title: D_HLTF+/+ cells  -/- mice

city: Lubbock

first: Beverly

middle: S

last: Chilton

department: Cell Biology & Biochemistry

institute: Texas Tech University HSC

data_processing:
data analysis of tissue images and sequencing files in FASTQ format with Space Ranger
space ranger aggr pipeline aggregated data from replicate samples and from replicate regions
read 2 sequences were mapped against the reference human genome (GRCh38/hg38) and read 1 sequences were used for UMI filtering to obtain spatial information
Spaceranger count combined a brightfield microscope slide image and FASTQ files from spaceranger mkfastq and performed alignment, tissue detection, fiducial detection, barcode/UMI counting, and prepared a full resolution slide image for visualization in Loupe Browser.
The pipeline used the Visium spatial barcodes to generate feature-spot matrices, determine clusters, and perform gene expression analyses. The pipeline used a probe aligner algorithm for FFPE tissues.
Assembly: GRCh38/hg38
Supplementary files format and content: Scalefactors, JSON
Supplementary files format and content: Image, PNG
Library strategy: Spatial Transcriptomics

source_name: primary CDX tumor

extract_protocol:
FFPE CDX tumors on capture areas of a Visium gene expression slide (V11D13-089-A1)
permeabilize tissue and construct barcoded libraries with a final sample index PCR
short-read sequencing (Illumina NovaSeq) of barcoded libraries by Genewiz single index
10x Visium Human Transcriptome Probe Set v1.0

value: primary CDX tumor

value: HLTF+/+

value: human CRC


title: 504_Pb-PRL_Vehicle

status: Public on Sep 13 2023

type: SRA

city: Paris

first: Mickael

middle: Mathieu

last: Menager

address: 24 Boulevard du Montparnasse

country: France

institute: Institut Imagine

library_source: transcriptomic single cell

data_processing:
Sequencing reads were demultiplexed and aligned to the mouse reference genome (mm10-2020-A), using the CellRanger Pipeline v5.0.1
Unfiltered RNA UMI counts were loaded into Seurat v4.0.1 (Stuart et al., 2019) for quality control, data integration and downstream analyses. Apoptotic cells and empty sequencing capsules were excluded by filtering out cells with fewer than 500 features or a mitochondrial content higher than 20%.
Data from each sample were log normalisedand scaled, before batch correction using Seurat’s FindIntegratedAnchors.
On this integrated dataset, we computed the principal component analysis on the 3000 most variable genes. UMAP was carried out using the 30 most significant PCs, and community detection was performed using the graph-based modularity-optimization Louvain algorithm from Seurat’s FindClusters function.
Cell types labels were assigned to resulting clusters based on a manually curated list of marker genes as well as previously defined signatures of the known Prostate subtypes.
Assembly: mm10-2020-A
Supplementary files format and content: h5 file containes the raw counts for each sample

molecule: total RNA

organism: Mus musculus

source_name: Prostate

extract_protocol:
The prostates were dissected and minced, then digested for one and a half hours with 1mg collagenase at 37°C in 10 ml DMEM + 10% SVF. The cells were then dissociated with trypsin and sieved using a 40µM cell sieve, then cleared of debris using histopaque centrifugation. Live ter119-negative cells were then isolated by flow cytometry.
The scRNA-seq libraries were generated using Chromium Single Cell Next GEM 3′ Library & Gel Bead Kit v.3.1 (10x Genomics) according to the manufacturer’s protocol. Briefly, cells were counted, diluted at 1,000 cells/µL in PBS+0,04% and 20,000 viable cells were loaded in the 10x Chromium Controller to generate single-cell gel-beads in emulsion. After reverse transcription, gel-beads in emulsion were disrupted. Barcoded complementary DNA was isolated and amplified by PCR. Following fragmentation, end repair and A-tailing, sample indexes were added during index PCR. The purified libraries were sequenced on a Novaseq (Illumina) with 28 cycles of read 1, 8 cycles of i7 index and 91 cycles of read 2.

treatment_protocol: daily gavage for 30 days with a dose of 60mg/kg/day of Anethole tritione or vehicle (coconut oil).

tag: tissue

value: Prostate

tag: genotype

value: Pb-PRL

tag: treatment

value: coconut oil


title: RNA Mock rep2

city: Riverside

first: Yinsheng

last: Wang

state: California

address: 501 Big Springs Road

country: USA

institute: University of California Riverside

library_source: transcriptomic

data_processing:
The sequencing reads were aligned to GRCh38 assembly using STAR (v.2.7.0) with default parameters. Transcript quantification was conducted using featureCounts (v.2.0.3). Differential gene expression analysis was performed with DESeq2 (v.1.36.0)
Assembly: GRCh38
Supplementary files format and content: xlsx files were generated with gene expression transcripts per million (TPM) data included.

molecule: polyA RNA

organism: Homo sapiens

growth_protocol: Cells were cultured at 37 degrees in a humidified incubator with 5% CO2

extract_protocol:
Total RNA was extracted from cells with Omega Total RNA Kit I.
Poly(A) RNA enrichment was conducted using NEBNext Poly(A) mRNA Magnetic Isolation Module following the manufacturer's instructions, and the sequencing library was constructed by using the NEBNext Ultra II RNA Library Prep Kit.

treatment_protocol: Mock treatment or 20uM PDS treatment for 24hrs

tag: cell line

tag: cell type

value: Human hepatocellular carcinoma

value: wild type


title: RNA PDS rep2

value: 20uM PDS, 24hrs


title: HiChIP PDS rep1

library_source: genomic

data_processing:
Paired-end reads were processed using HiC-Pro (v.3.1.0). Fastq files were aligned to GRCh38 assembly, deduplicated, and assigned to MboI restriction fragments. After filtration for valid interactions. Interaction matrices were constructed and visualized using HiCExplorer.
Assembly: GRCh38
Library strategy: HiChIP-seq

molecule: genomic DNA

growth_protocol: DMEM, 10% fetal bovine serum, 1% penicillin/streptomycin. Cells were cultured at 37 degrees in a humidified incubator with 5% CO2

extract_protocol:
Cells were fixed with 1% formaldehyde for 10 minutes. After quenching and cell lysis, chromatin were digested with MboI and ligated before sonication and antibody enrichment.
HiChIP sequencing library preparation was conducted using NEBNext Ultra DNA Library Prep Kit for Illumina following the manufacturer's instructions.

