version 1.4
Sequenced reads were aligned to the Hg38 human reference genomes using Bowtie2 (v2.3.4.1) and generated SAM files were converted to BAM files using Samtools (v.1.9)  using the view function.
Samtools was used to further sort, index and Picard tool MarkDuplicates (http://picard.sourceforge.net) was used to remove potential PCR duplicates from BAM files with the default parameters which were converted to BigWig files using Deeptools. BigWig files were visualized using the Integrative Genomics Viewer (Broad Institute).
HOMER suit of tools was used. Aligned bam files were subjected to peak calling using findPeaks tools with the -style factor.
Assembly: hg38
Supplementary files format and content: BigWig files were generated using deeptools and were visualized using the Integrative Genomics Viewer (Broad Institute).

molecule: genomic DNA

extract_protocol:
Cells were washed once with cold PBS prior to cross-linking with 2 mM DSG for 45 minutes followed by 1% formaldehyde (28908, Thermo) for 15 min at room temperature (except for the etoposide ChIP of TOP2A, cells were treated with 100mM etoposide for 10min). To quench the cross-linking reaction, 2.5 M glycine dissolved in PBS was added and cells were incubated at room temperature for a further 5 minutes. Cells were washed twice with ice-cold PBS and lysed using cell lysis buffer (50 mM Tris pH 8.0, 0.5% NP40, 50 mM NaCl) to remove the cytoplasmic proteins. The pellet was resuspended in nuclear lysis buffer (1% Triton X-100, 2 mM EDTA pH 8.0, 400 mM NaCl, 20 mM Tris pH 8.0, 0.1% SDS). Chromatin DNA was sheared to 300–500 bp average in size through sonication using a Bioruptor instrument (Diagenode). Fragmented chromatin was diluted 1:1 with dilution buffer (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 1% Triton X-100) and immunoprecipitated with IgG or indicated specific antibodies overnight at 4°C, followed by incubation with protein A/G magnetic Dynabeads for 4 h. Dynabeads were washed once each with ChIP wash buffer 1 (20 mM Tris pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and ChIP wash buffer 2 (20 mM Tris pH 8.0, 400 mM NaCl, 2 mM EDTA pH 8.0, 0.1% SDS, 1% Triton X-100) and washed twice with TE buffer (10 mM Tris pH 7.5, 1 mM EDTA pH 8.0). After washing and elution, the protein–DNA complex was reversed by heating overnight at 65°C. Immunoprecipitated DNA was purified by QIAquick spin columns. Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing.
Sequencing libraries were prepared using the KAPA DNA HyperPrep Kit and subjected to high-throughput sequencing. Briefly, Chip DNA was end-blunted and added with an ‘A’ base. Then 200–400 bp fragments are gel-isolated and purified. The library was amplified by 18 cycles of PCR.

tag: chip antibody

value: Fra-1 (Santa Cruz, sc-374091)


title: heterogenous_Rep2

city: Shenzhen

first: Wenyan

last: Chen

address: Yutang Street

institute: Shenzhen Bay Laboratory

data_processing:
RNA samples, namely, 4 samples of HEK293T cell lines under two different conditions (Control: WT; Case: heterogenous) with 2 biological replicates per condition, were obtained in FASTQ format. For each FASTQ file, quality checks were conducted using FastQC.
Contaminating data, such as low-quality reads, adaptor sequences, and poor-quality bases, were removed with Trimmomatic software.
The trimmed reads were mapped to the human reference genome (GRCh38) using STAR and were then sorted by SAMtools.
Assembly: GRCh38
Supplementary files format and content: Wig format for each sample

source_name: kidney

extract_protocol:
HEK293T cells were cultivated in Dulbecco's modified eagle medium (DMEM) supplemented with 1% penicillin/streptomycin and 10% fetal bovine serum (FBS) and were incubated in 5% CO2 with 37 ℃
Total RNA extracted from HEK293T cells was subjected to strand-specific RNA sequencing using the Illumina nova seq 6000 platform at Berry Genomics Co, Ltd (Beijing, China). Briefly, strand-specific RNA-Seq libraries were prepared by combining the Ribo-Zero rRNA Removal Kit (Epicentre, Madison, WI, USA) and the dUTP method to ensure strand specificity.

value: kidney

value: Anchorrage-dependent cells

value: heterogenous


title: FNN, PNAscr, 30min, rep B

description: Library name: Fnn23_PNAscr_30m_B

value: B


title: W303 strains, grr1-deficient, Tunicamycin 4 h, replicate 2 [Ribo-seq]

city: Tokyo

first: Nichika

last: Sato

address: 4-6-1, Shirokanedai, Minato-ku

department: The Institute of Medical Science

country: Japan

institute: The University of Tokyo

description:
Data was used for the following comparision(s) in Riboseq.2_FC_grr1_0_Ribovs_grr1_4_Ribo.csv: grr1_2 vs grr1_1,grr1_4 vs grr1_3. TE was calculated using the count from Ribo-seq data and the count from RNA-seq data shown in another file.
Riboseq.2_FC_grr1_0_Ribovs_grr1_4_Ribo.csv
TE_FC_grr1_0_vs_grr1_4.csv

library_source: other

data_processing:
Linker sequences were trimmed with Cutadapt v2.6 and reads were demultiplexed using FASTX-toolkit v0.0.14.
Demultiplexed reads longer than 20 nt were mapped against rRNA and noncoding RNA genes using Bowtie2 (Langmead and Salzberg, 2012) v2.3.5 with ‘–very-sensitive’.
The unmapped reads were then mapped to the R64 reference genome using STAR (Dobin et al., 2013) v2.7.3a with parameters ‘–outFilterMultimapNmax 1 –outFilterIntronMotifs RemoveNoncanonicalUnannotated –outSAMtype BAM Unsorted –quantMode TranscriptomeSAM GeneCounts’. Alignments to transcriptome were used for subsequent analysis.
The A-site offset was computed using the R package riboWaltz (Lauria et al., 2018). 27-29 nt  reads were then used for computation of A-site occupancy with the python package RiboPlot v0.3.1.
The read counts per gene outputs were proceeded to differentially expression analysis with the R package DEseq2 (Love et al., 2014).
Assembly: R64
Supplementary files format and content: Tab-delimited text file including raw counts and RPM (reads per million) of of A-site occurrences for each nucleotide across all transcripts within each sample
Library strategy: Ribosome profiling (Ribo-seq)

molecule: other

organism: Saccharomyces cerevisiae

source_name: Saccharomyces cerevisiae

growth_protocol: Yeast cells were cultured with synthetic complete (SC) medium with 2 % glucose at 30 ºC.

extract_protocol:
After 4 hr of tunicamycin treatment, yeast cells were harvested by filtration and frozen by liquid nitrogen. They were lysed by lysis buffer for Ribo-seq (20 mM Tris-HCl [pH 7.5], 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 1% Triton X-100, 0.1 mg/mL cycloheximide, 25 U/mL Turbo DNase (Invitrogen, AM2238)). Clear lysates were obtained by centrifugation at 20,000 xg for 10 min at 4 °C. Clear lysate containing 20 μg total RNA was treated with 1.25 unit of RNase I (#E0067-10D1, LGC Biosearch Technologies) per µg RNA for 45 min at 25°C. RNase I treatment was quenched by the addition of 200 units of SUPERase•In RNase Inhibitor (Invitrogen, AM2694). RNA-digested lysate was layered on a sucrose cushion (1 M sucrose, 20 mM Tris-HCl [pH 7.5], 150 mM NaCl, 5 mM MgCl2, 1 mM DTT, 0.1 mg/mL cycloheximide, 20 U/mL SUPERase•In RNase Inhibitor), followed by centrifugation in a TLA-110 rotor (Beckman) at 100,000 rpm for 1 hr at 4°C. The ribosomal pellet was resuspended in 120 µL of splitting buffer (20 mM Tris-HCl [pH 7.5], 300 mM NaCl, 5 mM EDTA, 1% Triton X-100, 1 mM DTT, 20 U/mL of SUPERase•In RNase Inhibitor) to dissociate ribosomes from the mRNA fragments, and then passed through the 100 kDa MWCO Amicon Ultra-0.5 device (Millipore, UFC5100). The non-ribosomal flow-through (approximately 100 µL) was collected and mixed with 300 µL TRIzol reagent (Invitrogen, 15596018). RNA fragments were extracted by Direct-zol RNA MicroPrep (Zymo Research).
Library preparation was performed as described (Matsuki and Matsuo et al., 2020) with following modifications. As linker DNA, 5’-(Phos)NNNNNIIIIITGATCGGAAGAGCACACGTCTGAA(ddC)-3’ where (Phos) indicated 5’ phosphorylation and (ddC) indicates a terminal 2’, 3’-dideoxycytidine, was used. The Ns and Is indicate random barcodes for eliminating PCR duplication and multiplexing barcodes, respectively. The linkers were pre-adenylated with 5’ DNA Adenylation kit (NEB), and then used for the ligation reaction. The rRNAs were removed using a mixture of riboPOOL (siTOOLs Biotech) and homemade customized biotinylated oligos. An oligo 5’-(Phos)NNAGATCGGAAGAGCGTCGTGTAGGGAAAGAG(iSp18)GTGACTGGA GTTCAGACGTGTGCTC-3’, where (Phos) indicated 5’ phosphorylation and Ns indicate random barcode, was used for reverse transcription. PCR was performed with oligos, 5’-AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTC-3’ and 5’- CAAGCAGAAGACGGCATACGAGATJJJJJJGTGACTGGAGTTCAGACGTGTG-3’, where Js indicate reverse complement of the index sequence discovered during Illumina sequencing. The libraries were sequenced on a HiSeq X Ten (Illumina) at Macrogen Japan corp.

treatment_protocol: Yeast cells were grown at 30 ºC  until OD600 = 0.2, then treated with 1 µg/ml of tunicamycin (Tm, #208-08243, Wako) for 4 hr.

