title: UHB2010-26, scRNA-seq

city: Indianapolis

first: Harikrishna

last: Nakshatri

state: IN

address: 980 W. Walnut St. R3C218C

department: General Surgery

institute: Indiana University School of Medicine

data_processing:
CellRanger 4.0.0 was utilized to process the raw sequence data generated. The filtered gene-cell barcode matrices generated by CellRanger were used for further analysis.
Assembly: GRCh38
Supplementary files format and content: filtered gene-barcode matrices in HDF5 format

source_name: breast

extract_protocol:
Cells were extracted from cryopreserved samples using tumor dissociation kit (human) Cat# 130-095-929, followed by red blood cell lysis.
Library was performed according to the manufacturer's instructions (single cell 3' protocol, 10x Genomics).

value: breast

value: epithelial


title: HFpEF + Veh_2305

status: Public on Jan 17 2024

type: SRA

city: South San Francisco

first: Farshad

last: Farshidfar

state: CA

address: 171 Oyster Point Blvd Ste 500

country: USA

institute: Tenaya Therapeutics Inc.

library_source: transcriptomic

data_processing:
Adapter trimming by FASTP (ver. 0.23.2)
Read alignment by Salmon (ver. 1.6.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT

molecule: polyA RNA

organism: Mus musculus

source_name: Left ventricle

extract_protocol:
Approximately 106 cells or 20-30 mg of mouse heart tissue were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Total RNA was extracted and washed from lysed cells using the Direct-zol-96 RNA Kit (Zymo Research) according to the manufacturer’s instructions. Samples were treated with DNase I for 15 min at room temperature. cDNA was reverse transcribed from approximately 1 μg of RNA through random hexamers using the SuperScript III First-Strand Synthesis System according to the manufacturer’s instructions (Thermo Fisher Scientific). Real-time qPCR reactions were performed using the TaqMan universal PCR master mix (Thermo Fisher Scientific) with the TaqMan probes listed. RT-qPCR reactions were performed using the QuantStudio7 Flex Real-Time PCR systems (Thermo Fisher Scientific). Each reaction was performed in triplicate for a given RT-qPCR run, and each condition had four experimental replicates. Relative expression of the gene of interest was normalized to GAPDH as the housekeeping control using the 2–ΔΔCT method. P values were calculated with Student’s t-tests.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina, Inc.. The RNA libraries were prepared using a TruSeq Stranded mRNA kit (Illumina), which also removes ribosomal RNA. The libraries were sequenced as 100 base pair single-end reads using Illumina NovaSeq SP with an average of 29.8 million reads per sample.

treatment_protocol: HFD+L-NAME mice were randomized to different groups to receive oral doses of 15 mg/kg TYA-018 or vehicle (5% DMSO + 45% PEG-300 + 50% purified water) at 10 mL/kig once per day for 6-9 weeks. TYA-018 was formulated in vehicle.

tag: tissue

value: Left ventricle

tag: disease state

value: HFD/L-NAME HFpEF model

tag: genotype

value: WT

tag: strain

tag: treatment

value: Vehicle


title: CD5C5ANXX_3#136773_CCGTCC [DEV sRNA]

city: Wien

first: Andreas

middle: B

last: Diendorfer

address: Leberstraße 20

country: Austria

institute: TAmiRNA GmbH

data_processing:
fastQ quality assessment
cutadapt adater trimming
bowtie1 genome alignment
miRDeep2 miRNA quantification (mirbase)
Assembly: GRCh38.p12; mirbase version v22.1
Supplementary files format and content: CSV with miRNA quantifications (raw and rpm)

molecule: total RNA

organism: Homo sapiens

source_name: LEC

extract_protocol:
Total RNA was extracted using the miRNeasy Mini Kit
RealSeq Biofluids Plasma/Serum miRNA Library Kit

tag: sample type

value: EV

tag: cell type

value: LEC

tag: donor

value: D

tag: molecule subtype

value: small RNA


title: RKO-CYP1B1 2

city: Shanghai

first: Lei

last: Jin

state: Shanghai

address: Shanghai Fenglin Road

country: China

institute: Fudan University

data_processing:
CLC Genomics Workbenchv 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed sequence reads were mapped to NCBI_GRCh38.p13 using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: NCBI_GRCh38.p13
Supplementary files format and content: tab-delimited text files include count and FPKM values for each Sample

source_name: colon tissue

growth_protocol: RKO and SW480 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was extracted using the TRIzol reagent according to the manufacturer's protocol. 1 ug of total RNA was used for the construction of sequencing libraries.
Then the libraries were constructed using TruSeq Stranded mRNALTSample Prep Kit(Ilumina,San Diego, CA, USA) . 1 ug of total RNA was used for the construction of sequencing libraries.

treatment_protocol: RKO and SW480 cells were transfected with CYP1B1 lentivirus for 24hpf

value: colon tissue

tag: cell line

value: RKO

value: Human colon cancer cells

value: CYP1B1 overexpression


title: HFpEF + Veh_2307


title: Ctrl_vehicle_V2501

library_source: transcriptomic single cell

data_processing:
After sequencing, clean reads were analyzed with mouse reference genome mm10-2020-A using Cell Ranger v6.1.2 software. Output from Cell Ranger in the form of filtered gene expression matrix h5 files were analyzed using R package Seurat version 4.
Assembly: mm10-2020
Supplementary files format and content: h5

extract_protocol:
Approximately 100 mg of mouse heart tissue were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Nuclei isolation was performed as per instructions from 10xGenomics "Nuclei Isolation from Cell Suspensions & Tissues for Single Cell RNA Sequencing" protocol (CG000124, Rev F) to reach the target concentration of 700-1,200 nuclei/µl. The suspension was processed using 10X Genomics Single Cell protocol (CG00053, Rev D).
We constructed 3’ single cell gene expression libraries (Next GEM v3.1) using the 10x Genomics Chromium system. Each library was sequenced with Illumina NovaSeq (PE150).
snRNA-seq

treatment_protocol: Control and HFD+L-NAME mice were randomized to different groups to receive oral doses of 15 mg/kg TYA-018, 10 mg/kg empagliflozin,  or vehicle (5% DMSO + 45% PEG-300 + 50% purified water) at 10 mL/kg once per day for 6-9 weeks. TYA-018 was formulated in vehicle.

value: Control


title: Hela-OLDN-fragments-rep2

city: Fukuoka

first: Yasuyuki

last: Ohkawa

address: 3-1-1 Maidashi

country: Japan

institute: Medical Institute of Bioregulation

description: 200-300 bp DNA fragmants were sampled

library_source: genomic

data_processing:
Adapter DNAs were trimmed using Trim Galore (version 0.6.7) with the options: --paired.
The paired-end reads were mapped to the GRCh38 for the Hela samples and the tandemly connected three Widom 601 sequences for the in vtiro sample using bowtie (version 2.3.5.1) with the default options.
Data of Hela samples were filtered using the following specifications; OLTN: 337 (+/- 5) bp, OLDN: 248 (+/- 5) bp and mono-nucleosome: 147 (+/- 5) bp, respectively.
For Hela data, the bigWig files were created by 50 bp intervals on the genome, and then the counts were normalized as CPM (Reads Per Million reads) using deepTools (version 3.5.1) with the option: -bs 1 --normalizeUsing CPM --minMappingQuality 60 --ignoreDuplicates --normalizeUsing CPM.
For in vitro data, a count file was created by counting fragments by lengths.
Assembly: GRCh38
Supplementary files format and content: bigwig files were genelated using deepTools (version 3.5.1, bamCoverage function)  with the option

molecule: genomic DNA

source_name: Hela cells

growth_protocol: The HeLa cells were commercially obtained and stored at -80ºC until use.

extract_protocol:
The HeLa cells were suspended in the washing solution containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, and a proteinase inhibitor (Roche). The detergent buffer containing 15 mM Tris-HCl (pH 8.0), 15 mM NaCl, 60 mM KCl, 300 mM sucrose, proteinase inhibitor (Roche), and 1% NP-40 was then added to the cell suspension, and the mixture was rotated at 4 ºC for 10 minutes. The HeLa nuclei were collected by centrifugation and were resuspended in the washing solution. A large amount of MNase (3 units/µL) and CaCl2 (2 mM) were added to the HeLa nuclei suspension. The MNase treatment was performed under 37 ºC for 30 minutes, and was terminated by EDTA (pH 8.0) addition. The MNase fragments were precipitated by ethanol, and were electrophoresed by 4% agarose gel.
Libraries were prepared using ThruPLEX DNA-Seq Kit (Clontech, #R400674).

value: Hela

tag: sample group

value: OLDN-fragments


title: CD5C5ANXX_3#136772_ATGTCA [CEV sRNA]

value: C


title: UHB2009-18B, scRNA-seq

value: breast

value: epithelial


title: Human endometrial organoids, mid-secretory phase, control 15 [B15-SEC]

city: Valencia

first: Hortensia

last: Ferrero

state: Valencia

address: Avenida Fernando Abril Martorell 106, Torre A

department: Reproductive Medicine

country: Spain

institute: Instituto de Investigación Sanitaria La Fe / Fundación IVI

description:
CONTROL15-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

data_processing:
Data was processed in R computing environment (version 4.1.3).
The quality of sequencing was evaluated by FastQC.
Raw FASTQ files from sequencing were processed to remove adapters and filter read sequences by size using BBDuk package.
mRNAs were aligned using Subread software and annotated using the human genome reference HG38.
The number of reads per sample was normalized using the geometric median method of ratios on each mRNA implemented in the DESeq2 R package.
Assembly: HG38
Supplementary files format and content: Raw_counts.xlsx, column-delimited excel file include raw count values for each sample
Supplementary files format and content: Normalized_counts.xlsx, column-delimited excel file include normalized count values for each sample

source_name: Human endometrial epithelial cells

growth_protocol: Established human endometrial organoids were cultured for 7 days at 37°C, 6% CO2 and 5% O2 in Organoid Expansion Medium (ExM).

extract_protocol:
Total RNA was extracted from the ADENO-SECorg, CONTROL-SECorg, ADENO-GESTorg and CONTROL-GESTorg groups (n=15/group) using the RNeasy Mini Kit (Qiagen) according to the manufacturer’s protocol, and quantified with a Qubit 3 Fluorometer (Invitrogen).
cDNA libraries were generated employing the TruSeq Stranded mRNA Library Prep (Illumina) and TruSeq RNA CD Index Plate (Illumina) according to manufacturer’s instructions.

treatment_protocol: Control and adenomyosis organoids were cultured in ExM treated with 10 nM estradiol (E2; Sigma-Aldrich), 1 µM progesterone (P4; Sigma-Aldrich) and 1 µM 8-bromoadenosine 3′,5′-cyclic monophosphate sodium salt (cAMP; Sigma-Aldrich) for mid-secretory phase differentiation. For gestational phase differentiation, control and adenomyosis organoids were treated with 10 nM E2, 1 µM P4, 1 µM cAMP, with an additional 20 ng/mL prolactin (Peprotech) and 20 ng/mL human placental lactogen (R&D).

value: Human endometrial epithelial cells

tag: differentiation phase

value: mid-secretory phase

value: None; contraol


title: HFpEF + Veh_2304

value: Left ventricle

value: HFD/L-NAME HFpEF model

value: WT

value: Vehicle


title: UHB2007-14B, scRNA-seq


title: Human endometrial organoids, gestational phase, control 14 [B14-GEST]

description:
CONTROL14-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: gestational phase


title: Human endometrial organoids, mid-secretory phase, control 14 [B14-SEC]

description:
CONTROL14-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: UHB1907-02, scRNA-seq


title: CD5C5ANXX_3#136770_AGTCAA [AEV sRNA]

value: EV

value: LEC

value: A

value: small RNA


title: UH2012-19D, scRNA-seq


title: Human endometrial organoids, gestational phase, control 15 [B15-GEST]

description:
CONTROL15-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: Human endometrial organoids, mid-secretory phase, control 13 [B13-SEC]

description:
CONTROL13-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HFpEF + Veh_2303


title: Control + Veh_2248

value: Control (non-failing)


title: Human endometrial organoids, gestational phase, control 13 [B13-GEST]

description:
CONTROL13-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: Control + Veh_2249


title: UH2012-19B, scRNA-seq


title: CD5C5ANXX_2#136767_TAGCTT [J sRNA]

value: Cells

value: J


title: Human endometrial organoids, gestational phase, control 12 [B12-GEST]

description:
CONTROL12-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: Control + Veh_2247


title: CD5C5ANXX_2#136768_GGCTAC [K sRNA]

source_name: HUVEC

value: HUVEC

value: K


title: CD5C5ANXX_2#136766_GATCAG [I sRNA]

source_name: BEC

value: BEC

value: I


title: Control + Veh_2246


title: CD5C5ANXX_2#136765_ACTTGA [H sRNA]

value: H


title: EHB2002-07_PN, scRNA-seq

value: breast

value: epithelial


title: HFpEF+Vehicle_TT-592

treatment_protocol: HFD+mTAC mice vehicle (5% DMSO + 45% PEG-300 + 50% purified water) at 10 mL/kig once per day for 6-9 weeks.