tag: chip antibody


title: HiChIP PDS rep2


title: RNA Mock rep1


title: C_HLTF+/+ cells  -/- mice

state: TX

tag: strain


title: HiChIP Mock rep2


title: cortex_wt_3

city: St Louis

first: Sridhar

last: Nonavinkere Srivatsan

address: 660 S Eucild Ave

institute: WashU School Of Medicine

description:
paired-end
group_cortex_ko-group_cortex_wt_GAGE_MSigDb_Human_Phenotype_Ontology_Results.tsv; group_cortex_ko-group_cortex_wt_Differential_Expression_sanitized.tsv

data_processing:
Basecalls and de-multiplexing were performed with Illumina’s bcl2fastq software and a custom Python demultiplexing program with a maximum of one mismatch in the indexing read.
RNA-Seq reads were then aligned to Ensembl GRCh38.76 or Ensembl GRCm38.76 assembly for human or mouse samples, respectively, with STAR version 2.7.9a
Gene counts were derived from the number of uniquely aligned unambiguous reads by Subread:featureCount version 2.0.3
Isoform expression of known Ensembl transcripts were quantified with Salmon version 1.5.2
All gene counts were then imported into the R/Bioconductor package EdgeR and TMM normalization size factors were calculated to adjust for samples for differences in library size.
Assembly: Ensembl GRCh38.76 or Ensembl GRCm38.76 assembly for human or mouse samples, respectively
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: Cortex

growth_protocol: Human cell lines (HeLa-S, and U2OS; both originally from ATCC) were cultured in Dulbecco’s modified eagle medium (Invitrogen), supplemented with 10% fetal bovine serum (Sigma), 100 U/ml of penicillin-streptomycin (GIBCO) at 37°C and 5% CO2.

extract_protocol:
RNA was purified from cell lines using the Qiagen miRNeasy mini kit to accomodate small RNA isolation (#217004). For RNA isolation from mouse cortex, cerebral cortex was dissected in ice-cold PBS from 5 female Ttdn1-/- and 5 WT littermates at 8 weeks of age, then flash frozen. RNA was purified from cortex using the Qiagen miRNeasy mini kit.
Samples for small RNA-sequencing were prepped with TruSeq Small RNA library preparations kits; otherwise all other samples were prepared according to library kit manufacturer’s protocol, indexed, pooled, and sequenced on an Illumina NovaSeq 6000 2x150bp with the Genome Technology Access Center at Washington University in St. Louis, typically yielding 200 million paired-end reads per sample.

treatment_protocol: Where indicated, cells were treated with 250 nM pladienolide-B for 24h.

value: Cortex

tag: age

value: 8 weeks


title: cortex_wt_5


title: cortex_wt_4


title: HiChIP Mock rep1


title: mice placenta, Arsenic, gestational day 18, biol rep 3

city: hefei

first: yaping

middle: Ya

last: Song

address: No. 81, Meishan Road, Hefei City

department: department of toxicology

country: China

institute: Anhui Medical University School of Public Health

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 mm10 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: mm10
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

source_name: placenta

growth_protocol: pregnant mice were administered with different concentrations of NaAsO2 (0, 0.15, 1.5 or 15 mg/L) by drinking water from gestational day (GD) 0 to GD18

extract_protocol:
Total RNA from mouse placentas was extracted by Trizol regent (Thermo Fisher Scientific) and then treated with DNase I (cat#: AM2222, Thermo Fisher Scientific).
RNA sequencing was done in Genesky using TruSeq Stranded mRNA Library Preparation (illumina, CA, USA).

treatment_protocol: All pregnant mice were anesthetized using a mixture of isoflurane and oxygen, and then sacriﬁced by in the morning of GD18. Placental tissues were obtained.

value: placenta

value: Arsenic

tag: time

value: gestational day 18


title: B_HLTF-/- cells  -/- mice

value: HLTF-/-


title: cortex_wt_1


title: mice placenta, Arsenic, gestational day 18, biol rep 2


title: cortex_ko_5


title: cortex_wt_2


title: cortex_ko_4


title: mice placenta, Arsenic, gestational day 18, biol rep 1


title: mice placenta, Control, gestational day 18,biol rep 3

value: Control


title: mice placenta, Control, gestational day 18,biol rep 2


title: cortex_ko_2


title: mice placenta, Control, gestational day 18,biol rep 1


title: A_HLTF-/- cells  -/- mice


title: Per2uORF mutant male, RiboProf ZT02-04, rep3

city: Suita

first: Arthur

last: Millius

state: Osaka

address: iFReC 6F

department: iFReC

country: Japan

institute: Osaka University

description:
M21D12_S12
RiboProf library

data_processing:
RNA was precipitated from the elution by the addition of 38.5 µl water, 1.5 µl GlycoBlue (ThermoFisher), and 10 µl 3 M sodium acetate pH 5.5 followed by 150 µl isopropanol, stored overnight at -80 °C, pelleted by centrifugation (20,000 × g for 30 min at 4 °C), and resuspended in 22 µl 10 mM Tris pH 8. Approximately 10 µg RNA was separated on a 15% (wt/vol) polyacrylamide TBE-urea gel at 200 V for 65 min in 1× TBE, and fragments between 26 and 34 nt were excised and recovered in 400 µl RNA gel extraction buffer (300 mM sodium acetate pH 5.5, 1 mM EDTA, and 0.25% (wt/vol) SDS) overnight. RNA was precipitated by the addition of 1.5 µl GlycoBlue and 500 µl, stored at -80 °C for >30 min, pelleted by centrifugation (20,000 × g for 30 min at 4 °C), and resuspended in 10 µl 10 mM Tris pH 8. RNA was dephosphorylated by T4 PNK (Takara Bio), precipitated and recovered as previously described, resuspended in 8.5 µl 10 mM Tris, and 1.5 µl of preadenylated and 3' blocked miRNA cloning linker (1/5rApp/CTGTAGGCACCATCAAT/3ddC/, IDT) was added. The linker mixture was denatured for 90 s at 80 °C, cooled to room temperature, ligated by T4 Rnl2 (NEB) for ~24 h at room temperature, precipitated, recovered, and separated by 15% TBE-urea gel electrophoresis. Ligation products were recovered overnight in RNA gel extraction buffer, precipitated, and recovered in 10 µl 10 mM Tris pH 8. Ligated RNA was reverse transcribed at 52 °C for 20 min using SuperScript IV (ThermoFisher) with the reverse transcription primer (5′-(Phos)-AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGC-(SpC18)-CACTCA-(SpC18)-TTCAGACGTGTGCTCTTCCGATCTATTGATGGTGCCTACAG-3′, where SpC18 indicates a hexa-ethyleneglycol spacer). Reverse transcription products were precipitated, recovered, separated by 15% TBE-urea gel electrophoresis, and recovered overnight in DNA gel extraction buffer (300 mM NaCl, 10 mM Tris pH 8, and 1 mM EDTA). The cDNA was precipitated, recovered, resuspended in 15 µl 10 mM Tris pH 8, and circularized by CircLigase (EpiCentre) for 1 h at 60 °C. rRNA was depleted by combining 5 µl circularization reaction with 1 µl of subtraction oligo pool, 1 µl 20× SSC, and 3 µl water, incubating at 37 °C for 15 min and binding to MyOne Streptavidin C1 DynaBeads (ThermoFisher) at 37 °C for 15 min with mixing at 1000 rpm. Eluate was precipitated, recovered, and resuspended in 5 µl 10 mM Tris pH 8. rRNA-depleted cDNA was PCR amplified by Phusion High-Fidelity DNA Polymerase (NEB) in a 20 µl reaction (denature 94 °C for 15 s, anneal 55 °C for 10 s, extend 72 °C for 10 s) for 12 cycles. PCR products were separated on a 8% TBE gel, recovered overnight in DNA gel extraction buffer, precipitated, recovered, and resuspended in 15 µl 10 mM Tris pH 8. Libraries were quantified using the high-sensitivity DNA chip on the Agilent BioAnalyzer according to the manufacturer's protocol, pooled, and amplified on the Illumina NovaSeq6000 system according to the manufacturer's protocol. RNAseq libraries were amplifed using the TruSeq stranded mRNA kit according to the manufacturer's instructions.
For RNAseq analysis, the data were processed using DESeq2. For ribosome profiling, the follow steps were taken: after quality control using FASTQC (https://www.bioinformatics.babraham.ac.uk/projects/fastqc/), reads were clipped using fastx_clipper (with parameters -Q33 -a CTGTAGGCACCATCAAT -l 25 -c -n) and processed with fastx_trimmer (with parameters -Q33 -f 2), both from the FASTX-Toolkit (http://hannonlab.cshl.edu/fastx_toolkit/).
We then used Bowtie 2.1.0.0 (Langmead and Salzberg, 2012) to map the resulting reads to rRNA sequences. Reads that were successfully aligned to these sequences are discarded, and only unaligned reads were used for downstream analysis.
These reads that did not align to rRNA were mapped to the mouse mm10 reference genome. Using samtools 0.1.19.0 and egrep, we extracted reads for which an exact match between the sequence and the reference could be found.
Using reads aligned to a unique location, we then calculated transcript density profiles. This relies on assignment each footprint alignment (i.e., each read) to a specific A site nucleotide based on the length of the fragment. The initial assumption is that this site will be close to the center of the read. To calculate the best offset, we considered a metagene that captured all reads and their position relative to the start site and calculated the offset that optimized phasing. The best results were obtained when the offset from the 5' end of the alignment was: 26 nt long, +13; 27-28 nt long, +15; 29-30 nt long, +16; 31-32 nt long, +17. Reads shorter than 26 or longer than 32 nucleotides were discarded. Using this offset, we assigned each read to a unique nucleotide, and constructed transcript density profiles by counting the number of reads whose A site was assigned to each nucleotide position.
For each transcript, non-overlapping five-codon windows were then tiled across the coding region and the transcript was considered well-translated if it had a median value of at least 2 reads per window (excluding the excluding the first fifteen and the last five codons).Using all well-translated transcripts, we created file where each transcript is represented across all samples by its RPKM value. We used this file in JTK_CYCLE (Hughes et al., 2010) to identify all rhythmic transcripts with a circadian period (i.e., period between 20 and 28 h). We used a threshold of 0.05 on the adjusted p-value to assess significance.
Assembly: mm10