value: Saccharomyces cerevisiae

value: Tunicamycin

value: 4 hr


title: ChIP_FosL1_KDL1


title: W303 strains, grr1-deficient, Tunicamycin 0 h, replicate 2 [Ribo-seq]

value: 0 hr


title: WT_Rep2


title: WT_Rep1


title: CoCult-Luva-I-II

value: human mast cell line LUVA

value: coculture


title: heterogenous_Rep1


title: W303 strains, grr1-deficient, Tunicamycin 4 h, replicate 1 [Ribo-seq]


title: WT-3

city: Shenyang

first: Zhang

last: Baocai

address: Shenyang

department: College of Life and Health Sciences

institute: Northeastern University

description: Library name: Sample 6

data_processing:
Clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content sequence of the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Assembly: NZ_CP053946.1
Supplementary files format and content: Excel file includes RPKM values for each sample

organism: Shewanella oneidensis MR-1

source_name: strain

extract_protocol:
Cells were harvested from the anode via centrifugation (4℃, 8000 rpm, 7741 × g, Avanti J26S XP, 30 min), which were immediately frozen in liquid nitrogen. The RNAprep pure Cell/Bacteria Kit (TIANGEN) was used to extract the total RNA
The NEBNext®UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) was used to construct the sequencing libraries, in which each sample was modified with the index codes. The index-coded samples were clustered using the TruSeq PE Cluster Kit v3-cBot-HS (Illumina) on a cBot Cluster Generation System

value: strain


title: FNN, PNA79, 30min, rep C

description: Library name: Fnn23_PNA79_30m_C

value: subspecies nucleatum ATCC 25586


title: ChIP_FosL1_CTL

value: melanoma

value: shCtrl


title: W303 strains, wild-type, Tunicamycin 4 h, replicate 2 [Ribo-seq]

description:
Data was used for the following comparision(s) in Riboseq.2_FC_WT_0_Ribovs_WT_4_Ribo.csv: WT_2 vs WT_1,WT_4 vs WT_3. TE was calculated using the count from Ribo-seq data and the count from RNA-seq data shown in another file.
Riboseq.2_FC_WT_0_Ribovs_WT_4_Ribo.csv
TE_FC_WT_0_vs_WT_4.csv

value: wild-tipe


title: R_DMSO2

description: PR_DMSO_DT_processed data.xls

value: WT

value: DMSO


title: FNN, PNA79, 30min, rep A

description: Library name: Fnn23_PNA79_30m_A

value: 30 minutes

value: A


title: Bottom position, R1 growth stage, biological replicate 1

description:
VuCanopy_001
B-R1-Rep1

value: Leaf

value: Bottom position

value: R1 growth stage


title: ChIP_seq_FosL1_P

value: Fra-1 (Santa Cruz, sc-374091)


title: ChIP_seq_H3K4me2_R_KDT21_fosl1

value: H3K4me2 (Millipore, 07-030)


title: W303 strains, wild-type, Tunicamycin 0 h, replicate 2 [Ribo-seq]

value: Saccharomyces cerevisiae

value: Tunicamycin

value: 0 hr


title: ChIP_FosL1_WT


title: FNN, H20, 16h, rep A

description: Library name: Fnn23_H2O_16h_A

value: 16 hours

value: Control


title: FNN, H20, 30min, rep C

description: Library name: Fnn23_H2O_30m_C

value: subspecies nucleatum ATCC 25586

value: C


title: W303 strains, grr1-deficient, Tunicamycin 0 h, replicate 1 [Ribo-seq]


title: ChIP_seq_H3K4me2_R_KDT21_ctl

value: melanoma


title: W303 strains, wild-type, Tunicamycin 4 h, replicate 1 [Ribo-seq]

value: wild-tipe

value: 4 hr


title: FNN, H20, 30min, rep A

description: Library name: Fnn23_H2O_30m_A

value: 30 minutes


title: FNN, H20, 30min, rep B

description: Library name: Fnn23_H2O_30m_B

value: B


title: ChIP_seq_H3K4me2_R

value: WT


title: W303 strains, wild-type, Tunicamycin 0 h, replicate 1 [Ribo-seq]


title: ChIP_seq_FosL1_R


title: SDV3-2

description: Library name: Sample 2

value: strain


title: ChIP_seq_H3K4me2_P


title: SDV3-1

description: Library name: Sample 1


title: No Pt-drug treatment on cisplatin-resistant A549

city: Beijing

first: Mingyang

last: Li

address: Yanyuan Subdistrict, Haidian District

institute: Peking University

description: Library name: ResistantA549_control

data_processing:
Pt-seq: All sequence reads were processed using trim_galore (v0.6.10) with paramters -q 30 --phred33 --length 25 --stringency 3 --paired. Reads with SbfI enzyme restriction sites in 5' terminal was removed. Cleaned reads were then aligned to CRGh38 human genome (CHO samples were aligned to Crigri-PICRH-1.0 genome) using bowtie2 (v2.5.1), and reads aligned to forward strand and reverse strand were split by samtools view -F 276 (for forward strand) and -F 260 -f 16 (for reverse strand). Aligned reads with MAPQ >= 40, or between 1 and 10, were kept. And others were filtered using sambamba (v1.0.0). For sample comparison, samples were all down-sampled to the volume of sample with the lowest volumn. Pearson correlation coefficient (PCC) across samples was calculated by deeptools multiBigwigSummary and plotCorrelation commands, with bin size 5 kb. Target-seq: Raw sequencing reads were first subjected to UMI extraction using umi_tools extract, where UMIs with specific patterns were identified and separated from the read sequences. The extracted reads were then trimmed using trim_galore to remove adapter sequences and low-quality bases, with stringent parameters including a quality score threshold of 30, a minimum read length of 25, and a stringency value of 3. Trimmed reads were aligned to the reference genome using the STAR aligner. STAR was configured to perform end-to-end alignment. Duplicate reads were subsequently removed based on UMIs using umi_tools dedup, which extracted UMIs from read IDs and deduplicated paired-end reads.
Assembly: Homo sapiens: hg38, t2tchm13. Cricetulus griseus: CriGri-PICRH-1.0

source_name: cell line

extract_protocol:
Pt-seq: Genomic DNAs were extracted using Universal Genomic DNA Kit (CWBIO, CW2298) following manufacturer's protocol. Target-seq: Total RNA of CHO cells was extracted by Total RNA Isolation Kit (Vayzme, RC112) and then reverse transcription was performed using 1st Strand cDNA Synthesis Kit (Vayzme, R312).
Pt-seq: Briefly, 500-1000 ng genomic DNA was fragmented by COVARIS S220 Focused-ultrasonicator (Covaris, Inc.) to generate DNA fragments with a medium size of 300 bp. DNA fragments with 1 ng model sequences were performed for library preparation by using End Repair/dA-Tailing Module (NEB, E7546). Adaptors with modifications used in Pt-seq were synthesized by Sangon Biotech, Shanghai and annealed by gradual cooling process. Ligation Module (NEB, E7595) was used to perform restriction-sites-contained-adaptor ligation. Then DNA fragments were denatured and placed on ice. Non-immunoprecipitated DNA was saved as input and stored at -20°C. Generally, 1 μg anti-Pt modified DNA antibodies (Abcam, ab103261) were added into IP buffer and incubated with the processed DNA fragments overnight at 4°C with gentle rotation. Dynabeads Protein G (Thermo Fisher, 10004D) were pre-washed and blocked with 0.1% BSA/PBS and then incubated with samples for 2 hours at 4°C with gentle rotation50. The immunoprecipitated DNA-antibody-Dynabeads complexes were washed three times with IP buffer. The immunoprecipitated DNA was eluted by Proteinase K (NEB, P8107S) with freshly made elution buffer at 56°C for 2 hours and then purified. Then un-ligated DNA was removed by RecJf (NEB, M0264) and Exonuclease I (NEB, M0293). Then the primer extension was performed using Q5 High Fidelity DNA Polymerase (NEB, M0544) and redundant primer was removed by Exonuclease I (NEB, M0293). DNA fragments were denatured and placed on ice. Second adaptor ligation was performed on sing strand DNA samples using T4 DNA Ligase (NEB, M0202) with PEG8000 at 16°C for overnight. PCR amplification was performed using Q5 High Fidelity DNA Polymerase (NEB, M0544) and DNA was amplified for 2 cycles at first time. The PCR products were cleaned up with 1.2× AMPure XP beads (Beckman Coulter). Restriction endonuclease digestion was performed using SbfI (NEB, R3642) at 37°C f. Target-seq: The cDNA was diluted and amplified with primers specially designed for HGPRT gene containing the paired adaptor sequences (Supplementary Table 1) using Q5 High Fidelity DNA Polymerase (NEB, M0544) for 5 cycles. The PCR products were purified with 1× AMPure XP beads (Beckman Coulter) and then the second round of amplification was performed with different index primers for about 25 cycles. The PCR products were purified with 0.8× AMPure XP beads (Beckman Coulter). Final library quality was measured as described before. Libraries were sequenced on and MGISEQ-2000 platform to generate 150 bp paired-end reads.

value: cisplatin-resistant


title: HFD_W8

city: 海淀区

first: YiRan

last: Liu

state: 北京市

department: Department of Biomedical Informatics, State Key Laboratory of Vascular Homeostasis and Remodeling, School of Basic Medical Sciences, Peking University, Beijing, China

institute: PKU

description:
Library name: Sample22
HFD.csv contains DEGs between SCARA3 KO and WT

data_processing:
Raw data (raw reads) of fastq format were firstly processed through fastp software and clean data with high quality were obtained.
Next, the clean reads were mapped with Mesocricetus auratus genome using Hisat2 v2.0.5. FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs) was used to estimate gene expression levels. Differential expression genes (DEGs) analysis was performed using DESeq2 R package (1.20.0).
Assembly: BCM_Maur_2.0
Supplementary files format and content: CD.csv,fCD.csv,HFD.csv contain DEGs between SCARA3 KO and WT in different treated samples
Supplementary files format and content: CD_rawcounts.xlsx,HFD_rawcounts.xlsx contains raw counts file in samples in each group, CD and fCD in CD_rawcounts.xlsx and HFD in HFD_rawcounts.xlsx

organism: Mesocricetus auratus

source_name: liver

growth_protocol: RNA was extracted from liver tissues of WT and SR-A3-/- hamsters CD-fed (n = 3/group) or HFHCD-fed for 8 weeks (n = 5/group).

extract_protocol:
After assessment of RNA integrity using the RNA Nano 6000 Assay Kit of the Bioanalyzer 2100 system (Agilent Technologies, CA, USA), the cDNA library was prepared following the Illumina protocol.
The library preparations were sequenced on an Illumina Novaseq platform and 150 bp paired-end reads were generated before clustering of the index-coded samples via cBot Cluster Generation System using TruSeq PE Cluster Kit v3-cBot-HS (Illumia).