value: Left ventricle

value: HFD/mTAC HFpEF model

value: WT


title: Human endometrial organoids, gestational phase, control 11 [B11-GEST]

description:
CONTROL11-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: gestational phase

value: None; contraol


title: EHB2002-07_HN, scRNA-seq


title: CD5C5ANXX_3#136771_AGTTCC [BEV sRNA]

source_name: HDMEC

value: EV

value: HDMEC

value: B

value: small RNA


title: HFpEF+Vehicle_TT-591

value: Vehicle


title: Human endometrial organoids, mid-secretory phase, control 11 [B11-SEC]

description:
CONTROL11-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase


title: EH1906-01B, scRNA-seq


title: HFpEF+Vehicle_TT-590


title: CD5C5ANXX_2#136763_GCCAAT [F sRNA]

value: Cells

value: LEC

value: F


title: Human endometrial organoids, gestational phase, control 10 [B10-GEST]

description:
CONTROL10-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HFpEF+Vehicle_TT-589


title: CD5C5ANXX_2#136762_ACAGTG [E sRNA]

source_name: LECtert

value: LECtert

value: E


title: Human endometrial organoids, mid-secretory phase, control 10 [B10-SEC]

description:
CONTROL10-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: HFpEF+Vehicle_TT-588

value: Left ventricle


title: CD5C5ANXX_2#136761_TGACCA [D sRNA]

value: D


title: CD5C5ANXX_2#136760_TTAGGC [C sRNA]

value: C


title: Human endometrial organoids, gestational phase, control 9 [B9-GEST]

description:
CONTROL9-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells


title: Human endometrial organoids, mid-secretory phase, control 12 [B12-SEC]

description:
CONTROL12-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: 20118a065

city: Hamburg

last: Neueder

address: Falkenried 94

department: Center for Molecular Neurobiology (ZMNH)

country: Germany

institute: University Medical Center Hamburg-Eppendorf

data_processing:
After demultiplexing, samples were trimmed using cutadapt v3.2 as follows: Read 1: Remove everything 3' of A10. Read 2: Remove everything 3' of AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT; on the reverse complementary reads remove everything 3' of A10. For final read pairs: In paired end mode keep only reads with a minimum length of 15 base pairs; remove 3 nucleotides from the 5' ends of the reads.
A merged gene annotation was prepared for use with salmon v1.5.2. To this end, the transcript fasta sequences from the GENCODE human release 38 (https://www.gencodegenes.org/human) and the human specific transcript fasta sequences from RNAcentral v19 release (https://rnacentral.org/) were merged. Together with primary assembly genome fasta file (GENCODE) and its decoys, these were used to generate a salmon index.
To quantify sense transcripts, salmon was run with the -l ISF option, for antisense transcripts with the -l ISR option. Common parameters were --validateMappings --softclip --softclipOverhangs --recoverOrphans --incompatPrior 0.0 --seqBias --gcBias --posBias --numBootstraps 100.
Quantification files were imported using tximport v1.20.0 and collapsed to gene level with the non-coding RNA transcripts of the RNAcentral database considered as 'genes'. Variance stabilizing transformed (VST)counts from an intercept matrix in DESeq2 v1.32.0 were used to correct for batch effects (site of sampling, BMI, sequencing batch, sex and age) in limma 3.48.3, and a Euclidean distance with a z of -3 was used to screen for outliers.
Assembly: GRCh38.p13
Supplementary files format and content: tab-delimited text file of normalized counts per sample, sense (ISF) mapping RNAs, DESeq2 output

source_name: plasma

extract_protocol:
RNAs were extracted from freshly purified EVs without any freeze/thaw steps in between. To this end, 350 μl of lysis buffer from the SeraMir Exosome RNA Amplification kit (System Biosciences) was added to the purified EVs, vortexed for 15 sec at maximum speed, incubated for 5 mins at room temperature and 200 μl of 100% ethanol (RNA grade) added. The sample was vortexed for 10 sec at maximum speed and the precipitating solution was transferred to an ExoRNA spin column. Samples were bound and washed twice (each 400 µl of wash buffer) with centrifugation steps of 1 min at > 15.000 g. Flow-throughs were discarded. Columns were dried 2 min at > 15.000 g and placed into a new DNA low-bind tube (Eppendorf). 23 μl of RNase free water was directly applied onto the middle of the column without touching it and incubated for 1 min at room temperature. RNAs were eluted by centrifugation for 2 min at < 400 g, followed by centrifugation for 1 min at > 15.000 g. RNA was aliquoted, frozen in liquid nitrogen and stored at -80°C. RNA quality assessment and quantification were carried out using a Agilent 2100 Bioanalyzer with RNA 6000 pico chips (Agilent Technologies).
The sequencing library was prepared using the SMARTer smRNA-Seq Kit (Takara Bio, Kusatsu, Japan) with 100 pg total RNA as input according to the manufacturer's protocol. In short, adenylation of the 3' ends enabled priming of the reverse transcription reaction using an oligo(dT) primer containing the Read 2 adapter sequence for sequencing. Subsequently, cDNA synthesis was performed, making use of the template-switching technology and adding the Read 1 sequencing adapter. Libraries were then amplified in a PCR with 21 cycles using barcoded primers. Eight differently barcoded forward (i5 index) primers and twelve different reverse (i7 index) primers provided in the kit were used in 66 different combinations to enable multiplexing of all 66 samples on one flowcell. After the PCR, samples were cleaned up using the column-based NucleoSpin Gel and PCR Clean-Up kit (Macherey-Nagel, Düren, Germany). The double two-sided size selection described in the user manual was omitted to also retain larger molecules. The molarity of the libraries was assessed using the High Sensitivity NGS assay of the FragmentAnalyzer (Agilent, Santa Clara, USA) for average fragment size, and fluorometric quantitation to measure library concentration with the dsDNA High Sensitivity assay on a Qubit 3.0 (both Thermo Fisher Scientific, Waltham, MA, USA). The libraries were pooled in an equimolar fashion, denatured according to the manufacturer's instructions and diluted to 270 pM. Sequencing was performed on a NovaSeq 6000 (Illumina, San Diego, CA, USA) as 150 bp paired-end reads with an average sequencing depth of 11 Mio clusters (i.e. read-pairs) per sample.

value: plasma

value: extracellular vesicles


title: 20118a064


title: UH1908-22B, scRNA-seq

value: breast

value: epithelial


title: Control_TT-586

value: Control (non-failing)

value: WT


title: CD5C5ANXX_2#136759_CGATGT [B sRNA]

value: HDMEC

value: B

value: small RNA


title: Human endometrial organoids, mid-secretory phase, control 9 [B9-SEC]

description:
CONTROL9-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase

value: None; contraol


title: CD5C5ANXX_2#136758_ATCACG [A sRNA]

value: Cells

value: LEC

value: A


title: CD5C5ANXX_2#136764_CAGATC [G sRNA]

value: G


title: Control_TT-585

value: Left ventricle

value: Vehicle


title: Human endometrial organoids, gestational phase, control 8 [B8-GEST]

description:
CONTROL8-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: Human endometrial epithelial cells

value: gestational phase


title: Human endometrial organoids, mid-secretory phase, control 8 [B8-SEC]

description:
CONTROL8-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: CD76FANXX_4#138279_GAGTCC [K mRNA]

data_processing:
fastQ quality assessment
cutadapt adater trimming
STAR genome alignment
htSeq quantification
Assembly: GRCh38.p12

extract_protocol:
QuantSeq 3′ mRNA-Seq Library Prep Kit FWD for Illumina
Total RNA was extracted using the miRNeasy Mini Kit

value: cells

value: HUVEC

value: K


title: 20118a062

value: plasma

value: extracellular vesicles


title: Human endometrial organoids, gestational phase, control 7 [B7-GEST]

description:
CONTROL7-GESTorg
Raw_counts.xlsx
Normalized_counts.xlsx


title: 20118a066


title: 20118a061


title: Control_TT-584

value: Control (non-failing)

value: WT


title: 20118a060


title: Control_TT-583


title: CD76FANXX_4#138278_TATGTC [J mRNA]

value: J


title: Human endometrial organoids, mid-secretory phase, control 7 [B7-SEC]

description:
CONTROL7-SECorg
Raw_counts.xlsx
Normalized_counts.xlsx

value: mid-secretory phase

value: None; contraol


title: Control_TT-587


title: CD76FANXX_4#138277_ATACTG [I mRNA]

value: BEC

value: I


title: 20118a063


title: 20118a058


title: OS tissue of lung metastatic patient

city: Kunming

first: Chenhong

last: Zheng

address: No. 174 Renmin West Road

institute: Yunnan Cancer Hospital

description: 10X Genomics

data_processing:
The Cell Ranger software pipeline provided b 10X Genomics was used to demultiplex cellular barcodes.
Raw reads were demultiplexed and mapped to the reference genome by UMI-tools (version 1.0.1, Smith et al., 2017) using default parameters.
All downstream single-cell analyses were performed using Seurat (version 3.1.0, Satija et al., 2015) unless specifically mentioned.
The Seurat R package (version 3.1.0) was used for cells filtering, data normalization, dimensionality reduction, clustering, differential expression.
Gene Ontology (GO) enrichment analysis of marker genes were implemented by the clusterProfiler R package, in which the bias of gene length was corrected.
Assembly: mm10
Supplementary files format and content: Matrix table with raw gene counts for every gene and every cell (barcodes.tsv, features.tsv, marix.mtx).

source_name: Osteosarcoma

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Cells were added to analysis by Illumina pipeline.
RNA libraries were prepared with Chromium Single cell 3' Reagent v3 Kits according to the manufacturer's protocol.

value: Osteosarcoma

tag: diagnosis

value: Osteosarcoma lung metastatic patient


title: WT1, B6, colon immune cells, scRNAseq

city: MONTREAL

first: David

last: Langlais

state: QC

address: 740 Ave Dr Penfield, rm 4203, McGill Genome Centre

department: Human Genetics

country: Canada

institute: McGill University

description: 10x Genomics Single Cell 3’ RNA (v3.1)

data_processing:
Raw gene expression matrices were generated for each sample by the Cell Ranger, and the output was analyzed using the Seurat package.
Low quality reads were filtered based on three criteria: number of detected genes per cell, number of UMIs expressed per cell and mitochondrial content, using the following threshold parameters: nGene (between 200 and 7500), nUMI (between 500 and 75,000), and percentage of mitochondrial genes expressed (< 7.5%).
Doublets were then identified by finding cells expressing markers of two cell lineages simultaneously, as well as using the DoubletFinder package.
Gene expression matrices were normalized using the NormalizeData function and scaled using the ScaleData function, regressing out effects of cell cycle and percentage of expressed mitochondrial genes. Identification of highly variable features, linear dimension reduction by PCA transformation, UMAP dimensionality reduction, and cell clustering were performed using standard Seurat package workflows.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Colon

growth_protocol: Colons from B6 mice were collected, cut into small pieces, and washed in gut buffer (1X Hank’s Balanced Salt Solution (HBSS) containing 2% heat-inactivated fetal bovine serum (FBS) and 15 mM of HEPES. Epithelial cells were removed by shaking in gut buffer with 5 mM EDTA for 30 minutes at 37°C, with occasional vortexing. Finally, tissues were treated with collagenase IV (20 mg/ml) and DNase I (10 mg/mL) in RPMI-1640 supplemented with 5% FBS and 15 mM of HEPES for 20 minutes at 37°C and passed through a 70 μM cell strainer to collect lamina propria cells. Cells were stained for viability using Zombie Viability Dye V500 (1:400), and surface stained with anti-CD45 APC (1:400, clone 30F11, Biolegend). Stained cell suspensions were sorted on a BD FACSAriaIII Cell Sorter (BD Biosciences) to obtain viable CD45+ cells.

extract_protocol:
Freshly sorted cells were washed and resuspended in 0.04% BSA in PBS for loading on the 10x Chromium G chip aiming to capture with 8000 cells per sample. Two mouse colons were processed and capture separately.
Single cell capture and cDNA preparation was done according to the 10x Genomics Single Cell 3’ RNA (v3.1) protocol. Libraries were sequenced on the NovaSeq 6000 (Illumina).