source_name: whole liver tissue

growth_protocol: Twelve-to-fourteen week-old wild-type male mice (C57BL/6N, Japan SLC) under 12-h light (400 lx) 12-h dark (LD) conditions were sacrificed between ZT02-04.

extract_protocol:
Frozen liver sections were rinsed in 3x PBS, homogenized in 1 mL polysome lysis buffer using dounce A (10 strokes) then dounce B (10 strokes), clarified by 15,000 x g centrifugation for 10 min., then divided into 200 uL + 1 mL trizol (RNAsequencing), 300 uL for ribosome profiling (see steps below), and remaining snap frozen for western blot.
Unbound RNA was digested by the addition of 7.5 µl RNAseIf (ThermoFisher) for 45 min and then stopped by 10 µl SUPERase In RNAse Inhibitor (ThermoFisher). The digestion was transferred to 13 mm × 51 mm polycarbonate ultracentrifuge tubes, layered on top of 0.9 ml sucrose cushion (150 mM NaCl, 20 mM Tris-HCl pH 7.4, 5 mM MgCl2, 5 mM DTT, 100 µg/ml cycloheximide, 1 M sucrose, 10 U/ml SUPERase In), centrifuged in a TLA100.3 rotor at 70,000 rpm at 4 °C for 4 h. Ribosome pellets were resuspended in 0.8 ml Trizol and mRNA was recovered according to the manufacturer's instructions.

treatment_protocol: Half-dime size liver sections were snap-frozen and stored at -80C until use.

value: whole liver tissue

value: 12-14 week-old

tag: gender

value: male


title: Per2uORF mutant male, RiboProf ZT02-04, rep2

description:
M20D12_S11
RiboProf library


title: cortex_ko_1


title: KO-MET TS 2

city: Barcelona

first: Antonio

last: Postigo

state: BARCELONA

address: Casanova 143. Cellex 1B

country: Spain

institute: IDIBAPS/ICREA

data_processing:
RNA-seq reads were mapped against Mus musculus reference genome with STAR (ENCODE parameters)
Genes were quantified with RSEM (default parameters)
Normalization and differential expression was performed with DESeq2
GO/KEGG enrichment analysis was performed with G:profiler
Assembly: GRCm38
Supplementary files format and content: txt file containing RSEM expected counts

source_name: Zeb1f/f LysM Peritoneal Macrophages-Set 2

growth_protocol: Freshly isolated peritoneal macrophages

extract_protocol:
Total RNA was isolated using Trizol
TruSeq® Stranded mRNA LT Sample Prep Kit

treatment_protocol: LPS treated peritoneal macrophages

value: Peritoneal lavage macrophages sorted by flow cytometry using CD11b and F4/80 markers