value: liver

value: 4 weeks HFD treatment

value: 20 weeks


title: No Pt-drug treatment on wiltype A549

description: Library name: WildtypeA549_control

value: wildtype


title: ICR-191 treatment CHO target-seq on HGPRT gene rep1, 9 days expression

description: Library name: ICR191_treatment_expression9days-target-1

organism: Cricetulus griseus

value: cell line

value: CHO


title: ICR-191 treatment CHO target-seq on HGPRT gene rep2, 9 days expression

description: Library name: ICR191_treatment_expression9days-target-2


title: WT-2

description: Library name: Sample 5


title: WT-1

description: Library name: Sample 4


title: ChIP_seq_LSD1_R_KDT21ctl

value: LSD1 (BETHYL, A300-215A)


title: HFD_W7

description:
Library name: Sample21
HFD.csv contains DEGs between SCARA3 KO and WT


title: SDV3-3

description: Library name: Sample 3


title: Cisplatin treatment on cisplatin-resistant A549 cell line rep2

description: Library name: ResistantA549_cisplatin-2

value: cisplatin


title: ICR-191 treatment CHO target-seq on HGPRT gene rep3, 9 days expression

description: Library name: ICR191_treatment_expression9days-target-3


title: ChIP_seq_LSD1_R


title: HFD_W6

description:
Library name: Sample20
HFD.csv contains DEGs between SCARA3 KO and WT


title: Cisplatin treatment on cisplatin-resistant A549 cell line rep1

description: Library name: ResistantA549_cisplatin-1


title: ChIP_seq_LSD1_R_KDT21_fosl1


title: HFD_W4

description:
Library name: Sample19
HFD.csv contains DEGs between SCARA3 KO and WT


title: ChIP_seq_LSD1_P


title: Cisplatin treatment on wildtype A549 cell line rep2

description: Library name: WildtypeA549_cisplatin-2


title: ICR-191 treatment CHO target-seq on HGPRT gene rep1, 7 days expression

description: Library name: ICR191_treatment_expression7days-target-1


title: ICR-191 treatment CHO target-seq on HGPRT gene rep2, 7 days expression

description: Library name: ICR191_treatment_expression7days-target-2


title: R_KDF12


title: R_KDF1


title: Cisplatin treatment on wildtype A549 cell line rep1

description: Library name: WildtypeA549_cisplatin-1


title: FNN, PNAscr, 30min, rep A

description: Library name: Fnn23_PNAscr_30m_A

value: subspecies nucleatum ATCC 25586

value: PNA scrambled

value: A


title: HFD_S7

description:
Library name: Sample17
HFD.csv contains DEGs between SCARA3 KO and WT

value: SCARA3 knockdown


title: HFD_W2

description:
Library name: Sample18
HFD.csv contains DEGs between SCARA3 KO and WT


title: R_KDL1

value: melanoma


title: HFD_S6

description:
Library name: Sample16
HFD.csv contains DEGs between SCARA3 KO and WT


title: wildtype CHO target-seq on HGPRT gene rep2

description: Library name: CHO-target-2


title: R_KDL12


title: Pt-Bio-I treatment on HeLa rep1

description: Library name: Pt-Bio-I-1

value: HeLa

value: Pt-Bio-I


title: Pt-Bio-I treatment on HeLa rep2

description: Library name: Pt-Bio-I-2


title: wildtype CHO target-seq on HGPRT gene rep1

description: Library name: CHO-target-1


title: No Pt-drug treatment on HeLa

description: Library name: control


title: ICR-191 treatment CHO target-seq on HGPRT gene rep3, 7 days expression

description: Library name: ICR191_treatment_expression7days-target-3


title: HFD_S5

description:
Library name: Sample15
HFD.csv contains DEGs between SCARA3 KO and WT


title: No Pt-drug treatment on ICR-191 treated CHO rep2

description: Library name: ICR191CHO_control-2


title: No Pt-drug treatment on ICR-191 treated CHO rep1

description: Library name: ICR191CHO_control-1


title: HFD_S3

description:
Library name: Sample14
HFD.csv contains DEGs between SCARA3 KO and WT


title: R_CTL1

value: shCtrl


title: R_CTL2


title: HFD_S2

description:
Library name: Sample13
HFD.csv contains DEGs between SCARA3 KO and WT


title: No Pt-drug treatment on wildtype CHO rep2

description: Library name: WildtypeCHO_control-2


title: Lobaplatin treatment on HeLa rep2

description: Library name: Lobaplatin-2

value: lobaplatin


title: wildtype CHO target-seq on HGPRT gene rep3

description: Library name: CHO-target-3


title: No Pt-drug treatment on wildtype CHO rep1

description: Library name: WildtypeCHO_control-1


title: P-L12


title: Oxaliplatin treatment on HeLa rep2

description: Library name: Oxaliplatin-2

value: oxaliplatin


title: Oxaliplatin treatment on HeLa rep1

description: Library name: Oxaliplatin-1


title: Cisplatin treatment on ICR-191 treated CHO rep2

description: Library name: ICR191CHO_cisplatin-2


title: CD_fW5

description:
Library name: Sample11
fCD.csv contains DEGs between SCARA3 KO and WT

value: liver

value: WT

value: Chow diet with 12h fasted treatment


title: P-CTL2


title: Cisplatin treatment on ICR-191 treated CHO rep1

description: Library name: ICR191CHO_cisplatin-1


title: CD_fS6

description:
Library name: Sample9
fCD.csv contains DEGs between SCARA3 KO and WT

value: 20 weeks


title: R_DT2

description: PR_DMSO_DT_processed data.xls

value: 250 nM Dabrafenib; 10 nM Trametinib


title: Cisplatin treatment on HeLa rep2

description: Library name: Cisplatin-2

value: wildtype


title: Cisplatin treatment on HeLa rep1

description: Library name: Cisplatin-1

value: cisplatin


title: CD_fS5

description:
Library name: Sample8
fCD.csv contains DEGs between SCARA3 KO and WT


title: Cisplatin treatment on wildtype CHO rep2

description: Library name: WildtypeCHO_cisplatin-2

value: CHO


title: Lobaplatin treatment on HeLa rep1

description: Library name: Lobaplatin-1


title: Cisplatin treatment on wildtype CHO rep1

description: Library name: WildtypeCHO_cisplatin-1


title: CD_fW4

description:
Library name: Sample10
fCD.csv contains DEGs between SCARA3 KO and WT


title: R_DT1

description: PR_DMSO_DT_processed data.xls


title: MDA-MB-468_Abemaciclib_12h_3

city: Ann Arbor

first: Weiping

last: Zou

state: Michigan

address: 109 Zina Pitcher Place

institute: University of Michigan

data_processing:
Reads were trimmed and clipped for quality control in FastQC.
Assembly: GCF_000001405.39_GRCh38.p13
Supplementary files format and content: FPKM value in txt format

source_name: breast cancer

growth_protocol: cultured in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS)

extract_protocol:
RNA was harvest using Direct-zol RNA Miniprep Kit (Zyme Research, R2050)
RNA libraries are generated with Optimal Dual-mode mRNA Library Prep Kit

value: breast cancer

value: metastatic breast adenocarcinoma

value: Abemaciclib 12h


title: MDA-MB-468_Abemaciclib_12h_2


title: CD_W3

description:
Library name: Sample6
CD.csv contains DEGs between SCARA3 KO and WT

value: Chow diet


title: CD3+ T cells EZH2 WT

city: Munich

first: Dorothee

last: Atzler

state: Bavaria

address: Pettenkoferstr. 9

department: IPEK

institute: LMU Munich

description: Library name: CD3+ T cells EZH2 WT

library_source: transcriptomic single cell

data_processing:
CellRanger (7.2.0)
Assembly: GRCm38,version M23(Ensembl 98)
Supplementary files format and content: matrix files (h5)

organism: Mus musculus

source_name: Spleen

growth_protocol: 50,000 CD3+ T cells were sorted (B200-Gr1-Ter119-CD45+CD3+Live/Dead-) using a FACSAria III (BD Biosciences) from spleens of EZH2Cd4-WT and -KO mice.

extract_protocol:
10,000 CD3+ T cells were targetted for RNA extraction using the Chromium Next GEM Single Cell 3’ Reagent Kit v3.1 according to manufacturer recommedations.
RNA libraries were constructed using the Chromium Next GEM Single Cell 3’ Reagent v3.1 according to manufacturer recommedations. To increase biological variability, 4 WT mice were pooled into one sample and 4 KO mice were pooled into one sample.

value: Spleen

value: CD3+ T cells


title: CD_fW6

description:
Library name: Sample12
fCD.csv contains DEGs between SCARA3 KO and WT


title: CD_fS4

description:
Library name: Sample7
fCD.csv contains DEGs between SCARA3 KO and WT

value: SCARA3 knockdown


title: P_DT2

description: PR_DMSO_DT_processed data.xls

value: melanoma


title: P_DT1

description: PR_DMSO_DT_processed data.xls


title: P-CTL

value: shCtrl


title: MDA-MB-468_con_3

value: no treatment


title: P-L1


title: MDA-MB-468_Abemaciclib_12h_1

value: WT


title: CD3+ T cells EZH2 KO

description: Library name: CD3+ T cells EZH2 KO

value: KO


title: CD_W2

description:
Library name: Sample5
CD.csv contains DEGs between SCARA3 KO and WT

value: liver

value: 20 weeks


title: MDA-MB-468_con_2


title: P_DMSO1

description: PR_DMSO_DT_processed data.xls

value: DMSO


title: CD_W1

description:
Library name: Sample4
CD.csv contains DEGs between SCARA3 KO and WT


title: WT, 2

city: Geneve

first: George

last: Allen

state: Geneve

address: Rue Michel-Servet 1

institute: University of Geneva

data_processing:
For the Ribo-Seq samples, all fastq files were adapter stripped using cutadapt. Only trimmed reads were retained, with a minimum length of 20 and a quality cutoff of 2 reads were retained if the trimmed size was between 28 and 31.
Reads were mapped, using default parameters, with HISAT2 to R64-1-1, using Ensembl release 84 gtf for transcript definitions. For the mapping, only primary alignments were retained and reads were removed if they mapped to rRNA, tRNA and dubious ORFs or non-genic regions. Reads mapping to UTRs were retained.
A full set of 6692 CDS sequences were established for R64-1-1 Ensembl release 84 and extended by UTR sequences. The filtered reads were then mapped to this transcriptome with bowtie2, using default parameters.
The P-site position of each read was predicted by riboWaltz and confirmed by inspection (reads were generally shifted 15 bases from the 3’ end). Counts were made by aggregating P-sites overlapping with the CDS and RPKMs were then generated through normalizing by CDS length and total counts for the sample.
Assembly: R64-1-1
Supplementary files format and content: RPKMs
Library strategy: Ribo-seq

source_name: yeast cells

growth_protocol: Yeast were grown in YPD to mid-log phase in accordance with standard protocols.