value: Colon

value: CD45+ cells


title: CD76FANXX_4#138276_CCGCAA [H mRNA]

value: H


title: CD76FANXX_4#138275_TCTTAA [G mRNA]

value: cells

value: HDMEC

value: G


title: WT2, B6, colon immune cells, scRNAseq

description: 10x Genomics Single Cell 3’ RNA (v3.1)


title: KO-PAX5 input_rep_2

city: Tianjin

first: Yan

middle: Xue

last: miao

state: Tianjin

address: 22 Qixiangtai Road,Heping District,Tianjin,China

department: Department of Immunologyc

institute: Tianjin Medical University

description: KO-PAX5 input_rep_2

data_processing:
Basecalls performed using CASAVA version 1.4
Data were filtered using Trimmomatic
ChIP-seq reads were aligned to the hg38 genome assembly using bowtie2-2.3.5
Determination of the normalized factor using deeptools
peaks were called using MACS2
Genome_build: hg38  and dm6

source_name: H1155 cell line konck out PAX5

growth_protocol: H1155 and KO-PAX5 cell line were cultred in DMEM medium containg 10%FBS

extract_protocol:
Lysates were clarified from sonicated nuclei and H3K9me3-DNA complexes were isolated with H3K9me3 antibody.
Libraries were prepared according to Illumina's instructions accompanying the Paired-End DNA Samples Prep Kit. Briefly, DNA fragment end repair, add A base to 3'end, and connect sequencing adapter. PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Illumina HiSeq 2500 following the manufacturer's protocols.

treatment_protocol: untreatment

value: neuroendocrine large cell lung cancer

tag: genotype/variation

tag: chip antibody

value: untreatment


title: 20118a057

value: plasma

value: extracellular vesicles


title: 20118a055


title: KO-PAX5 input_rep_1

description: KO-PAX5 input_rep_1


title: CD76FANXX_4#138274_TACCTT [F mRNA]

value: LEC

value: F


title: hippocampus, offspring of prenatal hypoxia, C57BL/6J, biol rep 4

city: soochow

first: Miao

last: Sun

institute: Institute for Fetology, The First Affiliated Hospital of Soochow University

data_processing:
CLC Genomics Workbench v 11.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter-Quality limit:0.05)
Trimmed sequence reads were mapped to GrCM38/mm10 using CLC genomic benchwork (parameters-mismath cost:2 insertion cost: 3 deletion cost: 3 lengthfraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: mm10
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text file include RPKM values for each Sample

source_name: hippocampus

extract_protocol:
Total RNA was extracted from hippocampal tissue using a TRIZOL reagent (Ambion, USA).
RNA libraries were generated using NEBNext® UltraTM RNA Library Prep Kit for Illumina® (NEB, USA) following manufacturer’s recommendations.

value: hippocampus

value: prenatal hypoxia


title: KO-PAX5 ChIP-seq_rep_2

description: KO-PAX5 ChIP-seq_rep_2

value: anti-H3K9me3 (ab8898,abcam), spike-in antibody (61686, Activemotif)


title: hippocampus, offspring of prenatal hypoxia, C57BL/6J, biol rep 5

address: The First Affiliated Hospital of Soochow University


title: hippocampus, offspring of prenatal hypoxia, C57BL/6J, biol rep 3


title: KO-PAX5 ChIP-seq_rep_1

description: KO-PAX5 ChIP-seq_rep_1


title: CD76FANXX_4#138273_GGCTGC [E mRNA]

value: LECtert

value: E


title: hippocampus, offspring of prenatal hypoxia, C57BL/6J, biol rep 2


title: CD76FANXX_4#138272_CACACT [D mRNA]

value: D


title: 20118a053


title: hippocampus, offspring of prenatal hypoxia, C57BL/6J, biol rep 1


title: 20118a052


title: 20118a059


title: CD76FANXX_4#138271_CCTAAG [C mRNA]

value: C


title: H1155-WT input_rep_1

description: H1155-WT input_rep_1


title: 20118a051


title: CD76FANXX_4#138270_ATGAAC [B mRNA]

value: B


title: hippocampus, offspring of control pregnancy, C57BL/6J, biol rep 5

value: control pregnancy


title: CD76FANXX_4#138269_TTAACT [A mRNA]

value: cells

value: A


title: 20118a050


title: hippocampus, offspring of control pregnancy, C57BL/6J, biol rep 4


title: 20118a049


title: 20118a054


title: hippocampus, offspring of control pregnancy, C57BL/6J, biol rep 3


title: H1155-WT ChIP-seq_rep_1

description: H1155-WT ChIP-seq_rep_1

value: neuroendocrine large cell lung cancer


title: 20118a047


title: Brassica rapa seedlings 1 day old, IBA-Ala treatment 3h, rep2

city: ZAGREB

first: Branka

last: Salopek Sondi

address: Bijenička cesta 54

department: Division of Molecular Biology

country: Croatia

institute: Ruđer Bošković Institute

description:
Brassica rapa L. ssp. pekinensis (Lour.) Hanelt cv. Cantonner Witkrop
Illumina sequencing provided by Brassica rapa L. ssp. pekinensis (Lour.) Hanelt cv. Cantonner Witkrop

data_processing:
STAR v.2.7.1a was used to clip first 9 bp of the reads (improving the mismatch rate per base statistic), as well as to align them to the reference genome. For reference genome and GO annotations we used the Brassica rapa Chiifu V3.0 obtained from the BRAD database.
Raw counts of reads aligning to genes were obtained using htseq-count v.1.99.2
Raw counts were used for differential expression analysis using deseq2 v.1.34.0. IAA-Ala, IBA-Ala and IPA-Ala treatments were processed and compared to the untreated control independently. The deseq2 was run in Rstudio v.2021.09.02 Build 382, running R v.4.2.0.
Assembly: Brassica rapa Chiifu v.3
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample obtained with htseq-count
Supplementary files format and content: Tab-delimited text file includes normalized counts obtained with deseq2 when comparing treatment (two biological replicates) to control (the two biological replicates)

organism: Brassica rapa

source_name: seedling

growth_protocol: Seeds of Chinese cabbage (Brassica rapa L. ssp. pekinensis (Lour.) Hanelt cv. Cantonner Witkrop) were purchased from ISP International Seed Processing GmbH, Quedlinburg, Germany. Following sterilization, seeds were germinated.

extract_protocol:
Whole seedlings were homogenized on Mixer Mill MM400 (Retsch GmbH, Germany) in three cycles of 1 minute at 30 Hz with zirconium oxide beads (Next Advance, USA). To each pulverized sample, 1 mL of RNAzol (Sigma Aldrich, USA) was added and after centrifugation, the same volume of ethanol (100%) was added to the supernatants, which were further processed through the Direct-zolTM RNA MiniPrep kit (Zymo Research, USA) according to the manufacturer instructions. The eluted total RNA samples were checked for concentration on Nanodrop 2000.
mRNA Library preparation commercially by Vienna BioCenter Core Facilities (VBCF.NGS), Lexogen SENSE (Lexogen QuantSeq V2 adaptors)

treatment_protocol: The 1-day-old seedlings were placed on 1 % agar plates, supplemented with the hormones indole-3-acetyl-L-alanine (IAA-Ala), indole-3-propionyl-L-alanine (IPA-Ala) and indole-3-butyryl-L-alanine (IBA-Ala) in 0.01 mM concentration. Seedlings on hormone-free agar plates were used as a control. Following incubation of the seedlings under continuous light for a further 24 h at 22 °C, total RNA was isolated from 100 mg of whole seedlings.

value: seedling

value: IBA-Ala


title: R-2A-2

city: Changsha

first: Haifei

last: Chen

address: nongda road

institute: Hunan Agricultural University

data_processing:
sequencing on an Illumina platform (San Diego, CA, USA)
Gene expression levels were caculated using the FPKM method (Fragments Per Kilobase per Million mapped reads.
Differentially expressed genes (DEGs) were defined as genes with |log2 (fold change) | >1 and a false discovery rate (FDR) < 0.05.
Supplementary files format and content: The txt files include FPKM values.

organism: Arabidopsis thaliana

source_name: root

growth_protocol: Surface-sterilized seeds were sown onto nutritional soil in a greenhouse (300 μmol photons m-2 s-1, 16 h photoperiod, 22 °C) for 7 d. Then, eight uniformly growing plants of each ecotype were grown hydroponically with 4 L of nutritional media per pot, containing 1 mM Ca(NO3)2 or 1 mM (NH4)2SO4.

extract_protocol:
The total RNA was then extracted from the roots of the NH4+-tolerant and -sensitive ecotypes.
The sequencing library was generated using the NEBNext Ultra™ RNA Library Prep Kit from Illumina (New York, NEB, USA)

treatment_protocol: The seedlings were grown in a nitrate nutrient solution for 5 d, then transferred to 1 mM Ca(NO3)2 or 1 mM (NH4)2SO4 for 1 d.

value: root

tag: ecotype

tag: phenotype


title: hippocampus, offspring of control pregnancy, C57BL/6J, biol rep 2

tag: tissue


title: R-2A-1


title: Brassica rapa seedlings 1 day old, IBA-Ala treatment 3h, rep1


title: 20118a046

value: plasma

value: extracellular vesicles


title: H1155-WT input_rep_2

description: H1155-WT input_rep_2

value: untreatment


title: Brassica rapa seedlings 1 day old, IPA-Ala treatment 3h, rep2

value: IPA-Ala


title: 20118a045


title: Brassica rapa seedlings 1 day old, IPA-Ala treatment 3h, rep1


title: 20118a044


title: R-2N-3


title: R-2N-2


title: HFpEF+SGLT2i_V2575

value: Left ventricle

tag: Sex

value: Female

value: WT

value: Empagliflozin


title: H1155-WT ChIP-seq_rep_2

description: H1155-WT ChIP-seq_rep_2

value: anti-H3K9me3 (ab8898,abcam), spike-in antibody (61686, Activemotif)


title: Brassica rapa seedlings 1 day old, IAA-Ala treatment 3h, rep2

value: IAA-Ala


title: HFpEF+SGLT2i_V2573

tag: genotype


title: 20118a043


title: R-2A-3


title: 20118a042


title: Brassica rapa seedlings 1 day old, IAA-Ala treatment 3h, rep1


title: Brassica rapa seedlings 1 day old, mock treatment 3h, rep2

value: no treatment control


title: 20118a041


title: HFpEF+SGLT2i_V2572

tag: strain


title: R-16N-2

tag: treatment


title: R-16N-3


title: HFpEF+SGLT2i_V2571


title: HFpEF+SGLT2i_V2566


title: R-16N-1


title: hippocampus, offspring of control pregnancy, C57BL/6J, biol rep 1

value: hippocampus

value: control pregnancy


title: 20118a038


title: 20118a039


title: R-16A-3


title: Arpp21 KO6

city: Ulm

first: Marcin

last: Lyszkiewicz

address: Eythstr. 24

department: Dpt. of  Pediatrics and Adolescent Medicine

institute: Ulm University Medical Center

data_processing:
data processing and initial analysis were done by Genohub
Supplementary files format and content: .xlsx files contain detailed information about each identified TCR alpha and TCR beta clone. This includes clone number, frequency, CDR3 nucleotide sequence and information on the V-fagment used.
Library strategy: TCR-seq

source_name: spleen

growth_protocol: primary cells

extract_protocol:
stabdard mRNA extraction kit
Library preparation kit: Takara SMARTer mouse TCR alpha beta profiling kit

treatment_protocol: FACS purified

value: spleen

value: primary cells

value: CD4 T cells

value: Arpp21 KO

value: FACS cell sodting, naive T cells


title: R-16A-2

value: root


title: 20118a037

value: plasma

value: extracellular vesicles


title: HFpEF+SGLT2i_V2565

source_name: Left ventricle

value: Left ventricle


title: HFpEF+SGLT2i_V2574

value: Female


title: Arpp21 KO7

description: Takara SMARTer mouse TCR alpha beta profiling kit


title: HFpEF+SGLT2i_V2564

value: WT


title: Arpp21 KO5


title: R-2N-1


title: HFpEF+SGLT2i_V2563

value: Empagliflozin


title: R-16A-1


title: Arpp21 KO4


title: 20118a035


title: HFpEF+SGLT2i_V2562


title: Arpp21 KO3


title: Brassica rapa seedlings 1 day old, mock treatment 3h, rep1

value: seedling


title: 20118a034


title: 20118a033


title: Arpp21 KO2


title: HFpEF+SGLT2i_V2561


title: Arpp21 KO1


title: HFpEF+TYA-018_V2559


title: 20118a031


title: 20118a036


title: HFpEF+TYA-018_V2570


title: WT7


title: 20118a030


title: HFpEF+TYA-018_V2555


title: 20118a029


title: HFpEF+TYA-018_V2552


title: WT6


title: WT5


title: Dataset 3 Fibroblasts  treated 4

type: RNA

city: Genova

first: Giuseppina

last: Conteduca

state: GE

address: Largo Rosanna Benzi 10

country: Italy

institute: IRCCS Ospedale San Martino

description: Skin fibroblasts were obtained by punch biopsy of the forearm skin.  Cells were maintained, in RPMI-1640 medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone S.p.a, Milan, IT). Cell lines were tested for mycoplasma with the Mycoplasma Detection Kit (Lonza, Basel, CH). In all experiments, cells between passages 2 and 15 were used.