value: Zeb1f/f LysM Cre

value: Metfromin pretreatment LPS single dose


title: Per2uORF mutant male, RiboProf ZT02-04, rep1

description:
M15D12_S10
RiboProf library


title: KO-MET TS 1

source_name: Zeb1f/f LysM Peritoneal Macrophages-Set 1


title: Wild-type-MET TS 3

source_name: Zeb1f/f Peritoneal Macrophages-Set 3


title: Wild-type-MET TS 2

source_name: Zeb1f/f Peritoneal Macrophages-Set 2


title: Wild-type male, RiboProf ZT02-04, rep2

description:
M3W12_S8
RiboProf library

value: wild-type


title: KO-MET TS 3

source_name: Zeb1f/f LysM Peritoneal Macrophages-Set 3


title: Wild-type male, RiboProf ZT02-04, rep3

description:
M6W12_S9
RiboProf library


title: Wild-type male, RiboProf ZT02-04, rep1

description:
M1W12_S7
RiboProf library


title: KO-TOL3

value: LPS two doses


title: Per2uORF mutant male, RNAseq ZT02-04, rep2

description:
M20D_RNA_S5
total RNA


title: Per2uORF mutant male, RNAseq ZT02-04, rep3

description:
M21D_RNA_S6
total RNA


title: KO-TOL1


title: Wild-type male, RNAseq ZT02-04, rep3

description:
M6W_RNA_S3
total RNA


title: Per2uORF mutant male, RNAseq ZT02-04, rep1

description:
M15D_RNA_S4
total RNA


title: KO-TOL2


title: Wild-type-TOL 3


title: Wild-type-TOL 2


title: Wild-type male, RNAseq ZT02-04, rep2

description:
M3W_RNA_S2
total RNA


title: 5xFAD, expr 2, scRNAseq

city: Daegu

first: Jaemyung

last: Jang

address: 61, Cheomdan-ro, Dong-gu

country: South Korea

institute: Korea Brain Research Institute

description:
inDrops
5xFAD_hippocampus_3m-b

data_processing:
Sequencing results were first processed through pipeline for processing inDrop sequencing data (https://github.com/indrops/indrops) based on Python 2.7 with default parameters, aligned to a mouse genome GRCm38 (release 102). The datasets were imported via indRop (https://github.com/caleblareau/indRop) into R environments and used for subsequent bioinformatic analysis with Seurat v4.2.
The initial dataset contained 147,371 barcoded beads with more than 1,000 reads. Cells with fewer than 500 unique molecular identifiers filtered mapped (UMIFM) counts and genes with fewer than 10 cells were excluded, as low UMIFM indicates dead or dying cells. The R package, scDblFinder, was employed to identify and eliminate probable doublets. We further filtered cells whose nFeature_RNA and nCount_RNA was more than five standard deviations from the median value, because a high nCount_RNA or a nFeature_RNA implies that the cell may be a doublet or multiplet. In addition, cells with mitochondrial genes whose expression was more than two standard deviations above the median value of their total transcripts were excluded from further analysis.
Assembly: GRCm38 (release 102)
Supplementary files format and content: Comma-separated values files and matrix files

source_name: hippocampus

extract_protocol:
Brain tissue was harvested and dissociated in less than an hour. Briefly, mice (12 ~ 24-week-old) were quickly decapitated after being CO2 anesthetized. The brain was cut into 1mm slices, and the hippocampus then was extracted. The samples were dissociated enzymatically to obtain a single-cell suspension with 0.05% papain and DNase 1 (DN25, Sigma-Aldrich, USA) in neurobasal media (Gibco, USA) at 37 °C for 30 min. After the enzymatic reaction was stopped by the addition of OIA, the cell suspension was passed through a 40-μm filter and washed by differential centrifugation to remove debris. The dissociated cells were put in Hank’s balanced salt solution containing 0.04% bovine serum albumin and diluted to 100 cells/μl.
Directly after cell counting, a cell suspension volume equivalent to 5000 target cells was used for further processing. Preparation of gel beads in emulsion and libraries were performed with the custom-made microfluidic device and inDropTM chemistry, according to the inDrop™ Library Preparation, Version 2.1 provided by the manufacturer. Libraries’ quality and quantity were verified with a High-Sensitivity DNA Kit (Agilent Technologies, USA) on a 2100 Bioanalyzer (Agilent Technologies, USA). Next, sequencing was run in the rapid run flow cell and paired-end sequenced on a NovaSeq6000 (Illumina, USA).

value: Brain cells

value: hippocampus

value: 12 weeks old


title: KO-TS 1

value: LPS single dose


title: 5xFAD, expr 4, scRNAseq

description:
inDrops
5xFAD_hippocampus_6m-a

value: 24 weeks old


title: KO-TS 3


title: WT, ctrl 1, scRNAseq

description:
inDrops
WT_hippocampus_3m


title: Wild-type-TS 3


title: 5xFAD, expr 1, scRNAseq

description:
inDrops
5xFAD_hippocampus_3m-a


title: Wild-type-MET TS 1

source_name: Zeb1f/f Peritoneal Macrophages-Set 1


title: Wild-type-TS 2


title: intestinal crypt stem cells, circEZH2_005-2

city: Guangzhou

first: Wen-Juan

last: Zhang

state: Guangdong

address: Guangzhou, 1838 Guangzhou Avenue North, Guangzhou 510515, China

institute: Nanfang Hospital, Southern Medical University

data_processing:
A cDNA library constructed by the pooled RNA was sequenced run with Illumina NovaseqTM 6000 sequence platform.Using the Illumina paired-end RNA-seq approach, we sequenced the transcriptome, generating a total of millon 2 x 150 bp paired-end reads.To get high quality clean reads, reads were further filtered by Cutadapt (https://cutadapt.readthedocs.io/en/stable/,version:cutadapt-1.9)
we aligned reads of all samples to the Gallus gallus reference genome(ftp://ftp.ensembl.org/pub/release-101/fasta/gallus_gallus/dna/) using HISAT2(https://daehwankimlab.github.io/hisat2/,version:hisat2-2.0.4) package
The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare The mapped reads of each sample were assembled using StringTie(http://ccb.jhu.edu/software/stringtie/,version:stringtie-1.3.4d) with default parameters. Then, all transcriptomes from all samples were merged to reconstruct a comprehensive transcriptome using gffcompare
After the final transcriptome was generated, StringTie and ballgown (http://www.bioconductor.org/packages/release/bioc/html/ballgown.html) were used to estimate the expression levels of all transcripts and perform expression abundance for mRNAs by calculating FPKM (fragment per kilobase of transcript per million mapped reads) value.
RNAs differential expression analysis was performed by Deseq2 software between two different group and two different samples. The genes/transcripts with the parameter of qvalue < 0.05 and fold change > 2 or fold change <0.5.
Assembly: mm10
Supplementary files format and content: gene expression text files include raw counts and FPKM values for each Sample

source_name: intestinal crypt stem cells

growth_protocol: We isolated Lgr5+ ISCs from Lgr5-green fluorescent protein (GFP) mice and and incubated them with IntestiCult medium  to generate crypt-villus organoids.

extract_protocol:
RNA was harvested using RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511). 5 ug of total RNA was used for the construction of sequencing libraries.
RNA libraries for RNA-seq were prepared using Dynabeads Oligo (dT) (Thermo Fisher, CA, USA) following manufacturer's protocols.

treatment_protocol: Lgr5+ ISCs are infected with circEZH2_005 adenovirus according to the manufacturer's instructions. After infection for 72h, cells were challenged with H/R, and different assays were conducted. To induce the organoid H/R model, organoids were placed in an anaerobic environment containing 5% CO2, 2% O2, and 93% N2 in a 37 °C incubator for 4 h.

value: intestinal crypt stem cells

value: circEZH2_005 overexpression

value: Hypoxia/reoxygenation


title: intestinal crypt stem cells, circEZH2_005-1


title: intestinal crypt stem cells, vector2

value: WT


title: intestinal crypt stem cells, vector1


title: 5xFAD, expr 5, scRNAseq

description:
inDrops
5xFAD_hippocampus_6m-b


title: Wild-type male, RNAseq ZT02-04, rep1

description:
M1W_RNA_S1
total RNA

value: whole liver tissue


title: intestinal tissue exosomes,S5(sham),rep4

data_processing:
TMM (trimmed mean of M-values) was used to normalize the gene expression
Sequencedreadsweretrimmedforadaptersequence,andmaskedforlow-complexityorlow-qualitysequence,thenmappedtomm10wholegenomeusingBowtie2v2.1.0
Assembly: mm10
Supplementary files format and content: tab-delimited txt files include TMM values for each Sample ...
Supplementary files format and content: Matrix table with circRNA reads count for every circRNA and every sample

source_name: small intestine

extract_protocol:
The total RNA of exosomes was extracted using the TRIzol method, and the extracted total RNA was sampled for quality inspection. The Agilent 2100 bioanalyzer was used to analyze the concentration and integrity of RNA. After passing the RNA quality inspection, 10 ng to 20 ng of RNA was digested with RNase R to remove linear RNA and used for library preparation.
The RNA was fragmented, the 5' end conversion template was added, and the first strand of cDNA was reverse-transcribed. After the first round of PCR plus the index connector, the ligation product was purified, and the ribosomal cDNA was removed with ZapR and R-probes. The library was amplified by selecting the appropriate number of cycles according to the initial amount. After amplification, the circRNA SEQ library was purified and isolated with magnetic beads. After library quality control, different libraries were pooled according to the requirements for effective concentration and target offline data volume.