extract_protocol:
Cells were harvested and extracts were prepared and processed as described for S. pombe samples in Subtelny et al., 2014 (GSE52809)
Libraries were constructed exactly as described in Subtelny et al., 2014 (GSE52809)

value: yeast cells


title: Prime-seq splenic T cells

description: Library name: Prime-seq library Ezh2cd4-WT and Ezh2cd4-KO - spleen

data_processing:
zUMIs v. 2.5.5 (https://github.com/sdparekh/zUMIs)
R1: Barcode 1-6 bp and UMI 7-16 bp, R2: cDNA 1-50 bp
Reads were filtered using fqfilter
Mapping was completed using STAR alignment tool
Reads were counted using Rsubread
Assembly: mm10/Mus_musculus.GRCm38.89
Supplementary files format and content: Excel File (.xlsx) - differential expression analysis (EdgeR)

growth_protocol: CD4+ T cells were isolated from spleens of EZH2cd4-WT and -KO mice using Dynabeads™ Untouched™ Mouse CD4 Cells Kit (11415D, ThermoFisherScientific) according to manufacturer´s instructions.

extract_protocol:
RNA was harvested using an Rneasy mini kit (Qiagen). Twenty-five ng of RNA was used for cDNA synthesis. Dnase I digestion was performed in well, rather than on column.
RNA libraries were constructed using  Prime-seq protocol (doi: 10.1186/s13059-022-02660-8). Briefly, extracted RNA was treated with DNAse I and then reverse transcribed into full-length cDNA using barcoded oligodT primers and template switching oligos. Following first strand synthesis, the samples were pooled, cleaned with magnetic beads, and the remaining primers were digested using Exonuclease I. Second strand synthesis and pre-amplification was performed, and the amplified cDNA was quantified using PicoGreen and qualified using a HS DNA chip on the Bioanalyzer (Agilent). High quality samples were used for library construction using the NEB Next Ultra II FS kit (NEB) according to prime-seq specifications. The libraries were quantified and qualified using the HS DNA chip on the Bioanalyzer (Agilent).

value: CD4+ T cells

value: Ezh2cd4-WT and Ezh2cd4-KO


title: CD_S3

description:
Library name: Sample3
CD.csv contains DEGs between SCARA3 KO and WT


title: MDA-MB-468_con_1

value: breast cancer

value: metastatic breast adenocarcinoma


title: Block_23-51283D1_002

city: San Francisco

first: Alan

middle: Hunter

last: Shain

state: California

address: 2340 Sutter St. N326

department: Dermatology

institute: University of California, San Francisco

description:
SkinSection2_slide0036996
Skin mount was located at the margin of a wide excision performed to remove melanoma

hyb_protocol: The probes were hybridized to the target mRNA in the skin sections at 50°C for 16-24 hours as per 10X defined standardized protocol.

scan_protocol: The slides were processed using the fully automated Xenium Analyzer. The skin samples were imaged over 15 cycles, where fluorescent probes targeting mRNA sequences and other reagents were added, imaged, and removed during each cycle. The image sensor captured 3D data across four fluorescence channels and multiple fields of view (FOV) throughout these cycles. The resulting images were stitched together to create a comprehensive spatial dataset for Xenium analysis.

data_processing:
The Xenium Analyzer then processed and decoded the transcript data using its onboard probabilistic model through the XOA pipeline (v3.0.2.0). This decoding utilized predefined fluorescent signal patterns, or codewords, to identify transcripts, with negative codewords included to ensure specificity. Once decoded, the transcripts were deduplicated, and the final data underwent secondary analysis to produce the XOA output. The analysis summary provided information on decoding accuracy, cell segmentation, gene expression and image quality control (QC). All the outputs were visualized using Xenium Explorer (3.1.0).
Read count per gene per cell with the spatial context.

label: Fluorescent

source_name: Normal human tissue mount

label_protocol: The gene expression were identified using Xenium skin panel and 100 custom panel. The targeted gene panel was based on the predesigned human skin panel (v1), which comprised of 260 genes. An additional 100 genes were incorporated to create a custom panel. These additional genes cover various melanocyte subtypes, including those enriched in high-mutation melanocytes (n = 20), low-mutation melanocytes (n = 15), adult melanocytes (n = 12), neonatal melanocytes (n = 9), fetal melanocytes (n = 3), melanocyte stem cells (n = 12), differentiated melanocytes (n = 6), transitional melanocytes (n = 3), neural crest cells (n = 17), hair follicle bulge cells (n = 2)  and Schwann cells (n = 1)

growth_protocol: We obtained a formalin-fixed paraffin-embedded (FFPE) skin sample from a 63-year-old male donor. The skin mount consisted of normal, non-cancerous tissue located at the margin of a wide excision performed to remove melanoma, ensuring the presence of normal melanocytes with a high mutation burden. A 5 µm section of the skin was mounted on a Xenium slide, with two skin sections positioned within the sample area (10.45 mm x 22.45 mm) such that the epidermis of each section faced the other along the length of the slide. Two adjacent sections were mounted on two separate Xenium slides for dual Xenium analysis.

extract_protocol: To confirm acceptable quality of RNA for Xenium analysis, the mRNA was first extracted using Qiagen RNAeasy Kit from adjacent skin sections and  subjected to high-sensitivity eukaryotic Pico RNA analysis (Agilent, 5067-1513) using an Agilent Bioanalyzer 2100.

treatment_protocol: To accurately identify the borders of each cell, immunofluorescence staining was performed using various cell structure markers, including boundary stains (TP1A1, CD45, E-Cadherin) and an interior RNA stain (18S). The staining was carried out by incubating the slides at 4°C for 16-24 hours using the Xenium Cell Segmentation Staining Reagents (10X Genomics, PN-1000661).

tag: gender

value: Male

tag: age

value: 63 years

value: Non-cancerous skin


title: CD_S2

description:
Library name: Sample2
CD.csv contains DEGs between SCARA3 KO and WT

value: SCARA3 knockdown

value: Chow diet


title: CAF130D, 2, GATCAG

value: Caf130 deletion


title: total tumor cells, Lobeline, scRNAseq

city: Nanjing

first: yang

last: sun

state: Jiangsu

address: Nanjing University Academy of Sciences, No. 163 Xianlin Avenue, Qixia District, Nanjing City, Jiangsu Province

department: Life Sciences

institute: Nanjing University

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v2.1.1 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: colon

extract_protocol:
After the tumor was removed, it was digested into single cell suspension with tumor tissue dissociation kit on ice, and 10x-RNA reagents were added
Library was performed according to the manufacter’s instructions (single cell 3’ v2 protocol, 10x Genomics). Briefly, cell suspension were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: colon

value: Tumor cells, Stromal cells, Immune cells

value: 10 weeks old

value: Lobeline


title: CD_S1

description:
Library name: Sample1
CD.csv contains DEGs between SCARA3 KO and WT

value: liver

value: 20 weeks


title: Block_23-51283D1_001

description:
SkinSection1_slide0036448
Skin mount was located at the margin of a wide excision performed to remove melanoma


title: total tumor cells, PBS, scRNAseq

description: 10x Genomics

value: PBS


title: CAF130D, 1, ACTTGA

value: yeast cells


title: PB_Treg_JIA_32

status: Public on Feb 12 2025

city: London

first: Anne

middle: M

last: Pesenacker

state: England

address: Pears Building, UCL Institute of Immunity and Transplantation, Rowland Hill Street

department: Div Infection and Immunity

country: United Kingdom

institute: UCL

description:
Cell lysate (total RNA)
failed QC, excluded

hyb_protocol: 65C thermal cycler, 18hrs

scan_protocol: nanoString nCounter

data_processing:
The raw data were normalised and QC performed in accordance to R script Pesenacker_Tregsig_nanostring_normalisation.R availble on PesenackerLab github
failed QC, excluded

source_name: PB

extract_protocol: RLT buffer +1% 2-ME

value: PB

value: Treg

tag: condition

value: JIA

tag: activity

value: Inactive

tag: age (years)

tag: Sex

value: F


title: PB_Treg_JIA_22

tag: tissue

value: Active

value: M


title: PB_Treg_JIA_16

value: unknown


title: P_DMSO2

description: PR_DMSO_DT_processed data.xls

value: melanoma

value: WT

value: DMSO


title: SF_MC_JIA_10

source_name: SF

value: SF

value: SFMC


title: PB_Treg_HC_11

value: ad HC


title: PB_Treg_HC_21


title: PB_Treg_JIA_17


title: PB_Treg_HC_5

value: ped HC


title: PB_Treg_HC_9


title: WT, 1


title: PB_MC_JIA_58

description: Cell lysate (total RNA)

data_processing: The raw data were normalised and QC performed in accordance to R script Pesenacker_Tregsig_nanostring_normalisation.R availble on PesenackerLab github

value: PBMC


title: SF_Treg_JIA_26

description: Cell lysate (total RNA)


title: PB_Treg_HC_30

description: Cell lysate (total RNA)


title: PB_MC_HC_24

description: Cell lysate (total RNA)


title: PB_MC_HC_25

description: Cell lysate (total RNA)


title: PB_Treg_JIA_58

description: Cell lysate (total RNA)


title: PB_MC_JIA_59

description: Cell lysate (total RNA)


title: PB_Treg_JIA_57

description: Cell lysate (total RNA)


title: PB_Treg_JIA_54

description: Cell lysate (total RNA)


title: PB_MC_JIA_56

description: Cell lysate (total RNA)


title: PB_MC_JIA_55

description: Cell lysate (total RNA)


title: PB_Treg_JIA_55

description: Cell lysate (total RNA)


title: PB_MC_JIA_57

description: Cell lysate (total RNA)


title: SF_Treg_JIA_25

description: Cell lysate (total RNA)


title: PB_MC_HC_23

description: Cell lysate (total RNA)


title: PB_Treg_HC_29

description: Cell lysate (total RNA)


title: PB_Treg_HC_31

description: Cell lysate (total RNA)


title: PB_Treg_JIA_56

description: Cell lysate (total RNA)


title: SF_MC_JIA_29

description: Cell lysate (total RNA)


title: PB_Treg_JIA_53

description: Cell lysate (total RNA)


title: PB_MC_JIA_52

description: Cell lysate (total RNA)


title: PB_Treg_JIA_50

description: Cell lysate (total RNA)


title: PB_Treg_JIA_51

description: Cell lysate (total RNA)


title: PB_MC_JIA_53

description: Cell lysate (total RNA)


title: PB_MC_JIA_51

description: Cell lysate (total RNA)


title: SF_MC_JIA_30

description: Cell lysate (total RNA)


title: PB_Treg_JIA_52

description: Cell lysate (total RNA)


title: PB_MC_JIA_54

description: Cell lysate (total RNA)


title: PB_Treg_JIA_49

description: Cell lysate (total RNA)


title: PB_MC_JIA_50

description: Cell lysate (total RNA)


title: PB_Treg_JIA_48

description: Cell lysate (total RNA)