hyb_protocol: Cyanine-3-CTP-labeled cRNA was hybridized onto the SurePrint G3 microarray chips  (Design ID: G4851C), which contained 50,599 probes for 32,776 human mRNA and 17,438 human lncRNAs, which are derived from authoritative databases, including RefSeq, Ensemble, GenBank, and the Broad Institute. After hybridization and washing, processed slides were scanned with the Agilent microarray scanner (Agilent Technologies).

scan_protocol: Raw data were extracted using Feature Extraction (version 12.0.1.1; Agilent Technologies).

data_processing: Data pre-processing including normalization and filters, were carried out by Genespring software (version 14.3; Agilent Technologies). Raw data was normalized by a 75 percentile shift, log2-transformed and shifted to the median of all samples.

source_name: Fibroblasts   treated

label_protocol: The microarray hybridization was performed using Agilent One Color  microarray gene expression kit and SurePrint G3, 8x60K Human Gene Expression V3 array (Agilent Technologies, Santa Clara, California, USA) following established protocols.

extract_protocol: Total RNA was extracted using Trizol reagent (Thermo Fisher Scientific, MA, USA). Total RNA from each sample was quantified by the NanoDrop ND-1000 and RNA integrity was assessed by Agilent 2100 Bioanalyser.

treatment_protocol: The cells were transfected with active siRNA3, as well as with anti-Cy3 siRNA and anti- PPIA and analysed at various time points, namely, 6, 24, and 48, hours post-transfection. Cells treated with the Cy3-specific and anti PPIA  siRNA were used as controls

value: skin sample

value: fibroblasts


title: 20118a028


title: HFpEF+TYA-018_V2551


title: WT4


title: 20118a027


title: HFpEF+TYA-018_V2550


title: WT3


title: 20118a026


title: Dataset 3 Fibroblasts Dataset 3 From control wild type3

source_name: Fibroblasts from Control subject

growth_protocol: Skin fibroblasts were obtained by punch biopsy of the forearm skin.  Cells were maintained, in RPMI-1640 medium (Life Technologies, Grand Island, NY, USA) supplemented with 10% fetal calf serum (FCS), 2 mM L-glutamine, 100 U/ml penicillin, 100 μg/ml streptomycin (Euroclone S.p.a, Milan, IT). Cell lines were tested for mycoplasma with the Mycoplasma Detection Kit (Lonza, Basel, CH). In all experiments, cells between passages 2 and 15 were used.


title: HFpEF+TYA-018_V2549


title: 20118a025


title: Dataset 3 Fibroblasts  treated 2

source_name: Fibroblasts  treated


title: Dataset 3 Fibroblasts  treated 1


title: HFpEF+TYA-018_V2548


title: 20118a023


title: HFpEF+TYA-018_V2547


title: WT1


title: 20118a022


title: T12_KO4

value: Rag1 3'UTR KO


title: Dataset 3 Fibroblasts Dataset 3 From control wild type4


title: 20118a021


title: T11_KO3


title: Dataset 3 Fibroblasts  treated 3


title: HFpEF+TYA-018_V2546


title: 20118a020


title: HFpEF+TYA-018_V2543


title: T10_KO2


title: Dataset 3 Fibroblasts Dataset 3 From control wild type2


title: Dataset 2 Fibroblasts  treated 4

treatment_protocol: The cells were transfected with active siRNA2, as well as with anti-Cy3 siRNA and anti- PPIA and analysed at various time points, namely, 6, 24, and 48, hours post-transfection. Cells treated with the Cy3-specific and anti PPIA  siRNA were used as controls


title: WT2


title: Dataset 2 Fibroblasts Dataset 2 From control wild type4


title: T9_HET5

value: Rag1 3'UTR het


title: HFpEF+Veh_V2532

value: Vehicle


title: Dataset 3 Fibroblasts Dataset 3 From control wild type1


title: Dataset 2 Fibroblasts  treated 3


title: Dataset 2 Fibroblasts Dataset 2 From control wild type3


title: T8_HET4

value: spleen


title: HFpEF+Veh_V2530


title: 20118a018


title: T7_WT3

value: CD4 T cells


title: 20118a017


title: T6_HET3


title: HFpEF+Veh_V2529


title: HFpEF+Veh_V2527


title: HFpEF+Veh_V2528


title: Dataset 2 Fibroblasts  treated 1


title: 20118a014


title: T5_KO1


title: 20118a016


title: 20118a019


title: Dataset 2 Fibroblasts  treated 2


title: T4_HET2


title: HFpEF+Veh_V2523


title: HFpEF+Veh_V2521


title: HFpEF+Veh_V2526


title: 20118a012


title: 20118a013


title: 20118a011


title: T2_WT2


title: T3_HET1


title: non_failing_V2510


title: T1_WT1


title: 20118a010


title: Dataset 1 Fibroblasts  treated 3

treatment_protocol: The cells were transfected with active siRNA1, as well as with anti-Cy3 siRNA and anti- PPIA and analysed at various time points, namely, 6, 24, and 48, hours post-transfection. Cells treated with the Cy3-specific and anti PPIA  siRNA were used as controls


title: non_failing_V2509


title: Dataset 2 Fibroblasts Dataset 2 From control wild type1


title: non_failing_V2508


title: 20118a009


title: Dataset 2 Fibroblasts Dataset 2 From control wild type2


title: Dataset 1 Fibroblasts  treated 4


title: 20118a008


title: Dataset 1 Fibroblasts Dataset 1 From control wild type3


title: Dataset 1 Fibroblasts Dataset 1 From control wild type4


title: Dataset 1 Fibroblasts Dataset 1 From control wild type2


title: Dataset 1 Fibroblasts  treated 1


title: HeLa cells, Cisplatin, rep3

city: Izmir

first: Bünyamin

last: Akgül

state: Urla

address: Gulbahce Campus

department: Molecular Biology and Genetics

country: Turkey

institute: Izmir Institute of Technology

description: 160701_SND393_B_L002_GDU-45, 160701_SND393_B_L003_GDU-45

data_processing:
Adapter removal by Trim Galore!
Mapping to the genome by STAR
Read counting by featureCounts
Differential expression analysis by DESeq2
Genome_build: GRCh38
Supplementary_files_format_and_content: raw_counts, normalized_counts_significant, results_significant_annotated

source_name: HeLa cells

growth_protocol: HeLa cells were routinely cultured in RPMI medium supplemented with 10% FBS and 1 % penicillin-streptomycin

extract_protocol:
Total RNA was extracted by TRIzol Reagent
RNA samples were subjected to DNAse treatment and poly(A) enrichment
Custom Illumina

treatment_protocol: Hela cells were treated with 80 uM cisplatin for 16 h

value: HeLa cells

value: cervix epithelial

tag: passages

value: Cisplatin (80 uM)


title: non_failing_V2507

data_processing:
Adapter trimming by FASTP (ver. 0.23.2)
Read alignment by Salmon (ver. 1.6.0)
tximport to generate gene expression matrix in Transcript Per Million (TPM)
Protein-coding genes identification by Ensembl human reference genome release 100
Exclusion of mitochondrial genes and renormalization to TPM.
Assembly: hg38 v.13
Supplementary files format and content: TXT

extract_protocol:
Approximately 106 cells or 20-30 mg of mouse heart tissue were lysed with TRI Reagent (Zymo Research) and frozen at -80 °C to ensure complete cell lysis. Total RNA was extracted and washed from lysed cells using the Direct-zol-96 RNA Kit (Zymo Research) according to the manufacturer’s instructions. Samples were treated with DNase I for 15 min at room temperature. cDNA was reverse transcribed from approximately 1 μg of RNA through random hexamers using the SuperScript III First-Strand Synthesis System according to the manufacturer’s instructions (Thermo Fisher Scientific). Real-time qPCR reactions were performed using the TaqMan universal PCR master mix (Thermo Fisher Scientific) with the TaqMan probes listed. RT-qPCR reactions were performed using the QuantStudio7 Flex Real-Time PCR systems (Thermo Fisher Scientific). Each reaction was performed in triplicate for a given RT-qPCR run, and each condition had four experimental replicates. Relative expression of the gene of interest was normalized to GAPDH as the housekeeping control using the 2–ΔΔCT method. P values were calculated with Student’s t-tests.
From each replicate, 100 ng total RNA was extracted via the polyA-tail-specific protocol according to Illumina, Inc.. The RNA libraries were prepared using a TruSeq Stranded mRNA kit (Illumina), which also removes ribosomal RNA. The libraries were sequenced as 100 base pair single-end reads using Illumina NovaSeq SP with an average of 29.8 million reads per sample.


title: non_failing_V2504


title: HeLa cells, Cisplatin, rep1

description: 160701_SND393_B_L002_GDU-43, 160701_SND393_B_L003_GDU-43

tag: cell type


title: HeLa cells, Cisplatin, rep2

description: 160701_SND393_B_L002_GDU-44, 160701_SND393_B_L003_GDU-44


title: HeLa cells, Negative control, rep 3

description: 160701_SND393_B_L002_GDU-33, 160701_SND393_B_L003_GDU-33

value: Negative GapmeR (40 nM)


title: HeLa cells, Negative control, rep 2

description: 160701_SND393_B_L002_GDU-32, 160701_SND393_B_L003_GDU-32


title: HH_2.1.2 vs HMHC_3.7

city: Sant Vicent del Raspeig

first: María José

middle: Antonio

last: Bonete

state: Alicante

address: Carretera San Vicente del Raspeig s/n

department: Agroquímica y Bioquímica

institute: Universidad de Alicante

hyb_protocol: Microarrays where hybridized and washed according to manufacturer's protocol

scan_protocol: Scanned on an Agilent G2505C scanner.

data_processing: Images were quantified using Agilent Feature Extraction Software (version 10.7.3.1).

organism: Haloferax mediterranei

label_protocol: Two-Color Microarray-Based Prokaryote Analysis Fair Play III Labeling v. 1.3 (Agilent)

growth_protocol: Hfx. mediterranei strains were grown in different culture media at 42 °C containing 25% (w/v) salt water (25% SW) (Rodriguez-Valera et al., 1983). The pH of all media was adjusted to 7.2-7.4, with NaOH. Hfx. mediterranei cells were grown in a defined medium with 40 mM NH4Cl and 10 g/L glucose supplemented with 0.0005 g/L FeCl3, 0.5 g/L KH2PO4, 100 mM MOPS, and 50 µg/mL uracil until the mid-exponential phase. Subsequently, cells were harvested by centrifugation for 10 min at 13000 g, washed twice with 25% SW, and transferred to a medium without nitrogen or carbon source.

extract_protocol: Total RNA was isolated from these samples by using RNeasy Mini Kit (Qiagen) following product specifications

tag: growth condition

value: nitrogen starvation (120 h)

value: carbon starvation (120 h)


title: N3KO-1year

city: Los Angeles

first: Feiyang

last: Ma

address: 610, Charles Young Dr East, TLSB 3000C

department: Molecular Biology Institute

institute: UCLA

data_processing:
Sequencing was performed on Illumina Novaseq 6000.
For scRNA-seq,  raw reads were aligned to the mouse genome (mm10), and the digital expression matrix was generated using cellranger count.
Assembly: mm10
Supplementary files format and content: Raw count expression matrix for scRNA-seq.

source_name: Brain meninges and associated vasculature

extract_protocol:
Mice were euthanized in a CO2 chamber following institutional guidelines. Following sacrifice, mouse brains were removed from the skull of the sacrificed animals and placed into a dish containing 1X PBS. Using dissecting microscope, the meninges were manually removed from the brain and placed in a 6 well plate containing 1mL of cell dissociation solution containing DNASE I, 1M HEPES,  Liberase TH (1.2mg/mL) in 1X HBSS. A small magnetic stir bar was placed in each well with the dissected meninges and the plate was placed on a stirring plate at 37 degrees for cell dissociation. The samples were removed from the stirring plate and manually mixed with a P1000 pipette once every 5 minutes until a single cell suspension was formed, approximately 20 min per sample. The single cell suspension was neutralized using DMEM + 10% FBS and the suspension was filtered through a 40uM filter and then centrifuged for 5 min at 10,000 x g. Following centrifugation, the cell pellet was resuspended in 0.4% BSA-PBS and assessed for viability prior to library preparation using trypan blue.
Single cell libraries were prepared using 10X Genomics Chromium™ Single Cell 3' Library & Gel Bead Kit v3 as per manufacturer’s protocol. For the generation of single-cell gel beads in emulsion, cells were loaded on to the Chromium single cell instrument (10x Genomics) with an estimated targeted cell recovery of ~5,000 cells.