value: small intestine

value: Sham operation control


title: intestinal tissue exosomes,S3(sham),rep2


title: intestinal tissue exosomes,S4(sham),rep3


title: KO-TS 2

value: Peritoneal lavage macrophages sorted by flow cytometry using CD11b and F4/80 markers


title: Activated 5

city: Bunkyo-ku

first: Yoshitaka

last: Shirasaki

state: Tokyo

address: Hongo 7-3-1

department: Graduate School of Pharmaceutical Science

institute: The University of Tokyo

description: 3' mRNA library: read1 file contains transcript; read2 file contains cell barcord

data_processing:
After library demultiplexing (SMART-Seq DE3 Demultiplexer; Clontech) and adaptor trimming (by deleting 7 bases from the end), read 1 sequences were aligned to reference sequences (human: GRCh38.90) using TopHat2, and the read counts were calculated using HTSeq3.
Single-cell libraries stochastically lose information on low copy number transcripts in a quantity-dependent manner in the starting resource. Note should be taken of the correction for counts to avoid cell-to-cell bias.
Assembly: hg38
Supplementary files format and content: Tab-separated values files and matrix files

source_name: peripheral blood

extract_protocol:
Peripheral blood was obtained from a healthy volunteer. Mononuclear cells were obtained using Lymphoprep (Serumwerk, Berunburg, Germany), according to the manufacturer’s protocols. Lineage-negative (CD3, CD14, CD16, CD19, CD20 and CD56) and CD45-, CD127-, CRTH2- and CD161-positive cells were sorted using a MoFlo XDP flow cytometer (Beckman Coulter, Brea, CA, USA) as ILC2s.
cDNA libraries were prepared using SMART-Seq v4 3’-DE Kits (Clontech) according to the manufacturer’s instructions, with some modifications. A total of 3,892 copies of ERCC spike-in RNA were added to each sample as a mixture of quantitative internal controls. The cDNA was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter). Library quality check was performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and Agilent High Sensitivity DNA Kits (5067-4626). Degraded or low-yield samples were removed. Qubit High Sensitivity assays (Thermo Fisher Scientific) were performed to quantify the cDNA in each library, and 5 or 6 libraries with different indexed primers were evenly pooled. Pooled cDNA (400 pg) was tagmented using Nextera XT DNA Library Prep Kits (Illumina, San Diego, CA, USA), as described in the protocol. Library size and cDNA amount were quantified using an Agilent High Sensitivity DNA Kit and Qubit High Sensitivity assays, respectively.

value: peripheral blood

value: incubated with IL-2/IL-33/TSLP


title: Activated 4


title: intestinal crypt stem cells, circEZH2_005-3


title: Wild-type-TS 1


title: intestinal tissue exosomes,I5(ischemia 1h/reperfusion 2h), rep4

value: Ligation of superior mesenteric artery for 1h, reperfusion for 5h


title: Activated 2


title: Activated 3


title: intestinal tissue exosomes,I4(ischemia 1h/reperfusion 2h), rep3

value: Ligation of superior mesenteric artery for 1h, reperfusion for 4h


title: Activated 1


title: intestinal crypt stem cells, vector3


title: Transient 5


title: intestinal tissue exosomes, I1(ischemia 1h/reperfusion 2h), rep1

value: Ligation of superior mesenteric artery for 1h, reperfusion for 2h


title: CAF2_siCtrl

type: RNA

city: Sapporo

first: Hiromu

last: Suzuki

state: Hokkaido

address: S1, W17, Chuo-ku

department: Department of Molecular Biology

institute: Sapporo Medical University

description: CAF2 with control siRNA

hyb_protocol: Hybridization was performed using a Gene Expression Hybridization kit (Agilent Technologies) according to manufacturer's instruction.

scan_protocol: Array was scanned with an Agilent G2565BA Microarray Scanner.

data_processing: Agilent Feature Extraction Software (v 10.7) was used for background subtraction.

label_protocol: Total RNA (100 ng) was labeled using a Low Input Quick Amp Labeling Kit One-Color (Agilent Technologies) according to manufacturer's instruction.

growth_protocol: CAFs were cultured in Fibroblast Growth Medium 2 (FGM2, PromoCell) with Fibroblast Growth Medium 2 Supplement Pack (PromoCell) and 1% antibiotic-antimycotic (Thermo Fisher Scientific) at 37°C and 5% CO2.

extract_protocol: Total RNA was extracted using RNeasy Mini Kit (Qiagen).

treatment_protocol: CAFs were transfected with a control siRNA (Silencer Select Negative Control No. 1 siRNA, Thermo Fisher Scientific) or siRNAs targeting AEBP1 (Silencer Select Pre-designed siRNA; AEBP1 siRNA1, s1145; AEBP1 siRNA2, s1146; Thermo Fisher Scientific) using a TransIT-X2 Dynamic Delivery System (Mirus Bio) and were incubated for 72h.

tag: sirna

value: control siRNA


title: CAF2_siAEBP1-1

description: CAF2 with AEBP1 siRNA1

value: AEBP1 siRNA1


title: CAF2_siAEBP1-2

description: CAF2 with AEBP1 siRNA2

value: AEBP1 siRNA2


title: CAF1_siCtrl

description: CAF1 with control siRNA


title: Transient 4


title: CAF1_siAEBP1-1

description: CAF1 with AEBP1 siRNA1


title: CAF1_siAEBP1-2

description: CAF1 with AEBP1 siRNA2


title: Skin organoid, Adult, Day4, Rescure

city: Taichung

first: Yung-Chih

last: Lai

address: 7F., No. 6, Xueshi Road, North District

department: Integrative Stem Cell Center

country: Taiwan

institute: China Medical University Hospital

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger)
Assembly: mm10
Supplementary files format and content: matrix.h5

source_name: Skin organoid

extract_protocol:
Cells were derived from the dorsal skin of neonatal mice within 24 hours of birth. The skin was floated in 0.25% trypsin solution at 4°C to separate into the dermis and epidermis. Epidermal cells were cut with scissors, pipetted, and filtered through a 70um cell strainer followed by centrifugation. The dermis was digested in 0.35% collagenase for 20 minutes, then filtered through a 70um cell strainer followed by centrifugation. The dissociated epidermal cells and dermal cells were mixed at a ratio of 1:9 and were dropped onto the upper chamber of a transwell culture insert, and the lower chamber was filled with 700ul DMEM/F12 (Corning) culture medium containing 10% FBS (Gibco). For adult cell culture, the growth factors were added from D0 to D4, followed by adding MMP14 recombinant protein from D4 to D7. PKC inhibitors were added throughout the cultivation period. The cells were cultured in a 5% CO2 at 37°C incubator, with the culture medium being changed every other day.
Library was performed according to the manufacter’s instructions (single cell 3’ v3 protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: Skin organoid