title: FNN, PNA79, 30min, rep B

description: Library name: Fnn23_PNA79_30m_B

data_processing:
RNA-seq raw reads were trimmed, filtered and mapped using the F. nucleatum ssp. nucleatum ATCC 23726 (NZ_CP028109.1) annotation file with costume annotation or the F. nucleatum ssp. vincentii 3_1_36A2 (NZ_ CP003700.1) file.
To remove adapter sequences and trim nucleobases BBduk was used before mapping the reads with BBMap (v38.84).
Differential gene expression was investigated using the featureCounts methods of the Subread (2.0.1) package. For further downstream analysis R/Bioconductor packages were used.
Assembly: NZ_CP028109.1, NZ_ CP003700.1
Supplementary files format and content: raw_counts_FNN.csv is csv table with genes as rownames and samples as colnames for FNN samples
Supplementary files format and content: raw_counts_FNV.csv is csv table with genes as rownames and samples as colnames for FNV samples

extract_protocol:
To isolate fusobacterial RNA, samples were incubated 1:1 (v:v) with RNAprotect Bacteria (Qiagen) for five minutes at RT, snap frozen in liquid nitrogen and stored at -80°C until further processing. To purify RNA the miRNeasy Micro kit (Qiagen) was used. Briefly, cell dilutions were thawed on ice, centrifuged at 4°C with 13,000 g for 20 minutes, the pellets resuspended in 100 μl 0.5 mg ml-1 lysozyme (Roth) in TE buffer pH 8.0 and incubated for two minutes at RT. The samples were then incubated with 700 μl Qiazol (Qiagen) for five minutes at RT and after addition of 160 μl chloroform shaken vigorously for 15 seconds to obtain phase separation. The upper aqueous phase was mixed 1:1.5 with 100% ethanol and loaded onto the Qiagen columns. Columns washes, DNase I digest and elution were performed according to the manual instructions. RNA concentrations were determined via NanoDrop measurements and samples were stored at -80°C until sequencing.
RNA quality was investigated using the 2100 Bioanalyzer together with the RNA 6000 Pico kit (Agilent Technologies). Risbosomal RNA (rRNA) depletion was performing using the RiboCop META rRNA depletion kit (Lexogen) according to the manufacturer’s instructions. Depleted RNA was further fragmented via ultrasound for 30 s at 4°C. After adapter ligation to the 3’ end, the first-strand cDNA was synthetized using the M-MLV reverse transcriptase. Following purification, 5’ Illumina TruSeq adapters were ligated to the cDNA, the cDNA amplified by PCR and the resulting product purified with the Agencourt AMPure XP kit (Beckman Coulter Genomics). After performing library quality control using the 2100 Bioanalyzer with the DNA High Sensitivity kit (Agilent Technologies), the cDNA was pooled, purified and sequenced using an Illlumina NextSeq 500 system with 10 million reads/sample in single end mode with 75 nt read length.

value: 30 minutes

value: subspecies nucleatum ATCC 25586

value: B


title: PB_MC_JIA_49

description: Cell lysate (total RNA)

value: PB

value: JIA


title: PB_Treg_HC_28

description: Cell lysate (total RNA)

value: Treg

value: F


title: PB_MC_HC_22

description: Cell lysate (total RNA)


title: PB_MC_JIA_48

description: Cell lysate (total RNA)

value: Active


title: SF_MC_JIA_28

description: Cell lysate (total RNA)


title: PB_Treg_JIA_46

description: Cell lysate (total RNA)


title: PB_Treg_JIA_44

description: Cell lysate (total RNA)


title: SF_Treg_JIA_23

description: Cell lysate (total RNA)


title: SF_MC_JIA_27

description: Cell lysate (total RNA)


title: PB_MC_HC_21

description: Cell lysate (total RNA)

value: unknown


title: PB_Treg_JIA_43

description: Cell lysate (total RNA)

value: Inactive


title: PB_MC_JIA_44

description: Cell lysate (total RNA)


title: PB_MC_JIA_42

description: Cell lysate (total RNA)


title: PB_Treg_JIA_42

description: Cell lysate (total RNA)

value: M


title: PB_MC_JIA_46

description: Cell lysate (total RNA)


title: PB_MC_JIA_43

description: Cell lysate (total RNA)


title: PB_MC_JIA_45

description: Cell lysate (total RNA)


title: PB_Treg_JIA_41

description: Cell lysate (total RNA)


title: PB_Treg_HC_27

description: Cell lysate (total RNA)


title: PB_Treg_JIA_45

description: Cell lysate (total RNA)


title: PB_Treg_JIA_40

description: Cell lysate (total RNA)


title: PB_Treg_HC_26

description: Cell lysate (total RNA)


title: PB_MC_HC_20

description: Cell lysate (total RNA)


title: SF_Treg_JIA_24

description: Cell lysate (total RNA)


title: PB_Treg_JIA_47

description: Cell lysate (total RNA)


title: SF_MC_JIA_26

description: Cell lysate (total RNA)


title: PB_Treg_JIA_39

description: Cell lysate (total RNA)


title: SF_Treg_JIA_22

description: Cell lysate (total RNA)


title: PB_MC_JIA_47

description: Cell lysate (total RNA)


title: PB_MC_JIA_40

description: Cell lysate (total RNA)


title: PB_Treg_JIA_38

description: Cell lysate (total RNA)


title: PB_MC_JIA_41

description: Cell lysate (total RNA)


title: PB_MC_JIA_39

description: Cell lysate (total RNA)


title: PB_MC_JIA_38

description: Cell lysate (total RNA)


title: SF_Treg_JIA_21

description: Cell lysate (total RNA)


title: PB_Treg_JIA_36

description: Cell lysate (total RNA)


title: PB_MC_JIA_36

description: Cell lysate (total RNA)


title: PB_Treg_JIA_35

description: Cell lysate (total RNA)


title: SF_Treg_JIA_20

description: Cell lysate (total RNA)


title: PB_Treg_JIA_31

description: Cell lysate (total RNA)


title: PB_MC_JIA_34

description: Cell lysate (total RNA)


title: PB_Treg_HC_25

description: Cell lysate (total RNA)


title: SF_MC_JIA_24

description: Cell lysate (total RNA)


title: SF_MC_JIA_25

description: Cell lysate (total RNA)


title: PB_Treg_JIA_34

description: Cell lysate (total RNA)


title: PB_MC_HC_19

description: Cell lysate (total RNA)


title: PB_MC_JIA_35

description: Cell lysate (total RNA)


title: PB_Treg_JIA_33

description: Cell lysate (total RNA)


title: PB_MC_JIA_32

description: Cell lysate (total RNA)


title: PB_MC_JIA_33

description: Cell lysate (total RNA)


title: PB_MC_HC_18

description: Cell lysate (total RNA)


title: PB_Treg_HC_24

description: Cell lysate (total RNA)


title: SF_Treg_JIA_19

description: Cell lysate (total RNA)


title: PB_Treg_JIA_30

description: Cell lysate (total RNA)


title: PB_MC_JIA_31

description: Cell lysate (total RNA)


title: PB_Treg_JIA_29

description: Cell lysate (total RNA)


title: PB_MC_JIA_37

description: Cell lysate (total RNA)


title: PB_Treg_JIA_37

description: Cell lysate (total RNA)


title: PB_Treg_JIA_28

description: Cell lysate (total RNA)


title: PB_Treg_HC_23

description: Cell lysate (total RNA)


title: PB_MC_HC_17

description: Cell lysate (total RNA)


title: SF_Treg_JIA_18

description: Cell lysate (total RNA)


title: SF_MC_JIA_22

description: Cell lysate (total RNA)


title: PB_MC_JIA_28

description: Cell lysate (total RNA)


title: PB_Treg_JIA_27

description: Cell lysate (total RNA)


title: PB_Treg_JIA_26

description: Cell lysate (total RNA)


title: SF_MC_JIA_23

description: Cell lysate (total RNA)


title: PB_Treg_JIA_25

description: Cell lysate (total RNA)


title: PB_MC_JIA_27

description: Cell lysate (total RNA)


title: PB_MC_JIA_26

description: Cell lysate (total RNA)


title: PB_MC_HC_16

description: Cell lysate (total RNA)


title: SF_MC_JIA_21

description: Cell lysate (total RNA)


title: SF_Treg_JIA_17

description: Cell lysate (total RNA)


title: PB_Treg_JIA_24

description: Cell lysate (total RNA)


title: PB_MC_JIA_30

description: Cell lysate (total RNA)


title: SF_Treg_JIA_16

description: Cell lysate (total RNA)


title: PB_MC_HC_15

description: Cell lysate (total RNA)


title: PB_MC_JIA_24

description: Cell lysate (total RNA)


title: PB_Treg_JIA_23

description: Cell lysate (total RNA)


title: PB_MC_JIA_23

description: Cell lysate (total RNA)


title: PB_MC_JIA_25

description: Cell lysate (total RNA)


title: SF_MC_JIA_20

description: Cell lysate (total RNA)


title: PB_Treg_JIA_21

description: Cell lysate (total RNA)


title: PB_Treg_JIA_20

description: Cell lysate (total RNA)


title: PB_MC_JIA_22

description: Cell lysate (total RNA)


title: PB_MC_JIA_21

description: Cell lysate (total RNA)


title: PB_MC_JIA_29

description: Cell lysate (total RNA)


title: PB_Treg_HC_19

description: Cell lysate (total RNA)


title: SF_MC_JIA_19

description: Cell lysate (total RNA)


title: SF_Treg_JIA_15

description: Cell lysate (total RNA)


title: PB_Treg_HC_22

description: Cell lysate (total RNA)


title: PB_MC_JIA_20

description: Cell lysate (total RNA)


title: PB_Treg_JIA_19

description: Cell lysate (total RNA)


title: PB_MC_HC_14

description: Cell lysate (total RNA)


title: PB_Treg_JIA_18

description: Cell lysate (total RNA)


title: PB_MC_JIA_18

description: Cell lysate (total RNA)


title: PB_MC_JIA_17

description: Cell lysate (total RNA)


title: SF_Treg_JIA_14

description: Cell lysate (total RNA)


title: PB_MC_JIA_19

description: Cell lysate (total RNA)


title: PB_Treg_HC_18

description: Cell lysate (total RNA)


title: SF_MC_JIA_18

description: Cell lysate (total RNA)


title: PB_MC_JIA_16

description: Cell lysate (total RNA)


title: PB_Treg_JIA_15

description: Cell lysate (total RNA)


title: SF_Treg_JIA_13

description: Cell lysate (total RNA)


title: PB_MC_JIA_15

description: Cell lysate (total RNA)


title: PB_Treg_HC_17

description: Cell lysate (total RNA)


title: SF_MC_JIA_16

description: Cell lysate (total RNA)


title: SF_Treg_JIA_12

description: Cell lysate (total RNA)


title: SF_MC_JIA_17

description: Cell lysate (total RNA)


title: PB_Treg_HC_16

description: Cell lysate (total RNA)


title: PB_Treg_HC_20

description: Cell lysate (total RNA)