value: Notch3 Knock-out


title: ASHN_1.4 vs ASHC_3.4

value: HM26-ΔSm1 (deletion mutant)


title: ASHC_1.3 vs HMHC_1.1


title: HMHC_4.7 vs HH_1.1.1


title: HMHC_2.6 vs ASHC_2.1


title: ASHN_3.3 vs HH_3.1.1


title: Dataset 1 Fibroblasts Dataset 1 From control wild type1


title: 20118a004

value: plasma

value: extracellular vesicles


title: 20118a007


title: 20118a003


title: non_failing_V2503

city: South San Francisco

last: Farshidfar

address: 171 Oyster Point Blvd Ste 500

institute: Tenaya Therapeutics Inc.

value: Left ventricle

value: Female

value: WT


title: Dataset 1 Fibroblasts  treated 2

value: skin sample

value: fibroblasts


title: 20118a002


title: non_failing_V2502

value: Vehicle


title: non_failing_V2501


title: Control-1year

value: Brain meninges and associated vasculature

value: Wild type


title: Disease37_ST

city: Philadelphia

first: Jonathan

last: Levinsohn

state: PA

address: 3400 Civic Center Blvd, Smilow 12-188

institute: University of Pennsylvania

description: processed data files include count matrix, metadata and umap files

data_processing:
RNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
RNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
RNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
RNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
RNA-Seq: The output files for 29 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
RNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 50%.
Assembly: RNA-Seq: GRCh38
Supplementary files format and content: scRNA-Seq: EXPORT_scRNAseq_counts.rds: combined count matrix of all 11 samples; EXPORT_snRNAseq_metadata.txt: combined metadata; EXPORT_snRNAseq_umap.txt: UMAP embedding values for identified cell types.
scRNA-Seq: Cell Ranger v. 6.0.1 (http://10xgenomics.com) was used to process Chromium single cell 3’ RNA-seq output.
scRNA-Seq: “cellranger count” aligned the Read2 to the human reference genome (GRCh38).
scRNA-Seq: Aligned reads were used to generate data matrix only when they have valid barcodes and UMI, map to exons (GRCh38)
scRNA-Seq: The data matrix of each sample was corrected in terms of ambient RNA using SoupX.
scRNA-Seq: The output files for 11 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Assembly: scRNA-Seq: Once the gene-cell data matrix was generated, poor quality cells were excluded, such as cells with <200 genes detected or with >3,000 unique expressed genes (as they are potentially cell doublets). Cells were also discarded if their mitochondrial gene percentages were over 15%.
Supplementary files format and content: scRNA-Seq: GRCh38
ATAC-Seq: Cell Ranger ATAC v. 2.0.0 (http://10xgenomics.com) was used to process Chromium single cell ATAC-seq output.
ATAC-Seq: The poor quality cells were removed from the matrix using the following criteria: peak_region_fragments < 3000 & peak_region_fragments > 20000 & pct_reads_in_peaks < 15 & nucleosome_signal > 4 & TSS.enrichment > 2
ATAC-Seq: The output files for 20 samples were aggregated into one matrix using Signac v. 1.3.0.
Assembly: ATAC-Seq: GRCh38
Spatial Transcriptomics: Space Ranger v1.0.0 (http://10xgenomics.com) was used to process Human FFPE Visium output
Spatial Transcriptomics: “spaceranger count” aligned thedata to the human reference genome (GRCh38) by using the human probe dataset (Visium_Human_Transcriptome_Probe_Set_v1.0_GRCh38) and data mapped to the H & E stained image.
Spatial Transcriptomics: Aligned data was loaded to Seurat object (Seurat . 4.0.1) and normalized by using SCT.
Spatial Transcriptomics: The objects of 7 samples were aggregated into one gene-cell matrix using Seurat v. 4.0.1.
Spatial Transcriptomics: The samples were merged together, using “merge” function of Seurat.  Next, the data was subjected to principle component analysis (PCA) for linear dimension reduction and Harmony was used to integrate the datasets.
Assembly: Spatial Transcriptomics: GRCh38
Supplementary files format and content: EXPORT_ST_counts.rds: combined count matrix of all 7 samples; EXPORT_ST_metadata.txt: combined metadata; EXPORT_ST_umap.txt: UMAP embedding values for identified cell types.

source_name: FFPE kidney tissue

extract_protocol:
RNA-Seq: 10X Genomics Chromium Prep (10X Genomics, PN-1000120). Barcoding and cDNA synthesis were performed according to the manufacturer's instructions.
RNA-Seq: The cDNA libraries were constructed using the Chromium Next GEM Single Cell 3′ GEM Kit v3.1 (10X Genomics, PN-1000121) according to the manufacturer’s original protocol.
ATAC-Seq: Chromium Single Cell ATAC Library & Gel Bead Kit (10X Genomics, PN-1000110). Transposing and barcoding were performed according to the manufacturer's instructions.
ATAC-Seq: The libraries were constructed using the Chromium Single Cell ATAC Library & Gel Bead Kit and Chromium i7 Multiplex Kit N (10X Genomics, PN-1000084) according to the manufacturer’s original protocol.
Spatial Transcriptomics: 5 µm tissue samples was cut and onto the Visium Spatial gene Expression Slide. After deparaffinization, H & E staining was performed. Keyence 1266 BZ-X810 microscope was used for whole slide imaging.
Spatial Transcriptomics: After scanning, de-crosslinking, probe hybridization, probe release and extension, library preparation was performed by single Index Kit TS Set A (10X Genomics, PN-3000511) according to the manufacturer’s protocol.

tag: disease

value: DKD

value: adult kidney

tag: age

tag: gender


title: 20118a005


title: HeLa cells, Negative control, rep 1

description: 160701_SND393_B_L002_GDU-31, 160701_SND393_B_L003_GDU-31

tag: cell line

value: HeLa cells

value: cervix epithelial

value: Negative GapmeR (40 nM)


title: 20118a001


title: Disease36_ST

value: HKD


title: C-β-LG/DSF2 [C3]

city: Shenzhen

first: Hongmei

last: Liu

address: No. 1088, Xueyuan Avenue

department: Department of Biomedical Engineering

institute: Southern University of Science and Technology

description:
C3_FPKM
Data processed.xlsx

data_processing:
HISAT2 version 2.1.0 used to alignment
cufflinks v2.2.1 used to quantification
Assembly: GENCODEm16
Supplementary files format and content: Data processed.xlsx

source_name: Areas of brain injury

extract_protocol:
Total RNA was isolated with Trizol Reagent (Invitrogen) according to the manufacturer’s protocol.
Illumina Stranded Total RNA Prep

value: Areas of brain injury

tag: group

value: C-beta-LG/DSF


title: C-β-LG/DSF3 [C5]

description:
C5_FPKM
Data processed.xlsx


title: ASHC_4.2 vs ASHN_2.11

value: carbon starvation (120 h)

value: HM26-ΔSm1 (deletion mutant)

value: nitrogen starvation (120 h)


title: 66_OC43_30hpi_CHX_rep3

city: Edinburgh

first: Stefan

last: Bresson

state: Scotland

address: Max Born Crescent, Swann 5.1

department: Wellcome Trust Centre for Cell Biology

country: United Kingdom

institute: University of Edinburgh

data_processing:
Removal of non-templates bases: flexbar -r file.fastq -a polyA.fasta -ao 4 -x 3 -m 1 -ae RIGHT -u 2 -f i1.8 -t file_filtered.fastq (where polyA.fasta is a single-entry fasta file with the sequence AAAAAAAAAA
Reads were aligned to a contacenated human (ENSEMBL hg38-101) and viral (ATCC_VR_1558) genome: STAR --genomeDir human_OC43_full_index --genomeLoad LoadAndRemove --readFilesIn file_R1.fastq file_R2.fastq
SAM to BAM: samtools view -bS file.sam
BAM sorting: samtools sort file.bam
BAM indexing: samtools index -b file.bam
Coverage map (+strand). Command: bamCoverage -b file.bam --binSize 1 --ignoreForNormalization 1 21 22 HCoV_OC43 --exactScaling --filterRNAstrand forward --normalizeUsing CPM
Coverage map (-strand). Command: bamCoverage -b file.bam --binSize 1 --ignoreForNormalization 1 21 22 HCoV_OC43 --exactScaling --filterRNAstrand reverse --normalizeUsing CPM
Assembly: ENSEMBL hg38-101 and ATCC_VR_1558
Supplementary files format and content: Ribosome footprint coverage maps across the human and OC43 genomes
Library strategy: Ribo-seq

source_name: human cells infected with HCoV-OC43

growth_protocol: MRC5 cells were grown on 15 cm plates at 33°C and infected with either HCoV-OC43 at a MOI of 7. As a control, cells were alternatively infected with heat-inactivated OC43.

extract_protocol:
The cells were then resuspended in 1mL of lysis buffer (10 mM Tris 7.5, 5 mM MgCl2, 100 mM KCl, 1% tritonX-100, 2 mM DTT, protease inhibitors (1 tablet / 10 mL), and 0.1 mg/mL CHX), and lysed by gently passing through a 25G syringe four times and incubating on ice for ~5 min. Subsequently, the cell lysates were cleared by centrifugation at 1300g/10 min/4°C and frozen at -80°C for later use. Subsequently, 80 µg of RNA was digested with 5 U of RNase I for 45 min at 25°C. Ribosomal complexes were separated by ultracentrifugation at 38000 RPM for 2hr at 4°C in a 14 mL 10-50% sucrose gradient. The sucrose gradients were separated into 200 µL fractions, and those corresponding to the monosome peak were combined, and Tri Reagent was used to extract RNA. The resulting RNA was resolved on a 15% TBE-urea gel and 26-34nt footprints were excised, purified, and concentrated.
The resulting RNA footprints were treated T4 PNK to generate 5′ and 3′ ends amenable to linker ligation. The resulting RNA was used as input for the SMARTer smRNA-Seq Kit for Illumina. cDNA libraries were prepared according to the manufacturer’s protocol, except an rRNA depletion step using biotinylated oligos was incorporated after the reverse transcriptase reaction.

treatment_protocol: Culture medium was removed, and cells were washed with ice-cold PBS supplemented with 0.1 mg/mL cycloheximide. For harringtonine-based profiling, the cells were first pretreated with 8 µg/mL harringtonine for 10 min.

value: wild type

tag: infection

tag: timepoint (hr)

tag: translation inhibitor

value: 0.1 mg/mL cycloheximide in lysis buffer

tag: fraction

value: ribosome protected fragments


title: C-β-LG/DSF1 [C2]

description:
C2_FPKM
Data processed.xlsx

tag: tissue


title: 64_OC43_18hpi_CHX_rep3


title: TBI3 [T4]

description:
T4_FPKM
Data processed.xlsx

value: TBI


title: Disease35_ST

value: Male


title: N3KO-Young

data_processing:
Sequencing was performed on Illumina Novaseq 6000.
For scRNA-seq,  raw reads were aligned to the mouse genome (mm10), and the digital expression matrix was generated using cellranger count.
Assembly: mm10
Supplementary files format and content: raw count expression matrix for scRNA-seq

source_name: Brain Meninges

tag: strain background

value: Notch3 knock out

value: Brain meninges and associated vasculature


title: N3KO-Old

tag: genotype

value: Wild type


title: visium_sham_male

city: St. Louis

first: Haojia

last: Wu

state: Missouri

address: 600 S Euclid Ave

department: Renal Division/Internal Medicine

institute: Washington University in St. Louis

description: 10X Visium

data_processing:
Visium data processing: Sequencing was performed on a NovaSeq S4, targeting 125 million reads using dual indexing. Resulting FASTQ files were aligned to mm10 reference, manually aligned to respective hematoxylin and eosin stained images. The counts were normalized using 10× Genomics Space Ranger (spatial 3′ v1; spaceranger-1.2.1). The gene-by-count matrix was input to CellScopes.jl for downstream analysis.
Cell segmentation: Cell segmentation was performed using Baysor https://github.com/kharchenkolab/Baysor.
Assembly: mm10
Library strategy: spatial transcriptomics

extract_protocol: 10X Visium protocol: After removing the renal capsule, the kidneys were bisected in a coronal manner to prepare for 10x Genomics Visium sample preparation. To preserve the high quality of RNA for processing, the fresh tissue was immersed in a bath of 2-methylbutane equilibrated with liquid nitrogen. The tissue samples were then stored at -80°C prior to embedding them in optimal cutting temperature compound (OCT). The remaining kidney tissue was fixed overnight in 10% formalin at room temperature, before being transferred to 70% ethanol for storage at 4°C. The tissue was subsequently embedded in paraffin by the Washington University Musculoskeletal Research Center Core. Frozen kidney samples were embedded in cryomolds using OCT on dry ice. The blocks were then stored at -80°C. For preparation of Visium, the blocks were equilibrated to -18°C, and 10 μm sections were mounted onto the active sequencing areas of the 10× Genomics Visium slides. The slides were stored in airtight containers at -80°C until used for spatial library generation. Hemotoxylin and eosin staining were performed according to the 10× Genomics Visium protocol. Visium libraries were prepared according to 10× Genomics Visium manufacturer’s instructions (PN-1000185, Lot No. 155614, Rev D).