value: Rescure

value: Adult


title: Skin organoid, Adult, Day4, Control

description: 10x Genomics

value: Control


title: Transient 2


title: Skin organoid, Newborn, Day4, Control

description: 10x Genomics

value: Newborn


title: Transient 1


title: Skin organoid, Newborn, Day2, Control

description: 10x Genomics


title: Skin organoid, Newborn, Day0, Control

description: 10x Genomics


title: Pre-stimulation 5


title: intestinal tissue exosomes,S2(sham),rep1

value: WT


title: Pre-stimulation 4


title: 3-154-5_Prog_N2: progenitors, IL-6 knock-out core // progenitors, rep 6

city: Zurich

first: Tino

last: Stauber

address: Lengghalde 5

country: Switzerland

institute: ETH Zurich

description: Illumina Truseq Total RNA (ribosomal depletion)

data_processing:
The raw reads were first cleaned by removing adapter sequences, trimming low quality ends, and filtering reads with low quality (phred quality <20) or reads shorter than 30nt using Fastp (v0.20).
Pseudoalignment and calculation of transcript abundance based on the high quality reads was performed with Kallisto (v0.46.1) using the GENCODE annotation of release M26 for the mouse genome GRCm39.
Differential expression analysis was performed with DESeq2 (R4.1.2, v1.34).
All previous steps were performed using the SUSHI framework at the Functional Genomics Center Zurich.
Assembly: GRCm39
Supplementary files format and content: .txt : text file containing trancript identifiers (ENSEMBL ID) and the match counts based on Kallisto
Supplementary files format and content: .xlsx : Microsoft Excel Worksheet containing the DEG data based on DESeq2 (i.e. gene_id, gene_name, GO, gnc_symbol, entrez_id, log2 ratio, pValue, fdr)

source_name: Isolated from wildtype Achilles tendon

growth_protocol: Hybrid explant // hydrogel constructs were clamped and maintained in DMEM/F12 supplemented with 10% fetal bovine serum (FBS), antibiotics, and L-ascorbic acid (200 μM) in humidified atmosphere with 5% CO2 at 37C for 7 days

extract_protocol:
The samples were snap-frozen in liquid nitrogen, pulverized by cryogenic grinding (FreezerMill 6870, SPEXTMSamplePrep), and further processed with the RNeasy micro kit (Qiagen)
The RNA libraries were prepared using Illumina's Stranded Total RNA Prep with Ribo-Zero Plus.

treatment_protocol: Treatment consisted of co-culture with different extrinsic cell populations and integration of core explants unable to express interleukin-6 (IL-6)

value: Isolated from wildtype Achilles tendon

value: Tendon progenitors (mixed)

value: in a hydrogel surrounding an IL-6 knock-out core explant


title: intestinal tissue exosomes,I2(ischemia 1h/reperfusion 2h), rep2

value: small intestine

value: Ligation of superior mesenteric artery for 1h, reperfusion for 3h


title: 3-154-5_Core_N2: core, IL-6 knock-out core // progenitors, rep 4

source_name: Tail tendon fascicle

value: Tail tendon fascicle

value: Tenocyte (mixed)

value: surrounded by collagen-1 hydrogel + progenitors


title: Pre-stimulation 1

value: peripheral blood


title: 3-154-5_Prog_N1: progenitors, IL-6 knock-out core // progenitors, rep 5


title: Pre-stimulation 3


title: Pre-stimulation 2


title: 3-154-2_Prog_N2: progenitors, wildtype core // progenitors, rep 6

value: in a hydrogel surrounding a wildtyp core explant


title: SA1, 36h, non-secreting

description: 3' mRNA library: read1 file contains transcript; read2 file contains cell barcode

data_processing:
After library demultiplexing (SMART-Seq DE3 Demultiplexer; Clontech) and adaptor trimming (by deleting 7 bases from the end), read 1 sequences were aligned to reference sequences (human: GRCh38.90) using TopHat, and the read counts were calculated using HTSeq.
The libraries were not demultiplexed. If the series of single cell data was required, it can be obtained by demultiplexing using SMART-Seq DE3 Demultiplexer from Takara-bio (https://www.takarabio.com/products/next-generation-sequencing/rna-seq/ultra-low-input-rna-seq/smart-seq-de3-demultiplexer).
Single-cell libraries stochastically lose information on low copy number transcripts in a quantity-dependent manner in the starting resource. Note should be taken of the correction for counts to avoid cell-to-cell bias.
Assembly: hg38
Supplementary files format and content: Comma-separated values files and matrix files

extract_protocol:
Peripheral blood was obtained from patients and healthy volunteers. Mononuclear cells were obtained using Lymphoprep (Serumwerk, Berunburg, Germany), according to the manufacturer’s protocols. Lineage-negative (CD3, CD14, CD16, CD19, CD20 and CD56) and CD45-, CD127-, CRTH2- and CD161-positive cells were sorted using a MoFlo XDP flow cytometer (Beckman Coulter, Brea, CA, USA) as ILC2s.
cDNA libraries were prepared using SMART-Seq v4 3’-DE Kits (Clontech) according to the manufacturer’s instructions, with some modifications. A total of 3,892 copies of ERCC spike-in RNA were added to each sample as a mixture of quantitative internal controls. The cDNA was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter). Library quality check was performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and Agilent High Sensitivity DNA Kits (5067-4626). Degraded or low-yield samples were removed. Qubit High Sensitivity assays (Thermo Fisher Scientific) were performed to quantify the cDNA in each library, and 5 or 6 libraries with different indexed primers were evenly pooled. Pooled cDNA (400 pg) was tagmented using Nextera XT DNA Library Prep Kits (Illumina, San Diego, CA, USA), as described in the protocol. Library size and cDNA amount were quantified using an Agilent High Sensitivity DNA Kit and Qubit High Sensitivity assays, respectively.

value: incubated with IL-2/IL-33


title: 3-154-4_Core_N2: core, IL-6 knock-out core // cell-free, rep 4

value: surrounded by collagen-1 hydrogel


title: SA1, before


title: 3-154-2_Core_N2: core, wildtype core // progenitors, rep 4


title: 3-154-2_Prog_N1: progenitors, wildtype core // progenitors, rep 5


title: SA1, 60h, non-secreting


title: 3-154-1_Core_N2: core, wildtype core // cell-free, rep 4


title: 3-154-3_Core_N2: core, wildtype core // macrophages, rep 4

value: surrounded by collagen-1 hydrogel + macrophages


title: H9, before


title: 3-152-5_Prog_N2: progenitors, IL-6 knock-out core // progenitors, rep 4


title: Transient 3

value: incubated with IL-2/IL-33/TSLP


title: H9, 60h non-secreting


title: SA1, 60h, secreting


title: SA1, 36h, secreting


title: 3-152-5_Core_N2: core, IL-6 knock-out core // progenitors, rep 3


title: 3-152-4_Core_N2: core, IL-6 knock-out core // cell-free, rep 3


title: SA1, real, secreting


title: 3-152-5_Core_N1: core, IL-6 knock-out core // progenitors, rep 2


title: 3-152-5_Prog_N1: progenitors, IL-6 knock-out core // progenitors, rep 3


title: H9, 36h, secreting


title: 3-152-3_Core_N2: core, wildtype core // macrophages, rep 3


title: 3-152-3_Core_N1: core, wildtype core // macrophages, rep 2


title: CKH4M3

city: guangzhou

first: Wu

last: Shuo

address: wushan

institute: South China Agricultural University

description: Corn silage inoculated with Aspergillus flavus spores and added with Neolamarckia cadamba essential oil, aerobic exposure, seven days,rep3