title: SF_Treg_JIA_11

description: Cell lysate (total RNA)


title: PB_MC_HC_13

description: Cell lysate (total RNA)


title: SF_MC_JIA_15

description: Cell lysate (total RNA)


title: PB_Treg_JIA_13

description: Cell lysate (total RNA)


title: PB_MC_JIA_14

description: Cell lysate (total RNA)


title: PB_MC_JIA_13

description: Cell lysate (total RNA)


title: Hut78 cells, PLCG1_WT_Stimulation

city: New Haven

first: Longhui

last: Zeng

state: CT

address: Yale University, 333 Cedar Street, SHM-C-434 Su lab

department: Cell biology

institute: Yale University

data_processing:
The raw data obtained from sequencing were filtered using SOAPnuke to remove: 1. Reads containing adapters (adapter contamination); 2. Reads with an unknown base 'N' content greater than 0.1%; 3. Low-quality reads (reads with a percentage of bases with a quality value less than 15 exceeding 20% of the total bases in the read).
The filtered data, referred to as clean data, were subsequently analyzed, visualized, and mined using Online Multi-Omics Data Mining System.
HISAT (Hierarchical Indexing for Spliced Alignment of Transcripts) is a software used for aligning RNA-seq reads to a reference genome.
Assembly: hg38
Supplementary files format and content: read acount for all samples
Supplementary files format and content: fpkm value for all samples

source_name: Hut78 cells

growth_protocol: Hut78 cells were maintained in RPMI 1640 medium with 10%FBS, 1%antibiotics in cell culture incubator at 37℃

extract_protocol:
Total RNA was extracted from Hut78 cells by Qiagen RNeasy Plus Mini kit.
mRNA enrichment was performed on total RNA using oligo(dT)-attached magnetic beads. The enriched mRNA with poly(A) tails was fragmented using a fragmentation buffer, followed by reverse transcription using random N6 primers to synthesize cDNA double strands. The synthesized doublestranded DNA was then end-repaired and 5'-phosphorylated, with a protruding 'A' at the 3' end forming a blunt end, followed by ligation of a bubble-shaped adapter with a protruding 'T' at the 3'end. The ligation products were PCR amplified using specific primers. The PCR products were denatured to single strands, and then single-stranded circular DNA libraries were generated using a bridged primer. The constructed libraries were quality-checked and sequenced after passing the quality control.

treatment_protocol: Hut78 PLCG1 wild type cells were incubated with 5 μg/ml Anti-CD3 antibody coated in plate and 2 μg/ml Anti-CD28 antibody in culture medium for 3 days.

value: Hut78 cells

value: Cutaneous T-lymphocyte cell

value: PLCG1 WT overexpression

value: Anti-CD3/CD28 antibodies for 3 days


title: PB_Treg_JIA_12

description: Cell lysate (total RNA)


title: SF_Treg_JIA_10

description: Cell lysate (total RNA)

value: SF


title: PB_Treg_HC_15

description: Cell lysate (total RNA)

value: ad HC


title: Hut78 cells, PLCG1_D1165H

value: PLCG1 D1165H overexpression

value: No treatment


title: PB_Treg_JIA_14

description: Cell lysate (total RNA)


title: Hut78 cells, PLCG1_S345F

value: PLCG1 S345F overexpression


title: SF_Treg_JIA_9

description: Cell lysate (total RNA)


title: SF_MC_JIA_14

description: Cell lysate (total RNA)

value: SFMC


title: SF_MC_JIA_13

description: Cell lysate (total RNA)

value: JIA


title: Hut78 cells, PLCG1_R48W

value: PLCG1 R48W overexpression


title: Hut78 cells, PLCG1_WT


title: Lung_Fed [RNA-Seq]

city: Bethesda

first: Haiming

last: Cao

state: MD

address: 9000 Rockville Pike

department: NHLBI

institute: NIH

data_processing:
The original FASTQ read files were trimmed and cleaned using fastp/0.23.2, then quality analysis was performed using FastQC/0.11.8.
The trimmed reads were aligned with default settings of HISAT2/2.2.1.0 and quantified using featureCounts (subread/2.0) with mouse GENCODE vm24.
Assembly: GRCm38
Supplementary files format and content: tab-delimited text files include raw counts for each sample

source_name: Lung

extract_protocol:
Tissue samples from the same experimental group were pooled equally and approximately 15-40 mg of pooled frozen tissue powder was homogenized 20-25 times in a Dounce homogenizer with 1.2 ml of Trizol reagent (Invitrogen, Catalog No. 15596018) on ice. The RNAs that have been extracted by Trizol were purified using the MagMAX RNA extraction kit (Thermo Fisher Scientific, Cat.AM1830).
RNA libraries were prepared for sequencing using standard Illumina kit and protocols; strand-specific

value: Lung

value: Male

value: Fed


title: Lung_Fasting [RNA-Seq]

value: Fasting


title: PB_Treg_JIA_10

description: Cell lysate (total RNA)

value: PB

value: Treg

value: Active

value: F


title: PB_MC_JIA_12

description: Cell lysate (total RNA)

value: PBMC

value: Inactive


title: Kidney_Fed [RNA-Seq]

source_name: Kidney

value: Kidney


title: PB_MC_JIA_11

description: Cell lysate (total RNA)


title: Kidney_Fasting [RNA-Seq]


title: SF_Treg_JIA_8

description: Cell lysate (total RNA)

value: SF

value: unknown


title: PB_Treg_HC_14

description: Cell lysate (total RNA)

value: ad HC


title: SF_MC_JIA_12

description: Cell lysate (total RNA)

value: SFMC


title: Spleen_Fasting [RNA-Seq]

value: Spleen


title: SF_Treg_JIA_7

description: Cell lysate (total RNA)

value: JIA


title: PB_Treg_HC_13

description: Cell lysate (total RNA)


title: Brown_Adipose_Fasting [RNA-Seq]


title: Spleen_Fed [RNA-Seq]


title: PB_Treg_JIA_11

description: Cell lysate (total RNA)


title: Heart_Fed [RNA-Seq]

source_name: Heart

value: Heart


title: SF_MC_JIA_11

description: Cell lysate (total RNA)


title: Heart_Fasting [RNA-Seq]

value: Male


title: PB_Treg_JIA_9

description: Cell lysate (total RNA)


title: Brown_Adipose_Fed [RNA-Seq]

value: Fed


title: PB_MC_HC_12

description: Cell lysate (total RNA)


title: PB_MC_JIA_10

description: Cell lysate (total RNA)


title: PB_Treg_JIA_8

description: Cell lysate (total RNA)


title: PB_Treg_HC_12

description: Cell lysate (total RNA)


title: White_Adipose_Fed [RNA-Seq]


title: White_Adipose_Fasting [RNA-Seq]

value: Fasting


title: Liver_Fasting [RNA-Seq]

source_name: Liver

value: Liver


title: Liver_Fed [RNA-Seq]


title: PB_MC_JIA_9

description: Cell lysate (total RNA)

value: PB


title: PB_MC_HC_11

description: Cell lysate (total RNA)


title: SF_Treg_JIA_6

description: Cell lysate (total RNA)

value: Treg

value: Active


title: PB_MC_JIA_8

description: Cell lysate (total RNA)

value: PBMC

value: F


title: Kidney_Fed

data_processing:
The raw FASTQ reads were processed using the pipeline from Kundaje Laboratory [https://github.com/kundajelab/atac_dnase_pipelines], which included adapter trimming, alignment with genome using Bowtie2, and peak calling using MACS2.
Assembly: GRCm38
Supplementary files format and content: narrowPeak

extract_protocol:
Transposase-accessible chromatin DNA were purified using the MinElute Reaction Cleanup Kit (Qiagen) according to the manufacturer's instructions. The purified DNAs were stored at -80 °C or processed to ATAC-Seq library preparation.
Libraries were constructed according to the Illumina TruSeq  protocol.

value: Kidney


title: Kidney_Fasting


title: PB_Treg_JIA_7

description: Cell lysate (total RNA)

value: Inactive


title: Lung_Fasting

value: Lung


title: PB_Treg_JIA_6

description: Cell lysate (total RNA)

value: unknown


title: PB_MC_JIA_7

description: Cell lysate (total RNA)


title: Lung_Fed


title: PB_MC_JIA_6

description: Cell lysate (total RNA)

value: M


title: Heart_Fasting


title: SF_Treg_JIA_5

description: Cell lysate (total RNA)

value: SF


title: White_Adipose_Fasting


title: SF_MC_JIA_9

description: Cell lysate (total RNA)

value: SFMC

value: JIA


title: Spleen_Fasting

value: Spleen

value: Male


title: Heart_Fed

value: Heart

value: Fed


title: Brown_Adipose_Fed


title: Muscle_Fasting [RNA-Seq]

source_name: Muscle

value: Muscle

value: Fasting


title: Muscle_Fasting


title: Muscle_Fed [RNA-Seq]


title: Liver_Fasting

value: Liver


title: SF_Treg_JIA_4

description: Cell lysate (total RNA)

value: Treg

value: Active


title: PB_MC_HC_9

description: Cell lysate (total RNA)

value: PB

value: PBMC

value: ped HC

value: F


title: White_Adipose_Fed


title: PB_Treg_JIA_5

description: Cell lysate (total RNA)

value: unknown

value: M


title: Spleen_Fed


title: PB_MC_HC_7

description: Cell lysate (total RNA)


title: Muscle_Fed


title: SF_MC_JIA_7

description: Cell lysate (total RNA)

value: SF

value: SFMC


title: PB_Treg_JIA_4

description: Cell lysate (total RNA)

value: JIA


title: Liver_Fed

value: Male


title: ctrl_19

city: Seoul

first: Murim

last: Choi

address: 103 Daehakro, Jongrogu

country: South Korea

institute: Seoul National University

description:
Library name: ctrl_19
10X Genomics

data_processing:
Reads were aligned, filtered, and counted by Cellranger software. Reference genome was obtained from Cellranger website (refdata-gex-GRCh38-2020-A)
Assembly: GRCh38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Frozen liver tissue sample from donor ctrl_19 processed for snRNA-seq

extract_protocol:
Frozen liver tissues were processed to generate 10x Genomics-based snRNA-seq data in GENINUS (Seoul, Republic of Korea). Tissues were homogenized, and isolated nuclei was counted using flow cytometry (BD: FACSMelodyTM Cell sorter)
10x Genomics chromium instrument and cDNA synthesis kit v3 were used to generate barcoded cDNA libraries. cDNA library quality was determined using an Agilent Bioanalyzer.