tag: Sex

value: male

tag: surgery

value: sham

value: Kidney


title: 62_OC43_6hpi_HAR_rep3

value: 8 µg/mL harringtonine for 10 min, then 0.1 mg/mL cycloheximide in lysis buffer


title: TBI2 [T2]

description:
T2_FPKM
Data processed.xlsx

value: Areas of brain injury


title: CTRL-Old


title: Disease34_ST

value: DKD

value: adult kidney

value: Female


title: Disease33_ST

value: HKD


title: Sham2 [S4]

description:
S4_FPKM
Data processed.xlsx

source_name: Brain tissue

value: Brain tissue

value: Sham


title: Sham3 [S5]

description:
S5_FPKM
Data processed.xlsx


title: 61_OC43_6hpi_CHX_rep3

value: wild type

value: 0.1 mg/mL cycloheximide in lysis buffer

value: ribosome protected fragments


title: 60_OC43_3hpi_CHX_rep3


title: HH_3.1.2 vs ASHN_4.8

value: nitrogen starvation (120 h)

tag: strain


title: TBI1 [T1]

description:
T1_FPKM
Data processed.xlsx

value: TBI


title: 63_OC43_12hpi_CHX_rep3


title: 65_OC43_24hpi_CHX_rep3


title: Control34_snATACseq

source_name: whole kidney tissue

value: Control


title: CTRL-Young

value: Notch3 knock out

value: Brain meninges and associated vasculature


title: Sham1 [S3]

description:
S3_FPKM
Data processed.xlsx


title: Control36_ST

value: Male


title: Control33_snATACseq


title: 58_OC43_30hpi_CHX_rep2


title: Control35_ST


title: Control32_snATACseq


title: Esophageal squamous cell carcinoma_Normal tissue adjacent to cancer_rep3

city: Urumqi

first: Qingchao

state: Xinshi District

address: 137 Liyushan South Road

institute: The First Affiliated Hospital of Xinjiang Medical University

description: Gene expression after esophageal squamous cell carcinoma normal tissue adjacent to cancer

hyb_protocol: 1.5 ug of Cy3-labelled cRNA (specific activity >10.0 pmol Cy3/ug cRNA) was fragmented at 60°C for 30 minutes in a reaction volume of 250 ml containing 1x Agilent fragmentation buffer and 2x Agilent blocking agent following the manufacturers instructions. On completion of the fragmentation reaction, 250 ml of 2x Agilent hybridization buffer was added to the fragmentation mixture and hybridized to Agilent Whole Human Genome Oligo Microarrays (G4112A) for 17 hours at 65Â°C in a rotating Agilent hybridization oven.  After hybridization, microarrays were washed 1 minute at room temperature with GE Wash Buffer 1 (Agilent) and 1 minute with 37Â°C GE Wash buffer 2 (Agilent), then dried immediately by brief centrifugation.

scan_protocol: The labeled cRNA was hybridized to the chip, eluted and scanned with Agilent Scanner G2505C(Agilent Technologies) to obtain the original image.

data_processing:
Feature Extraction software (version10.7.1.1, Agilent Technologies) was used to process the original image and extract the original data.Then Genespring software (version13.1, Agilent Technologies) was used for quantile standardization and subsequent processing.
The normalized data were filtered so that at least one set of probes 100% labeled as Detected from each set of samples used for comparison was left for subsequent analysis.

source_name: Esophageal squamous cell carcinoma,Normal tissue adjacent to cancer,replicate3

label_protocol: Cyanine-3 (Cy3) labeled cRNA was prepared from 0.5 ug RNA using the One-Color Low RNA Input Linear Amplification PLUS kit (Agilent) according to the manufacturer's instructions, followed by RNAeasy column purification (QIAGEN, Valencia, CA).  Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.

extract_protocol: RNA was prepared using the lysis/binding buffer（1mL lysis/binding buffer/0.1g tissue）following the manufacturer's recommendations.  RNA was quantified using a NanoDrop-1000 spectrophotometer and quality was monitored with the Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA).

treatment_protocol: The tissue is between 0.5 and 250mg, and the tissue removed from the living body should be rapidly cooled by immersion in liquid nitrogen within 15 minutes, and liquid nitrogen is transported. Smaller tissues are best preserved with RNA later and transported on dry ice.

value: Normal tissue adjacent to cancer

value: male


title: 57_OC43_24hpi_CHX_rep2


title: Esophageal squamous cell carcinoma_Normal tissue adjacent to cancer_rep2

source_name: Esophageal squamous cell carcinoma,Normal tissue adjacent to cancer,licaterep2

value: female


title: Control31_snATACseq

value: adult kidney


title: Esophageal squamous cell carcinoma_Normal tissue adjacent to cancer_rep1

source_name: Esophageal squamous cell carcinoma,Normal tissue adjacent to cancer,replicate1


title: 56_OC43_18hpi_CHX_rep2


title: 59_uninfected_CHX_rep3

source_name: human cells


title: Disease32_snATACseq


title: Esophageal squamous cell carcinoma_tumor tissue_rep2

description: Gene expression after esophageal squamous cell carcinoma tumor tissue

source_name: Esophageal squamous cell carcinoma,tumor tissue,replicate2

value: tumor tissue


title: Esophageal squamous cell carcinoma_tumor tissue_rep3

source_name: Esophageal squamous cell carcinoma,tumor tissue,replicate3


title: Disease31_snATACseq

value: HKD


title: Control30_snATACseq

value: Female


title: 54_OC43_6hpi_HAR_rep2

value: 8 µg/mL harringtonine for 10 min, then 0.1 mg/mL cycloheximide in lysis buffer


title: 55_OC43_12hpi_CHX_rep2

value: wild type


title: 53_OC43_6hpi_CHX_rep2

value: 0.1 mg/mL cycloheximide in lysis buffer


title: Control29_snATACseq


title: 52_OC43_3hpi_CHX_rep2

value: ribosome protected fragments


title: R-2A ROR2 KD day21, biological rep3

city: Kawasaki City

first: Takuya

last: Kuroda

state: Kanagawa

address: 3-25-26 Tonomachi, Kawasaki Ward,

institute: National Institute of Health Sciences

hyb_protocol: Hybridization was performed in a Gene Chip Hybridization Oven 645 for 16 h at 45 °C.

scan_protocol: Gene chips were scanned using the GeneChip Scanner 3000.

data_processing: Array-Quality Control was done using the Transcriptome Analysis Console (TAC) Software (version 4.0.3.14). Gene expression intensities were normalized and summarized with SST robust multiarray average algorithm (Affymetrix): SST-RMA.

label: Biotin

source_name: Human induced pluripotent stem cell

label_protocol: Labeling extracted total RNA was performed using the Gene ChipTM WT PLUS Reagent Kit (Thermo Fisher Scientific) according to manufacturer’s instructions.

growth_protocol: Undifferentiated hiPSCs were maintained on iMatrix-511 in StemFit AK02 medium.

extract_protocol: Total RNA was extracted from the hiPSC-derived NPC cells using RNeasy Mini Kit (QIAGEN), according to the manufacturer instructions.

treatment_protocol: HiPSCs were differentiated into NPCs by using the STEMdiff SMADi Neural Induction Kit (Stem Cell Technologies), according to the manufacturer instructions. The cells were passaged every 7 days until day 21 post-differentiation.

tag: cell type

value: Human induced pluripotent stem cell

tag: treatment

value: hiPSC-derived neural progenitor cell day21


title: R-2A ROR2 KD day21, biological rep2


title: R-2A ROR2 KD day21, biological rep1


title: Control27_snATACseq

tag: disease

value: Control


title: Control26_snATACseq

tag: age


title: 50_uninfected_CHX_rep2


title: Control25_snATACseq

tag: gender


title: Esophageal squamous cell carcinoma_tumor tissue_rep1

source_name: Esophageal squamous cell carcinoma,tumor tissue,replicate1


title: Disease30_snATACseq

value: DKD


title: Disease29_snATACseq


title: R-2A ROR2 KD day7, biological rep2

tag: cell line

value: hiPSC-derived neural progenitor cell day7


title: R-2A ROR2 KD day14, biological rep3

value: hiPSC-derived neural progenitor cell day14


title: 47_OC43_18hpi_CHX_rep1


title: C42B miR-410

city: Augusta

first: Sang Ho

last: Kwon

state: Georgia

address: 1120 15th Street

department: Cellular Biology and Anatomy

institute: Augusta Univeristy

description: Gene expression data from C42B cell line stably transfected with miR-410

hyb_protocol: Labeled samples were hybridized to the Clariom S Human array (Applied Biosystems) for 16 hours. The arrays were washed and stained using Affymetrix GeneChip Fluidics Station 450 systems.

scan_protocol: The stained arrays were scanned on Affymetrix GeneChip Scanner 3000.

data_processing: Data was obtained in CEL file and imported into Partek Genomic Suites version 6.6 (Partek) using the standard imprt tool with an RMA normalization. The differential expressions were calculated using ANOVA of Partek package and filtered with a p-value cut-off of 0.05.

source_name: Prostate cancer cell line, C42B

label_protocol: RNA was used to generate cDNAs and cDNAs were biotin-labeled according to the GeneCHip WT Plus reagent kit protocol.

growth_protocol: Cell lines stably expressing miR-CON/miR-410 were grown in RPMI media with 1 microgram/ml puromycin till logarithmic phase.

extract_protocol: RNA were extracted using miRNAeasy minikit (Qiagen) according to manufacturer's instructions.

treatment_protocol: miRNA vector (pMIR) with CMV promoter-driven expression of human pre-miRNA hsa-miR-410-GFP reporter and the corresponding scrambled construct were stably transfected into PC3 and C42B cell lines followed by puromycin selection.

value: Prostate cancer cell line

value: stably transfected with miR-410


title: R-2A ROR2 KD day14, biological rep1


title: 48_OC43_24hpi_CHX_rep1


title: R-2A ROR2 KD day7, biological rep3


title: Disease28_snATACseq

value: Male


title: R-2A ROR2 KD day14, biological rep2


title: 46_OC43_12hpi_CHX_rep1


title: C42B miR-CON

description: Gene expression data from C42B cell line stably transfected with miR-CON

value: stably transfected with miR-CON


title: Disease27_snATACseq

value: adult kidney


title: PC3 miR-410

description: Gene expression data from PC3 cell line stably transfected with control microRNA

source_name: Prostate cancer cell line, PC3


title: R-2A ROR2 KD day7, biological rep1


title: CD34 treated with  0.5 mM of Denatonium  biological rep2

city: Bologna

first: Maria Antonella

last: Laginestra

address: Via di Barbiano 1/10

department: Experimental Oncology Laboratory

institute: IRCCS Istituto Ortopedico Rizzoli, Bologna, Italy

description: Gene expression data from umbilical cord blood (UCB)-derived CD34+ cells after denatonium benzoate treatment

hyb_protocol: The cDNA fragments were hybridized on cartridge array using the GeneChipTM Hybridization Oven 645 set ON at 60 rpm and 45°C.