data_processing:
The library  was  sequenced on Illumina sequencing platform. According to the unique barcode and primer sequences, paired-end reads were accurately assigned to the relevant samples.
High-quality clean reads were generated by removing the adaptor sequences and low-quality sequences (SLIDINGWINDOW:5:15,HEADCROP:3,AVGQUAL:15,LEADING:5,TRAILING:5,MINLEN:80) using Trimmomatic (V0.38).
Host DNA was removed according to the Human Sequence Removal protocol of the National Center for Biotechnology Information (NCBI) using a host reference genome.
Clean rerads were annotated with taxonomic information using Kraken2 & Bracken based on the Kraken2 Virus database.
Assembly: AGPv4
Supplementary files format and content: tab-delimited text file includes species abundance for each Sample
Library strategy: Metagenome-seq

organism: silage metagenome

source_name: Fermentation microorganism

growth_protocol: All samples were exposed to oxygen at room temperature for seven days.

extract_protocol:
Total genome DNA was extracted Genome DNA Extraction kit (BBI) according to the manufacture instructions.
1ug of genomic DNA was fragmented by sonication using a Bioruptor (Diagenode) to a mean size of approximately 250 bp for library construction.

treatment_protocol: CK, the control; CKH, inoculated with Aspergillus flavus; CK4M, added with Neolamarckia cadamba essential oil; CKH4M, added with Neolamarckia cadamba essential oil and inoculated with Aspergillus flavus spores. All treatments were exposed to oxygen at room temperature for seven days.

value: All kinds of microorganisms


title: CKH4M2

description: Corn silage inoculated with Aspergillus flavus spores and added with Neolamarckia cadamba essential oil, aerobic exposure, seven days,rep2


title: H9, 36h, non-secreting


title: 3-152-2_Prog_N1: progenitors, wildtype core // progenitors, rep 3


title: CKH3

description: Corn silage inoculated with Aspergillus flavus spores, aerobic exposure, seven days,rep3


title: H9, real, secreting


title: 3-152-2_Prog_N2: progenitors, wildtype core // progenitors, rep 4


title: CK4M3

description: Corn silage with  Neolamarckia cadamba essential oil,aerobic exposure, seven days,rep3


title: 3-152-2_Core_N1: core, wildtype core // progenitors, rep 2


title: 3-152-1_Core_N2: core, wildtype core // cell-free, rep 3


title: CK4M1

description: Corn silage with  Neolamarckia cadamba essential oil,aerobic exposure, seven days,rep1


title: 3-150-5_Prog_N2: progenitors, IL-6 knock-out core // progenitors, rep 2


title: H9, 60h, secreting


title: CK4M2

description: Corn silage with  Neolamarckia cadamba essential oil,aerobic exposure, seven days,rep2


title: 3-152-2_Core_N2: core, wildtype core // progenitors, rep 3


title: 3-152-4_Core_N1: core, IL-6 knock-out core // cell-free, rep 2


title: CKH2

description: Corn silage inoculated with Aspergillus flavus spores, aerobic exposure, seven days,rep2


title: CKH1

description: Corn silage inoculated with Aspergillus flavus spores, aerobic exposure, seven days,rep1


title: CK3

description: Corn silage, aerobic exposure, seven days,rep3


title: CK2

description: Corn silage, aerobic exposure, seven days,rep2


title: CK1

description: Corn silage, aerobic exposure, seven days,rep1


title: 3-150-5_Prog_N1: progenitors, IL-6 knock-out core // progenitors, rep 1


title: 3-150-3_Core_N2: core, wildtype core // macrophages, rep 1


title: Midgut, 24 hours after feeding, replicate 6

city: Gent

first: Laurentijn

last: Tilleman

address: Ottergemsesteenweg 460

country: Belgium

institute: Ghent University

description: Midgut, equal male/female ratio, day 5 of the 5th (final) nymphal stage, animals grown in a clean (gregarine-free) environment, each replicate contains tissues from 6 individuals

data_processing:
Illumina® adapter sequences were trimmed from sequence reads at the 3’ end using Cutadapt (version 1.11)
Next, short sequencing reads were mapped to S. gregaria whole body transcriptome (2.3.3) (GenBank accession number GJPN000000000.1 ) using Bowtie2 (version 2.2.5).
Transcript abundance was quantified using the RSEM software package (RNA-seq by Expectation Maximization, version 1.2.31).
Mapped transcripts were annotated using Trinotate (http://trinotate.github.io). Transdecoder (http://transdecoder.github.io) was first used to translate the nucleotide sequences to their predicted best CDS. Next, all transcript sequences and their predicted CDS were used as query for BLAST in the annotated UniProtKB/Swiss-Prot databases. Standard parameters for BLAST were used, with BLAST e-value cut-off set at 1e-5.
Assembly: Sequence reads were mapped to an in-house S. gregaria whole body transcriptome (GenBank accession number GJPN000000000.1 ).
Supplementary files format and content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample

organism: Schistocerca gregaria

source_name: midgut

growth_protocol: Animals were kept at 30°C and RH 40-60% and were fed twice a day for one hour periods on cabbage (Brassica oleracea). Animals were kept in incubators, eggs were disinfected in ethanol and transferred to autoclaved soil to ensure that animals were gregarine-free (gut parasite).

extract_protocol:
Total RNA was extracted using the RNeasy lipid tissue extraction kit (Qiagen) according to the manufacturer’s protocol. An additional DNaseI treatment (Qiagen) was performed to remove potential genomic DNA contamination.
For Illumina® deep sequencing, mRNA was first purified from the total RNA mixture in every sample. From each sample, 1 μg of RNA was used to perform an Illumina® sequencing library preparation using the TruSeq® Stranded mRNA Library prep kit (Illumina®) according to the manufacturer's protocol.

treatment_protocol: Animals were fed for 10 minutes ('10 minutes after feeding') or 2 hours ('2 hours after feeding'). Animals were dissected 10 minutes after removing the food.  For the '24 hours after feeding' treatment food was removed and animals were dissected 24 hous later.