tag: disease group

value: ctrl

value: male


title: PB_MC_JIA_5

description: Cell lysate (total RNA)

tag: cell type


title: PB_MC_HC_8

description: Cell lysate (total RNA)

value: ad HC


title: SF_MC_JIA_8

description: Cell lysate (total RNA)


title: ctrl_18

description:
Library name: ctrl_18
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_18 processed for snRNA-seq


title: ctrl_16

description:
Library name: ctrl_16
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_16 processed for snRNA-seq


title: SF_MC_JIA_6

description: Cell lysate (total RNA)


title: PB_Treg_HC_7

description: Cell lysate (total RNA)


title: SF_Treg_JIA_3

description: Cell lysate (total RNA)


title: ctrl_20

description:
Library name: ctrl_20
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_20 processed for snRNA-seq


title: ctrl_14

description:
Library name: ctrl_14
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_14 processed for snRNA-seq


title: Brown_Adipose_Fasting

value: Fasting


title: ctrl_13

description:
Library name: ctrl_13
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_13 processed for snRNA-seq

value: Liver


title: PB_MC_HC_10

description: Cell lysate (total RNA)


title: PB_MC_JIA_4

description: Cell lysate (total RNA)


title: PB_Treg_HC_10

description: Cell lysate (total RNA)

value: Treg


title: ctrl_15

description:
Library name: ctrl_15
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_15 processed for snRNA-seq


title: PB_Treg_HC_8

description: Cell lysate (total RNA)


title: ctrl_21

description:
Library name: ctrl_21
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_21 processed for snRNA-seq


title: SF_MC_JIA_5

description: Cell lysate (total RNA)

value: Active


title: ctrl_11

description:
Library name: ctrl_11
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_11 processed for snRNA-seq

value: female


title: ctrl_17

description:
Library name: ctrl_17
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_17 processed for snRNA-seq


title: ctrl_10

description:
Library name: ctrl_10
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_10 processed for snRNA-seq


title: ctrl_12

description:
Library name: ctrl_12
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_12 processed for snRNA-seq


title: PB_Treg_HC_6

description: Cell lysate (total RNA)

source_name: PB

value: PB


title: ctrl_09

description:
Library name: ctrl_09
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_09 processed for snRNA-seq


title: SF_Treg_JIA_2

description: Cell lysate (total RNA)

source_name: SF


title: PB_MC_HC_5

description: Cell lysate (total RNA)

value: PBMC

value: ped HC


title: SF_MC_JIA_4

description: Cell lysate (total RNA)

value: unknown


title: ctrl_08

description:
Library name: ctrl_08
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_08 processed for snRNA-seq


title: PB_MC_JIA_3

description: Cell lysate (total RNA)

value: F


title: PB_Treg_JIA_3

description: Cell lysate (total RNA)


title: ctrl_07

description:
Library name: ctrl_07
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_07 processed for snRNA-seq


title: ctrl_06

description:
Library name: ctrl_06
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_06 processed for snRNA-seq


title: ctrl_05

description:
Library name: ctrl_05
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_05 processed for snRNA-seq


title: PB_MC_HC_6

description: Cell lysate (total RNA)


title: PB_Treg_HC_4

description: Cell lysate (total RNA)

value: M


title: PB_MC_HC_4

description: Cell lysate (total RNA)


title: ctrl_04

description:
Library name: ctrl_04
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_04 processed for snRNA-seq


title: PB_MC_HC_3

description: Cell lysate (total RNA)


title: FL36

description:
Library name: FL36
10X Genomics

source_name: Frozen liver tissue sample from donor FL36 processed for snRNA-seq

value: aMASH


title: FL774

description:
Library name: FL774
10X Genomics

source_name: Frozen liver tissue sample from donor FL774 processed for snRNA-seq


title: SF_MC_JIA_3

description: Cell lysate (total RNA)

value: SF

value: SFMC

value: JIA


title: PB_MC_JIA_2

description: Cell lysate (total RNA)


title: PB_Treg_HC_3

description: Cell lysate (total RNA)


title: PB_Treg_JIA_2

description: Cell lysate (total RNA)


title: SF_MC_JIA_2

description: Cell lysate (total RNA)


title: FL265

description:
Library name: FL265
10X Genomics

source_name: Frozen liver tissue sample from donor FL265 processed for snRNA-seq


title: FL111

description:
Library name: FL111
10X Genomics

source_name: Frozen liver tissue sample from donor FL111 processed for snRNA-seq


title: FL836

description:
Library name: FL836
10X Genomics

source_name: Frozen liver tissue sample from donor FL836 processed for snRNA-seq

value: male


title: PB_Treg_HC_2

description: Cell lysate (total RNA)

value: ad HC


title: FL804

description:
Library name: FL804
10X Genomics

source_name: Frozen liver tissue sample from donor FL804 processed for snRNA-seq


title: PB_MC_HC_2

description: Cell lysate (total RNA)


title: SF_MC_JIA_1

description: Cell lysate (total RNA)


title: FL799

description:
Library name: FL799
10X Genomics

source_name: Frozen liver tissue sample from donor FL799 processed for snRNA-seq


title: PB_Treg_HC_1

description: Cell lysate (total RNA)


title: ctrl_02

description:
Library name: ctrl_02
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_02 processed for snRNA-seq

value: ctrl


title: FL747

description:
Library name: FL747
10X Genomics

source_name: Frozen liver tissue sample from donor FL747 processed for snRNA-seq

value: Liver


title: FL758

description:
Library name: FL758
10X Genomics

source_name: Frozen liver tissue sample from donor FL758 processed for snRNA-seq


title: PB_Treg_JIA_1

description: Cell lysate (total RNA)

source_name: PB

value: Treg


title: ctrl_01

description:
Library name: ctrl_01
10X Genomics

source_name: Frozen liver tissue sample from donor ctrl_01 processed for snRNA-seq


title: PB_MC_HC_1

description: Cell lysate (total RNA)


title: PB_MC_JIA_1

description: Cell lysate (total RNA)


title: TST cells, Day 8, rep2

city: Boston

first: Chunyao

last: Wei

state: MA

address: 185 Cambridge St.

department: Molecular Biology

institute: Massachusetts General Hospital

description:
ES_Diff_Genecounts.txt
ES_Day8_TEcounts.txt

data_processing:
Adapters were removed from raw data using Trim Galore with the following parameters: (--stringency 5 -e 0.2 --length 35 --r1 36 --r2 36). The VCF files reporting SNP sites of two parental strains CAST/EiJ (Cast) and  129S1/SvlmJ (Mus) based on mm10 were downloaded from Sanger Institute and used to reconstruct the pseudo-Cast and pseudo-Mus genomes, respectively, from the mm10 genome assembly.
After PCR duplicates removal, pre-processed reads were aligned to two parental mouse genomes separately using STAR (v2.7.10a) in the 2-pass mode, with the allowance of 1 mismatch in every 20 bases and a maximum of 8 mismatches per read pair. Non-canonical introns were not considered, and read alignment spanning introns more than 60kb were filtered out. Reads with overlapping mates were only considered with at least 5 nucleotide overlap. All discordant read pairs where two mates were aligned to different chromosomes were discarded.
All uniquely aligned read pairs overlapping with gene exons were counted using featureCounts (v1.5.0-p1). For allelic gene analyses, each uniquely aligned read that covered strain specific SNPs or indels was analyzed and the alignment quality scores of each given read between two parental genomes (pseudo-Cast and pseudo-Mus) were compared to determine its allelic origin. Pairs that differed significantly in alignment score due to mismatches/gaps were classified as allele-specific and the better alignment retained. Pairs with identical alignment scores or scores that differed only slightly due to fragment length penalties were classified as neutral.
For allelic TE analysis, a de novo assembled CAST/EiJ genome (GenBank assembly: GCA_921999005.2) and 129S1/SvImJ genome (GenBank assembly: GCA_921998555.2) was used as parental genomes for read alignment. Only reads with less than 200 hits in the genome were considered. The TE in the genomes (LINE, SINEs, LTR and DNA repeats) were determined by RepeatMasker with default paramenters. For total TE expression analysis, reads with alignment overlapping with annotated TE were retained and used to quantification. For allelic reads in TE, only the reads that were uniquely aligned in both two genomes and that overlapped with TE were considered for downstream analyses. Reads that were uniquely aligned in one genome but had multiple or no hits in the other gnome were discarded.  The alignment qualities of each single read between to parental genomes were compared to determine its allelic origin. The significance of mono allelic or biallelic expression of a given repeat element was determined using the Binomial distribution with Bernoulli p=0.5.
For reanalyzed embryo RNAseq data, raw data was first examined using Trim Galore to remove adapters from reads using the following parameters: (--stringency 8 --phred33 -e 0.2 --paired --length 43 --r1 44 --r2 44), followed by the PCR duplication removal based on sequences of attached RNA identifier and subsequent base trimming from the 5’end of reads (22nt from read1 and 5nt from read2). The STAR alignment was the same as described above, except that Mus parental genome is either mm10 or GCA_921998555.2 depending on the mice used in the crosses and a maximum of 6 mismatches were allowed per read pair in the alignment.
Assembly: mm10 (Mus: C57BL/6J )
Assembly: GCA_921998555.2 (Mus: 129S1/SvImJ)
Assembly: GCA_921999005.2 (Cast: CAST/EiJ)
Supplementary files format and content: Tab-delimited text files include raw gene and TE (allelic and total) counts  for each Sample
Supplementary files format and content: Bed files of Mus or Cast allelic TE reads in Mus (muscoordinate) or Cast (castcoordinate) genome, respectively.

organism:
Mus musculus
Mus musculus castaneus

source_name: TST

growth_protocol: TST ES cells were grown in feeder-free 2i medium (50% DMEM/F12 media, 50% Neurobasal media, 2% Hyclone FBS, 0.5x N2 and 0.5x B27 supplements, 0.25x Glutamax, 100U/mlPen/Strep, 0.1mM βME, and 1000U/mL ESGRO recombinant mouse Leukemia Inhibitory Factor (LIF) protein supplemented with 1uM PD0325901 and 3uM of CHIR99021) at 37°C with 5% CO2

extract_protocol:
RNA was harvested using TRIZOL. 5 ug of total RNA was used for the construction of sequencing libraries.
RNA-seq libraries were prepared using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer’s protocols.