scan_protocol: The microarrays were finally scanned on a GeneChipTM Scanner 3000 System (Affymetrix).The fluorescent signals relative to hybridized probes were obtained as DAT files and were converted into CEL digital signal by Affymetrix GeneChip Command Console (AGCC) software

data_processing: CEL files' raw data were normalized using Robust Multi-array Average normalization (RMA) and  log-transformed using Oligo R package.Normalized data were  annotated by pd.clariom.s.human

source_name: umbilical cord blood derived CD34+ cells

label_protocol: The fragmented cDNA is labeled by terminal deoxynucleotidyl transferase (TdT), according to the manufacturer’s instructions

growth_protocol: UCB-derived CD34+ cells were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% Penicillin/Streptomycin (Pen/Strep) (MP Biomedicals), 1% Hepes buffer , SCF (50 ng/ml), IL-3 (50 ng/ml), GM-CSF (10 ng/ml)  and maintained at 37°C in a humidified 5% CO2 incubator, with or without increasing doses of Denatonium Benzoate (DEN)

extract_protocol: Total RNA was isolated using a Rneasy Micro kit,according to the manufacturer’s instructions

treatment_protocol: Denatonium Benzoate (DEN) treatment

value: 0.5 mM of Denatonium


title: PC3 miR-CON

description: Gene expression data from PC3 cell line stably transfected with miR-410


title: R-2A ROR2 KD day0, biological rep3

value: Undifferentiated state


title: CD34 treated with  0 mM of Denatonium  biological rep1

description: Gene expression data from umbilical cord blood (UCB)-derived CD34+ cells

value: control


title: CD34 treated with  0 mM of Denatonium  biological rep2

value: umbilical cord blood (UCB)-derived CD34+ cells


title: 51_uninfected_HAR_rep2

value: wild type

value: 8 µg/mL harringtonine for 10 min, then 0.1 mg/mL cycloheximide in lysis buffer


title: R-2A ROR2 KD day0, biological rep1

value: Human induced pluripotent stem cell


title: 44_OC43_3hpi_CHX_rep1

value: 0.1 mg/mL cycloheximide in lysis buffer

value: ribosome protected fragments


title: Disease25_snATACseq

value: HKD


title: ATE_B_II

city: Plymouth, Devon

first: vengamanaidu

last: modepalli

address: The Laboratory,Citadel Hill

department: Cell and Molecular

institute: Marine Biological Association of the UK

data_processing:
The De-multiplexing fastQ  files were filtering high-quality sequencing reads, and the adapter contamination was removed using fastp an ultra-fast all-in-one FASTQ preprocessor
The quality of the reads was verified using FastQC
Processed reads from each sample were mapped to the respective genome and gene models (indexed bowtie2) by using STAR
The number of reads mapping to the respective gene model were extracted from STAR output using the featureCounts tool
Assembly: Nematostella vectensis (ASM20922v1); Aurelia aurita (GCA_004194395.1);  Acropora tenuis  ( GCA_014633955.1); Acropora millepora (GCF_013753865.1)
Supplementary files format and content: Tab-delimited text files include read counts

organism: Acropora tenuis

source_name: larval body tissue

growth_protocol: Nematostella: Polyps were grown in 16 ‰ artificial seawater at 18°C in the dark and fed with freshly hatched Artemia nauplii. Aurelia aurita: Ephyras were collected using a plankton net in the vicinity of Plymouth Sound, UK and cultured in seawater at 18°C in a 12:12 light and dark cycle. The jellyfish were fed twice a day with freshly hatched Artemia nauplii. Acropora millepora and Acropora tenuis: The corals were cultured in ex-situ. During the annual spawning, the embryos were collected after fertilisation. The larvae are maintained in artificial seawater and collected for experimentation at the planula stage.

extract_protocol:
For RNA isolation, due to the sheer size, samples collected from multiple batches were combined to acquire an adequate amount of RNA for sequencing. Total RNA was isolated using the TRI Reagent® according to the manufacturer’s protocol. RNA quality was assessed using Agilent RNA 6000 Nano Kit on Agilent 2100 Bioanalyzer (Agilent, USA), and samples with RNA integrity number ≥ 8.0 were used for sequencing.
The CORALL RNA-Seq Library Prep Kit (Lexogen GmbH) was used for library preparation. Before sequencing, the libraries were pre-assessed by Agilent High Sensitivity DNA Kit (Agilent, USA) and quantified using Qubit™ 1X dsDNA HS Assay Kit (Invitrogen™).
The sequencing was outsourced (GENEWIZ Illumina NovaSeq™ 2x150 bp sequencing), generating 15 million paired-end reads per replicate.

treatment_protocol: To separate the apical region from the rest of the larval body, we performed microdissection on Nematostella, Aurelia aurita, Acropora millepora and Acropora tenuis larvae as described in our previous study in Nematostella. Apical tissue containing the apical organ was isolated using 34 gauge needles under a stereomicroscope with 10X magnification. Motile larvae were placed into a fresh plastic Petri dish filled with Nematostella medium or filtered seawater. The larvae tend to adhere briefly to the bottom of a new plastic Petri dish, allowing enough time to separate the apical tissue by cutting. Each sample was pooled from a minimum of 100 individual larvae. For each planula prior to dissection, the frontal region is identified by means of the direction of larvae swimming. The samples were carefully collected using glass Pasteur pipettes, the excess medium was removed, and the samples were snap-frozen in liquid nitrogen and stored at -80°C until further processing.

value: larval body tissue

tag: developmental stage

value: planula

value: wild type (WT)


title: 45_OC43_6hpi_CHX_rep1

tag: infection


title: ATE_AO_II

source_name: larval aboral tissue

value: larval aboral tissue


title: Disease24_snATACseq

value: Male


title: ATE_B_I


title: 43_uninfected_HAR_rep1

tag: timepoint (hr)


title: 42_uninfected_CHX_rep1

tag: translation inhibitor


title: Control24_snATACseq

value: Control


title: R-2A sh-C day21, biological rep2

value: shControl

value: hiPSC-derived neural progenitor cell day21


title: Disease23_snRNAseq

value: DKD

value: adult kidney


title: ATE_AO_I


title: R-2A sh-C day21, biological rep1


title: 40_OC43_HI_18hpi_rep2

data_processing:
Reads were aligned to a contacenated human (ENSEMBL hg38-101) and viral (ATCC_VR_1558) genome: STAR --genomeDir human_OC43_full_index --genomeLoad LoadAndRemove --readFilesIn file_R1.fastq file_R2.fastq
SAM to BAM: samtools view -bS file.sam
BAM sorting: samtools sort file.bam
BAM indexing: samtools index -b file.bam
Coverage map (+strand). Command: bamCoverage -b file.bam --binSize 1 --ignoreForNormalization HCoV_OC43 --exactScaling --filterRNAstrand forward --normalizeUsing CPM
Coverage map (-strand). Command: bamCoverage -b file.bam --binSize 1 --ignoreForNormalization HCoV_OC43 --exactScaling --filterRNAstrand reverse --normalizeUsing CPM
Assembly: ENSEMBL hg38-101 and ATCC_VR_1558
Supplementary files format and content: RNA coverage maps across the human and OC43 genomes

source_name: human cells infected with heat-inactivated HCoV-OC43

growth_protocol: MRC5 cells were grown on 6-well plates at 33°C and infected with either HCoV-OC43 at a MOI of 7. As a control, cells were alternatively infected with heat-inactivated OC43.

extract_protocol:
Cells were harvested using 1mL Tri Reagent, and RNA was extracted according to the manufacturer's protocol.
Following RNA extraction, 3µg of RNA was treated with Turbo DNase. The resulting RNA was ribodepleted using the NEBNext rRNA Depletion Kit. Libraries were prepared using the NEBNext rRNA Depletion Kit for Human/Mouse/Rat .

value: heat-inactivated HCoV-OC43

tag: fraction

value: ribodepleted RNA


title: 41_OC43_6hpi_CHX_rep0

source_name: human cells infected with HCoV-OC43

value: wild type


title: Disease22_snRNAseq

tag: tissue


title: 39_OC43_HI_6hpi_rep2


title: Disease26_snATACseq


title: 38_OC43_HI_3hpi_rep2


title: R-2A sh-C day14, biological rep2

value: Human induced pluripotent stem cell

value: hiPSC-derived neural progenitor cell day14


title: R-2A ROR2 KD day0, biological rep2

value: Undifferentiated state


title: Larvae-1,scRNAseq

city: Hefei

first: Ziguang

last: Wang

state: Anhui

address: Changjiang West Road

department: School of Plant Protection

institute: Anhui Agricultural University

description: 10x Genomics

data_processing:
Raw reads were aligned against the S. marcescens FY genome and counted by StarSolo. Sequencing data was further analyzed using the Scanpy software.
We initially reduced dimensionality of the dataset using principal components analysis (PCA), retaining 20 principal components.
Subsequent steps, like low-dimensional UMAP visualization and cell clustering via Leiden algorithm, were based on the initial PCA.
Finally, Wilcoxon rank sum was used to analyze the difference between different cluster cells.
Assembly: S. marcescens FY genome
Supplementary files format and content: tsv files include gene counts for each Sample

organism: Serratia marcescens

source_name: Serratia marcescens FY

extract_protocol:
Up to half a million S. marcescens cells were collected by centrifuging at 4000 rpm for 5 min at 4℃.The supernatant was removed and cell pellets were resuspended in 2 mL ice-cold 4% formaldehyde (Sigma, 47608) and incubated with shaking overnight at 4℃. The fixative was removed by centrifuging at 4000 rpm for 5 min at 4℃ and cells were washed twice by 1 mL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.1 U/mL Murine RNase inhibitor (Vazyme, R 301)). The supernatant was removed and cells were resuspended in 200 μL PBS-TRI (1x PBS supplemented with 0.1% Tween-20 and 0.2 U/mL Murine RNase inhibitor (Vazyme, R 301)).
The cell suspensions were counted with a Moxi cell counter (ORFLO Technologies, Ketchum, Idaho) and diluted according to the manufacturer’s instructions to obtain 2000-4000 single-cell per sample. Random primers were added to amplify the full length of RNA, and the resulting cDNA fragment was added with adaptor. The microbeads with cell barcode, UMI, and the cDNA fragments linked to the adaptor were combined with the mixture of enzymes and extended in the microfluidic system to obtain the labeled cDNA chain. The beads were lysed and the cDNA was used as a template for PCR amplification. All products were pooled to construct a standard sequencing library.

value: Serratia marcescens FY

value: WT

value: bacteria and larvae were co-cultured for 24 h


title: R-2A sh-C day21, biological rep3


title: R-2A sh-C day14, biological rep3


title: Disease19_snRNAseq

source_name: whole kidney tissue

value: Female


title: 37_OC43_30hpi_rep4


title: Force-2,scRNAseq

description: 10x Genomics

value: 24h physicalforce


title: R-2A sh-C day14, biological rep1


title: R-2A sh-C day7, biological rep3

value: hiPSC-derived neural progenitor cell day7


title: Force-1,scRNAseq

description: 10x Genomics


title: R-2A sh-C day7, biological rep2


title: NVE_B_II

organism: Nematostella vectensis

value: larval body tissue

value: planula

value: wild type (WT)


title: Control23_scRNAseq

value: Control

value: Male


title: Disease20_snRNAseq

value: HKD

value: adult kidney


title: 36_OC43_24hpi_rep4

value: wild type

value: ribodepleted RNA


title: Control-2,scRNAseq

description: 10x Genomics

value: 24h single cultivation


title: NVE_AO_II

value: larval aboral tissue


title: Larvae-2,scRNAseq

description: 10x Genomics

value: Serratia marcescens FY


title: 35_OC43_18hpi_rep4


title: Control22_scRNAseq


title: Control-1,scRNAseq

description: 10x Genomics

value: WT


title: R-2A sh-C day7, biological rep1

value: Human induced pluripotent stem cell

value: shControl


title: R-2A sh-C day0, biological rep3

value: Undifferentiated state


title: Control21_scRNAseq

value: Female


title: 34_OC43_12hpi_rep4


title: Control20_scRNAseq


title: NVE_B_I

value: larval body tissue


title: R-2A sh-C day0, biological rep2


title: 12S-1,scRNAseq

description: 10x Genomics

value: 12h single cultivation


title: 49_OC43_30hpi_CHX_rep1

value: 0.1 mg/mL cycloheximide in lysis buffer

value: ribosome protected fragments


title: rpb1-84 rrp6∆ rep2

city: Jaen

first: Ana I.

last: Garrido-Godino

address: Paraje Las Lagunillas s/n

institute: University of Jaen

data_processing:
Input DNAs were sequenced in an Illumina HiSeq 2000 instrument+B40:H46
The quality metrics of the Fastq sequencing datasets were obtained with FastQC and inspected visually
Sequencing adapters were removed from raw reads with Fastx Clipper
The resulting high-quality sequences were mapped to the S. cerevisiae S288c genome (SGD R64) with Hisat2
Resulting BAM,  were analyzedusing featurecounts and DEseq2 in Galaxy
Assembly: R64-1-1
Supplementary files format and content: .txt count files

organism: Saccharomyces cerevisiae

growth_protocol: Two independent biological replicates of each Saccharomyces cerevisiae strain were cultured in YPD liquid medium at 30ºC  until OD600 of about 0.8.

extract_protocol:
RNA extraction was performed with the Rneasy Mini Kit (Quiagen) according to the manufacture’s indications.
Sequencing cDNA libraries were performed using the QuantSeq 3' mRNA-Seq Library Prep Kit form Illumina following the manufacturer instructions; as above, they were sequenced in an Illumina HiSeq 2000 instruments.