treatment_protocol: ES cell differentiation was induced by replacing 2i medium with differentiation medium (DMEM, 10% FBS, 25mM HEPES, 1x MEM NEAA, 100U/ml Pen/Strep, 0.1mM βME)

value: TST

value: embryonic stem cells

tag: genotype

value: TsixTST/+

value: LIF withdrawal differentiation


title: SF_Treg_JIA_1

description: Cell lysate (total RNA)

source_name: SF

value: Active


title: TST cells, Day 10, rep2

description:
ES_Diff_Genecounts.txt
ES_Day10_TEcounts.txt

tag: time


title: FL477

description:
Library name: FL477
10X Genomics

source_name: Frozen liver tissue sample from donor FL477 processed for snRNA-seq

value: eMASH


title: FL330

description:
Library name: FL330
10X Genomics

source_name: Frozen liver tissue sample from donor FL330 processed for snRNA-seq


title: TST cells, Day 8, rep1


title: FL793

description:
Library name: FL793
10X Genomics

source_name: Frozen liver tissue sample from donor FL793 processed for snRNA-seq

value: female


title: FL762

description:
Library name: FL762
10X Genomics

source_name: Frozen liver tissue sample from donor FL762 processed for snRNA-seq


title: TST cells, Day 6, rep2

description:
ES_Diff_Genecounts.txt
ES_Day6_TEcounts.txt


title: FL745

description:
Library name: FL745
10X Genomics

source_name: Frozen liver tissue sample from donor FL745 processed for snRNA-seq


title: TST cells, Day 4, rep2

description:
ES_Diff_Genecounts.txt
ES_Day4_TEcounts.txt


title: FL556

description:
Library name: FL556
10X Genomics

source_name: Frozen liver tissue sample from donor FL556 processed for snRNA-seq


title: FL543

description:
Library name: FL543
10X Genomics

source_name: Frozen liver tissue sample from donor FL543 processed for snRNA-seq


title: TST cells, Day 4, rep1


title: TST cells, Day 3, rep2

description:
ES_Diff_Genecounts.txt
ES_Day3_TEcounts.txt


title: TST cells, Day 3, rep1


title: FL284

description:
Library name: FL284
10X Genomics

source_name: Frozen liver tissue sample from donor FL284 processed for snRNA-seq


title: FL723

description:
Library name: FL723
10X Genomics

source_name: Frozen liver tissue sample from donor FL723 processed for snRNA-seq


title: FL531

description:
Library name: FL531
10X Genomics

source_name: Frozen liver tissue sample from donor FL531 processed for snRNA-seq

value: MASL


title: TST cells, Day 2, rep2

description:
ES_Diff_Genecounts.txt
ES_Day2_TEcounts.txt


title: FL324

description:
Library name: FL324
10X Genomics

source_name: Frozen liver tissue sample from donor FL324 processed for snRNA-seq


title: TST cells, Day 2, rep1


title: FL423

description:
Library name: FL423
10X Genomics

source_name: Frozen liver tissue sample from donor FL423 processed for snRNA-seq


title: FL391

description:
Library name: FL391
10X Genomics

source_name: Frozen liver tissue sample from donor FL391 processed for snRNA-seq


title: TST cells, Day 10, rep1


title: TST cells, Day 1, rep2

description:
ES_Diff_Genecounts.txt
ES_Day1_TEcounts.txt


title: FL559

description:
Library name: FL559
10X Genomics

source_name: Frozen liver tissue sample from donor FL559 processed for snRNA-seq


title: FL511

description:
Library name: FL511
10X Genomics

source_name: Frozen liver tissue sample from donor FL511 processed for snRNA-seq


title: TST cells, Day 0, rep2

description:
ES_Diff_Genecounts.txt
ES_Day0_TEcounts.txt

source_name: TST


title: TST cells, Day 1, rep1


title: FL777

description:
Library name: FL777
10X Genomics

source_name: Frozen liver tissue sample from donor FL777 processed for snRNA-seq


title: Huh7 cells, 3D bioprinted in VEGF sustained-release system with HUVEV cells, replicate 3

city: Hangzhou

first: Zhichao

last: Ye

address: Huajiachi Campus

institute: Zhejiang University

data_processing:
Prior to differential gene expression analysis, for each sequenced library, the read counts were adjusted by edgeR program package through one scaling normalized factor. Differential expression analysis of two samples was performed using the EBSeq R package. The resulting FDR (false discovery rate) were adjusted using the PPDE(posterior probability of being DE).The FDR < 0.05 & |log2（foldchange）| ≥1 was set as the threshold for significantly differential expression.
Assembly: hg38
Supplementary files format and content: Quantification of gene expression levelsGene expression levels were estimated by fragments per kilobase of transcript per million fragments mapped.

source_name: Human Liver

extract_protocol:
RNA was isolated with TRIzol
RNA libraries for RNA-seq were prepared using VAHTS Universal V6 RNA-seq Library Prep Kit for Illumina® following manufacturer's protocols.

value: Human Liver

value: Hepatocytes

value: WT


title: TST cells, Day 0, rep1


title: FL566

description:
Library name: FL566
10X Genomics

source_name: Frozen liver tissue sample from donor FL566 processed for snRNA-seq


title: FL740

description:
Library name: FL740
10X Genomics

source_name: Frozen liver tissue sample from donor FL740 processed for snRNA-seq


title: Huh7 cells, 3D bioprinted in VEGF sustained-release system with HUVEV cells, replicate 2


title: Huh7 cells, 3D bioprinted in VEGF sustained-release system with HUVEV cells, replicate 1


title: FL514

description:
Library name: FL514
10X Genomics

source_name: Frozen liver tissue sample from donor FL514 processed for snRNA-seq


title: TST cells, Day 6, rep1


title: Huh7 cells, 3D bioprinted in VEGF sustained-release system, replicate 3


title: Huh7 cells, 3D bioprinted in VEGF sustained-release system, replicate 2


title: T24 Hypoxia without glucose

city: Porto

first: Andreia

middle: Ferreira

last: Peixoto

address: Rua Dr. António Bernardino de Almeida

country: Portugal

institute: Portuguese Oncology Institute of Porto (IPO Porto)

description: Library name: T24 Hypoxia without glucose

data_processing:
HiSeq Control Software and Subread package v.1.5.2
Image analysis and base calling were conducted using HiSeq Control Software. One mismatch was allowed for index sequence identification. Garbage reads were trimmed from raw data and BAM files were generated. Unique gene hit counts were calculated using feature Counts from the Subread package v.1.5.2.
Assembly: Homo sapiens GRCh38 reference genome
Supplementary files format and content: counts

source_name: Bladder

growth_protocol: Human BLCA cell lines were maintained with complete RPMI 1640 GlutaMAX™ medium (Gibco) supplemented with 10% FBS (Gibco, 10500-064). Cells were kept at 37 °C in a 5% CO2 humidified atmosphere.

extract_protocol:
Total RNA was pooled from five biological replicates of T24 and 5637 cells exposed to normoxia or hypoxia plus glucose restriction using the Qiagen RNeasy Plus Mini kit (Qiagen, 74134).
RNA sequencing library were prepared using the NEBNext Ultra RNA Library Prep Kit for Illumina following manufacturer’s recommendations

treatment_protocol: Cells were kept at 37 °C in a 5% CO2 humidified atmosphere (Normoxia) or were grown for 24h under hypoxia and nutrient deprivation (Hypoxia -Glc) at 37 °C in a 5% CO2, 99.9% N2 and 0.1% O2 atmosphere, using a BINDER C-150 incubator (BINDER GmbH).

value: Bladder

value: bladder cancer cell

value: Hypoxia and glucose restriction


title: 5637 Hypoxia without glucose

description: Library name: 5637 Hypoxia without glucose


title: T24

description: Library name: T24

value: Normoxia and standard glucose levels


title: SK36 EMV-inoculated TIGK cells, biological replicate 3

city: Portland

first: Emily

last: Helliwell

state: Oregon

address: 3181 SW Sam Jackson Park Rd, MRB433

institute: Oregon Health and Science University

description: Library name: SK36_3

data_processing:
RNA-Seq libraries were sequenced on an Illumina NovaSeq to a sequencing depth of at least 30 million read pairs (150 bp paired-end sequencing) per sample
Quality control of raw reads was carried out using FastQC v0.11.9. Adapter and low-quality sequences were trimmed from raw reads using Trim Galore! v0.6.6
Trimmed reads were aligned to the reference genome Homo sapiens GRCh38 using STAR v2.6.1d
BAM file filtering and indexing was carried out using SAMtools v1.9
RNAseq library quality control was implemented using RSeQC v4.0.0 and QualiMap v2.2.2-dev; Duplicate reads were marked using Picard tools v2.23.9, Library complexity was estimated using Preseq v2.0.3, Duplication rate quality control was performed using dupRadar v1.18.0
Assembly: Reads overlapping with exons were assigned to genes using featureCounts v2.0.1
Supplementary files format and content: CSV file includes DEseq2-normalized counts across all samples "normalized_counts.csv"

source_name: TIGK CRL3397

growth_protocol: Gingival epithelial cell line TIGK CRL3397 was maintained in KBM Gold Keratinocyte Growth Basal Medium (Lonza) at 37°C, 5% CO2. 5x105 cells were seeded into each well of a 6-well plate and incubated for 24hr before inoculation.  KBM was replaced by RPMI prior to inoculation.

extract_protocol:
RNA was extracted from whole cells using a Trizol-based protocol, genomic DNA was digested using TURBO DNaseI according to manufacters protocol and samples were cleaned using Qiagen RNeasy kit. Total RNA was used for the construction of sequencing libraries.
Libraries were prepared using the Zymo-Seq RiboFree Total RNA Library Prep Kit (Cat # R3000) according to the manufacturer’s instruction manual v1.3.0
RNA was reverse-transcribed into cDNA, which was followed by ribosomal RNA depletion. After that partial P7 adapter sequence was ligated at 3’ end of cDNAs, followed by second strand synthesis and partial P5 adapter ligation to 5’ end of the double stranded DNAs.  Lastly, libraries were amplified to incorporate full length adapters under the following conditions: initial denaturation at 95°C for 10 min; 10 - 16 cycles of denaturation at 95°C for 30 sec, annealing at 60°C for 30 sec, and extension at 72°C for 60 sec; and final extension at 72°C for 7 min

treatment_protocol: Streptococcus sanguinis SK36 was grown for 18hrs in chemically-defined media (CDM) for 18hrs, until late log-growth phase.  EMVs were isolated using differential centrifugation and quantified using nanoparticle tracking analysis.  Concentration was adjusted to 4x1011 particles per ml in 1X PBS, and 250μl of this suspension was used to inoculate 5x105 TIGK cells.  Control-treated cells were inoculated with 250μl of 1X PBS

value: TIGK CRL3397

value: Gingival epithelial cell

value: S. sanguinis SK36 EMVs (1011 particles)


title: Huh7 cells, 3D bioprinted in VEGF sustained-release system, replicate 1


title: Huh7 cells, 3D bioprinted with HUVEV cells, replicate 3


title: 5637

description: Library name: 5637


title: PBS-inoculated TIGK cells, biological replicate 3

description: Library name: PBS_3

value: PBS (control)


title: PBS-inoculated TIGK cells, biological replicate 2

description: Library name: PBS_2


title: SK36 EMV-inoculated TIGK cells, biological replicate 2

description: Library name: SK36_2