value: MAT{alpha} his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220-84 (2mm LEU rpb1-84) rrp6{delta}::KanMX4


title: NVE_AO_I

value: planula

value: wild type (WT)


title: Disease17_snRNAseq

value: HKD

value: adult kidney


title: Control19_scRNAseq

value: Control

value: Male


title: 33_OC43_9hpi_rep4

value: wild type

value: ribodepleted RNA


title: rpb4∆ rep1

description: This sample was analysed used a wt previosly publised: GSM3772984 and GSM3772985

value: MATa his3-{delta}1 leu2-{delta}0 met15-{delta}0 ura3-{delta}0 rpb4 {delta}::kanMX4


title: 12H-2,scRNAseq

description: 10x Genomics

value: Serratia marcescens FY

value: WT

value: heat-shock after 12h single cultivation


title: Control18_scRNAseq


title: 12H-1,scRNAseq

description: 10x Genomics


title: rpb4∆ rep2


title: Larvae5

data_processing:
For annotation, the genome of S. marcescens FY was used as reference.
The significant differentially expressed genes were determined in different groups using the DESeq software, with the standards of P-value ≤0.05, and fold change |log2FC| ≥1.2.
KEGG B class database was used to classify the genes with significantly differential expression based on their functions using the tool Omicshare.
Assembly: Genbank: CP053378.1
Supplementary files format and content: txt files include gene count values for each Sample

extract_protocol:
RNA was harvested using Bacteria RNA Extraction Kit (Vazyme). 1 ug of total RNA was used for the construction of sequencing libraries.
With Ribo-off rRNA Depletion Kit (Vazyme), the total bacterial RNA was subjected to rRNA removing to obtain mRNA.And then RNA libraries for RNA-seq were prepared using VAHTS Universal V8 RNA-seq Library Prep Kit for Illumina (Vazyme) following manufacturer's protocols.

value: bacteria and larvae were co-cultured

tag: replicate

value: replicate=larvae group biological replicate 5


title: R-2A sh-C day0, biological rep1

value: Human induced pluripotent stem cell

value: shControl

value: Undifferentiated state


title: Disease18_snRNAseq

value: Female


title: Larvae4

value: replicate=larvae group biological replicate 4


title: 32_OC43_6hpi_rep4

tag: genotype


title: 28_OC43_HI_18hpi_rep1

value: heat-inactivated HCoV-OC43


title: 31_OC43_3hpi_rep4


title: rpb1-84 rrp6∆ rep1

value: MAT{alpha} his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220-84 (2mm LEU rpb1-84) rrp6{delta}::KanMX4


title: CD34 treated with  0.5 mM of Denatonium  biological rep1

value: umbilical cord blood (UCB)-derived CD34+ cells

value: 0.5 mM of Denatonium


title: rrp6∆ rep2

value: MAT{alpha} his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220 (2mm LEU RPB1) rrp6{delta}::KanMX4


title: 12S-2,scRNAseq

description: 10x Genomics

value: 12h single cultivation


title: Larvae3

value: replicate=larvae group biological replicate 3


title: 30_OC43_1.5hpi_rep4

value: wild type

value: ribodepleted RNA


title: Disease16_snRNAseq

value: HKD

value: adult kidney

value: Male


title: 27_OC43_HI_6hpi_rep1


title: rrp6∆ rep1


title: wt (for rrp6 experiment) rep2

value: MAT{alpha} his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220 (2{micro}m LEU2 RPB1)


title: wt (for rrp6 experiment) rep1


title: Control17_scRNAseq

value: Control


title: Larvae1

value: Serratia marcescens FY

value: WT

value: bacteria and larvae were co-cultured

value: replicate=larvae group biological replicate 1


title: 25_OC43_30hpi_rep3


title: 26_OC43_HI_3hpi_rep1

value: heat-inactivated HCoV-OC43


title: 24_OC43_24hpi_rep3


title: 29_uninfected_rep4


title: Control16_scRNAseq


title: Disease14_snRNAseq


title: rpb1-84 rep2

description: This sample was analysed used a wt previosly publised: GSM4603016 and GSM4603018.

value: MAT{alpha} his3-{delta}200 leu2-3,112 trp1-{delta}63 ura3-52 rpb1-{delta}187::HIS3 + pYEB220-84 (2{micro}m LEU2 rpb1-84) RPB4::TAP::TRP1


title: Control3

value: single cultivation

value: replicate=control group biological replicate 3


title: Larvae2

value: replicate=larvae group biological replicate 2


title: rpb1-84 rep1


title: 23_OC43_18hpi_rep3


title: Control15_scRNAseq


title: 22_OC43_12hpi_rep3


title: Control2

value: replicate=control group biological replicate 2


title: Control14_scRNAseq


title: N2 wild-type, Kombucha microbe mix, biol rep 3

city: Chapel Hill

first: Robert

middle: Houston

last: Dowen

state: NC

address: 321 Fordham Hall, CB7100

department: Cell Biology and Physiology

institute: University of North Carolina at Chapel Hill

description:
Column_names: op50_r1, op50_r2, op50_r3, ht115_r1, ht115_r2, ht115_r3, acetob_r1, acetob_r2, acetob_r3, komb_1g_r1, komb_1g_r2, komb_1g_r3, komb_5g_r1, komb_5g_r2, komb_5g_r3, komb_mix_r1, komb_mix_r2, komb_mix_r3
raw_gene_read_counts.txt
DESeq2_norm_gene_counts.txt
DESeq2_DEGs_komb_mix_v_op50.txt

data_processing:
The adapter-trimmed mRNA-Seq reads were mapped to the WS260 genome using the STAR aligner. The mapping was performed using a GTF obtained from Wormbase (c_elegans.PRJNA13758.WS260.canonical_geneset.gtf) with the parameter --outFilterIntronMotifs RemoveNoncanonical.
The gene-level read counts were calculated using the featureCounts algorithm of the subread package (Liao et al., Bioinformatics, 2014), using the following flags: -p -t exon -g gene_id -a c_elegans.PRJNA13758.WS260.canonical_geneset.gtf.
Differential expression was calculated relative to the E. coli OP50 sample using the DESeq2 package using a 1% FDR cutoff (Love et al., 2014).
Assembly: WS260
Supplementary files format and content: raw_gene_read_counts.txt: A tab-delimited text file that includes gene level unnormalized read counts for each sample in matrix format
Supplementary files format and content: DESeq2_norm_gene_counts.txt: A tab-delimited text file that includes gene level normalized read counts for each sample in matrix format
Supplementary files format and content: DESeq2_DEGs_sample_v_op50.txt: A tab-delimited text file that includes a list of differentially expressed genes, the log2 FC values, and the p values called by DESeq2 at a 1% FDR threshold for each sample relative to the OP50 sample.

organism: Caenorhabditis elegans

source_name: Whole animals

growth_protocol: C. elegans N2 wild-type L1 animals were synchronized by egg prep and grown at 20°C on 10cm NGM Agarose plates (1000 animals/plate) seeded with either E. coli OP50, E. coli HT115, Acetobacter tropicalis, or Kombucha-associated microbes for ~72 hours when they reached day 1 of adulthood.

extract_protocol:
Animals were harvested in M9 buffer, washed three times, and flash frozen in liquid Nitrogen. Total RNA was isolated using Trizol.
mRNA-Seq libraries were prepared by Novogene Inc.

treatment_protocol: The individual microbes were cultured at 25°C, concentrated by centrifugation, plated on NGM Agarose plates, and incubated at room temperature for 4 days before dropping animals on the lawn.

value: wild-type

value: fed a mix of Kombucha microbes

value: Day 1 adults

value: Whole animals

tag: sample type

value: Hermaphrodites


title: Disease15_snRNAseq

value: HKD

value: adult kidney

value: Male


title: Control1

value: Serratia marcescens FY

value: WT

value: replicate=control group biological replicate 1


title: N2 wild-type, Kombucha microbe mix, biol rep 1


title: Control13_scRNAseq

value: Control


title: N2 wild-type, Kombucha microbe mix, biol rep 2


title: 21_OC43_9hpi_rep3

value: wild type

value: ribodepleted RNA


title: F8Exon16G351A_B_2A3_S4

city: Santa Cruz

first: Guillermo

middle: A

last: Chacaltana

address: 1156 High Street

department: Chemistry

institute: University of California, Santa Cruz

data_processing:
Paired-end reads were mapped onto reference sequence using rf-map module from RNA-FRAMEWORK V.2.8.2 (modular toolkit developed to deal with RNA structure probing and post-transcriptional modifications mapping high-throughput data)
Mutation counts were then counted using rf-count module on RNA-FRAMEWORK
Resulting mutation count files were normalized using rf-norm module on RNA-FRAMEWORK
Final .txt output files were then supplied to rf-fold module on RNA-FRAMEWORK to drive structural predictions
Supplementary files format and content: Processed .txt data files contain normalization parameters used in rf-norm, reference sequence used as a reference for each read used to obtain mutational counts, and reactivity values computed for each nucleotide position on the reference sequence
Assembly: reference_sequence.txt

extract_protocol:
in vitro transcribed RNA was first synthesized and PAGE purified prior to modification with 2A3 and then reverse transcribed. Resulting cDNA was used as input material for library assembly.
RNA is first modified with 2A3 or treated with DMSO control, then fragmented to a median length of 150nt. The fragmented material is used as input for a random hexamer reverse transcription reaction, afterwhich the resulting cDNA is used as starting material for NEBNext Ultra II DNA library prep kit for Illumina.
2'-hydroxyl acylation analyzed by primer extension (SHAPE) Mutational Profiling via High Throughput Sequencing (MaP-seq).

value: SHAPE probed

tag: molecule subtype

value: IVT RNA


title: 20_OC43_6hpi_rep3


title: Control12_scRNAseq

value: Female


title: Control4

value: single cultivation

value: replicate=control group biological replicate 4


title: Control11_scRNAseq


title: 19_OC43_3hpi_rep3


title: N2 wild-type, Kombucha, 5 generation, biol rep 2

description:
Column_names: op50_r1, op50_r2, op50_r3, ht115_r1, ht115_r2, ht115_r3, acetob_r1, acetob_r2, acetob_r3, komb_1g_r1, komb_1g_r2, komb_1g_r3, komb_5g_r1, komb_5g_r2, komb_5g_r3, komb_mix_r1, komb_mix_r2, komb_mix_r3
raw_gene_read_counts.txt
DESeq2_norm_gene_counts.txt
DESeq2_DEGs_komb_v_op50.txt

tag: strain

value: wild-type

value: fed Kombucha for five generations

value: Day 1 adults


title: Control9_scRNAseq


title: F8Exon16G351A_B_DMSO_S2


title: 18_OC43_1.5hpi_rep3


title: N2 wild-type, Kombucha, 1 generation, biol rep 3

value: fed Kombucha for one generation

value: Whole animals

value: Hermaphrodites


title: Control8_scRNAseq

value: adult kidney

value: Male


title: F8Exon16C348T_B_2A3_S24


title: F8Exon16G351A_A_2A3_S3


title: Control10_scRNAseq


title: 16_OC43_30hpi_rep2


title: F8Exon16C348T_A_2A3_S23


title: N2 wild-type, Kombucha, 5 generation, biol rep 1


title: N2 wild-type, Acetobacter tropicalis, biol rep 3

description:
Column_names: op50_r1, op50_r2, op50_r3, ht115_r1, ht115_r2, ht115_r3, acetob_r1, acetob_r2, acetob_r3, komb_1g_r1, komb_1g_r2, komb_1g_r3, komb_5g_r1, komb_5g_r2, komb_5g_r3, komb_mix_r1, komb_mix_r2, komb_mix_r3
raw_gene_read_counts.txt
DESeq2_norm_gene_counts.txt
DESeq2_DEGs_acetob_v_op50.txt

value: fed Acetobacter tropicalis


title: F8Exon16C348T_A_DMSO_S21


title: 14_OC43_18hpi_rep2


title: 15_OC43_24hpi_rep2


title: 17_uninfected_rep3


title: F8Exon16C348T_B_DMSO_S22


title: Disease11_scRNAseq

value: HKD


title: N2 wild-type, Kombucha, 1 generation, biol rep 2


title: N2 wild-type, Kombucha, 1 generation, biol rep 1


title: F8Exon16C321A_B_2A3_S28


title: Disease12_scRNAseq


title: 13_OC43_12hpi_rep2

value: wild type


title: N2 wild-type, Acetobacter tropicalis, biol rep 2


title: F8Exon16G351A_A_DMSO_S1


title: N2 wild-type, Kombucha, 5 generation, biol rep 3


title: 12_OC43_9hpi_rep2

value: ribodepleted RNA