value: midgut

value: 24 hours after feeding


title: Midgut, 24 hours after feeding, replicate 5

value: WT


title: CKH4M1

description: Corn silage inoculated with Aspergillus flavus spores and added with Neolamarckia cadamba essential oil, aerobic exposure, seven days,rep1


title: 3-150-2_Prog_N2: progenitors, wildtype core // progenitors, rep 2

value: Isolated from wildtype Achilles tendon

value: Tendon progenitors (mixed)


title: 3-150-2_Core_N2: core, wildtype core // progenitors, rep 1


title: 3-150-2_Prog_N1: progenitors, wildtype core // progenitors, rep 1


title: Midgut, 24 hours after feeding, replicate 4


title: 3-152-1_Core_N1: core, wildtype core // cell-free, rep 2


title: Midgut, 24 hours after feeding, replicate 3


title: 3-150-1_Core_N2: core, wildtype core // cell-free, rep 1


title: Midgut, 24 hours after feeding, replicate 2


title: Ring1AKO, replicate 1, scRNAseq

city: Shenzhen

first: Zhen

address: DaPeng

institute: AGIS

description: 10x Genomics

data_processing:
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software: cellranger-6.0.2 (https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger) .We applied the Seurat [https://satijalab.org/seurat/] package for cell normalization and cell filtering considering the MT percentage, minimum and maximum gene numbers, and then performed dimensional reduction, clustering and annotation based on the standard criteria.
Assembly: mm39
Supplementary files format and content: Tab-separated values files and matrix files

source_name: totoal colon

extract_protocol:
colons were opened longitudinally and washed with PBS to remove fecal contents, and then were incubated in PBS containing 5mM EDTA on shaker at 220 rpm for 12min at 37℃. After that, ephithelium was removed, colons was minced and digested in 3ml RPM1640 containing 10% FBS, 1mg/ml Type IV Collagenase and 40 µg/ml DNase I at 220 rpm for 60min at 37℃. After centrifugation and filtration, the colonic lamina propria cells were collected and sustained with 7-AAD and CD45. Then 7-AAD-CD45+ cells were sorted by FACS for scRNA-seq.
Library was performed according to the manufacter’s instructions (Single Cell 3' v3  protocol, 10x Genomics). Briefly, GCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.

value: immune cells

value: totoal colon

value: 8-10 weeks old


title: Midgut, 24 hours after feeding, replicate 1


title: Midgut, 2 hours after feeding, replicate 5

value: 2 hours after feeding


title: Midgut, 2 hours after feeding, replicate 6


title: 3-150-5_Core_N2: core, IL-6 knock-out core // progenitors, rep 1

value: Tail tendon fascicle

value: Tenocyte (mixed)

value: surrounded by collagen-1 hydrogel + progenitors


title: Midgut, 2 hours after feeding, replicate 4


title: 3-150-4_Core_N2: core, IL-6 knock-out core // cell-free, rep 1


title: Midgut, 2 hours after feeding, replicate 3


title: Midgut, 2 hours after feeding, replicate 2


title: RNA-Seq_MCF7_siCTL_CTL_6h

city: Xiamen

first: Jiancheng

last: Ding

state: Fujian

address: School of Pharmaceutical Sciences, Xiamen University Xiang`an South Road

institute: Xiamen University

data_processing:
Basecalling was performed using CASAVA version 1.4
Reads were aligned to the hg19 genome assembly using STAR version 2.7.10.
To generate bigwig files, first generate bedGraph files for each chain using the STAR options "--outWigStrand" and "--outWigStrand" at the time of aligning, and then sort and convert bedGraph files to bigwig files using bedSort and bedGraphToBigWig.
Assembly: hg19
Supplementary files format and content: bigwig

growth_protocol: MCF7 cells were maintained in DMEM supplemented with 10% fetal bovine serum (FBS) and antibiotics in humidified atmosphere with 5% CO2 at 37℃.

extract_protocol:
Total RNA was isolated using RNeasy Mini Kit (Qiagen) following the manufacturer’s protocol. DNase I in column digestion was included to ensure the RNA quality.
RNA library preparation was performed by using NEBNext® Ultra™ Directional RNA Library Prep Kit for Illumina (E7420L). Paired-end sequencing was performed with Illumina HiSeq platform at RiboBio Co., Ltd. or Amogene Biotech Co., Ltd.

treatment_protocol: MCF7 cells were maintained in stripping DMEM supplemented with 5% charcoal-treated fetal bovine serum (FBS) for 72 hours before treated with ethanol or estrogen (10-7 M) for 6 hours.

value: epithelial cells

value: siCTL

value: CTL


title: RNA-Seq_MCF7_siLINC02568_CTL_6h


title: RNA-Seq_MCF7_siCTL_E2_6h


title: RNA-Seq_MCF7_siLINC02568_E2_6h


title: 402_Batch6_43_560237976601_S123_L008

city: Atlanta

first: Gregory

middle: K

last: Tharp

state: GA

address: 954 Gatewood Dr

department: Developmental and Cognitive Neuroscience

institute: Yerkes National Primate Research Center

data_processing:
The sequencing data was demultiplexed using Illumina bcl2fastq version 2.20.0.422 BCL to FastQ file converter.
The quality of raw reads was assessed with FastQC version 0.11.8
Reads were mapped to the GRCh38 human genome assembly [https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/] using STAR version 2.5.2b with default alignment parameters.
Abundance estimation of raw read counts per transcript was done internally with STAR using the htseq-count algorithm
DESeq2 version 1.22.1 R package was used to produce Raw read counts.
Genome_build: GRCh38
Supplementary_files_format_and_content: tab delimited text file containing Raw read counts for each sample (in columns) and each annotated transcript (in rows).

source_name: endocervical cells

growth_protocol: Cervical cytobrush samples collected at the baseline and the one month follow-up visit from 188 matched participants (n=376) were processed for RNA sequencing of cervical cells. The cervical cells were collected using a Digene cervical sampler (Digene Corporation, Gaithersburg, MD, USA). A cervical cytobrush was inserted into the endocervical os, rotated through 360 degrees and placed in a 15ml tube containing 3ml R10 media (10% heat-inactivated fetal calf serum (FCS) in RPMI supplemented with L-glutamine (50 ng/μl), anti-fungin (0.8 ng/μl), penicillin (50 U) and streptomycin (50 ng/μl)) and transported to the laboratory within 6 hours.

extract_protocol:
RNA was extracted from the endocervical cytobrush samples collected at the crossover visit using RNeasy Micro kit (Qiagen, CA) with DNase digest and QIAcube automation stations. The RNA was quantified, and the quality was assessed by Bioanalyzer analysis (Agilent Technologies, Santa Clara, CA)
Libraries were prepared using the Illumina (Illumina Inc. San Diego, CA, USA) TruSeq RNA Exome kit, as per manufacturer’s instructions, with 20 ng of total RNA as input. The libraries were quantified using Qubit dsDNA HS before normalization and pooling. The amplified libraries were assessed for their quality and sizing information by capillary electrophoresis on the Agilent 4200 TapeStation. The libraries were normalized, pooled and sequenced on the Illumina HiSeq3000 system employing a single-end 101 cycles run at average read depths of 23 million reads/sample.

treatment_protocol: Upon arrival of the cytobrush at the laboratory, the cytobrush was rotated against the side of the tube to dislodge the cells and the transport medium was used to flush the cytobrush bristles 30 times. The tubes were centrifuged at 1200 rpm for 10 mins to pellet cells. The supernatant was removed from the tube leaving about 50 μl and the pellet gently dislodged by vortexing. 350 μl RLT buffer (QIAGEN) with 1% beta-mercaptoethanol was added to sample. The samples were vortexed for one min to disrupt cells and immediately stored at -80℃.

tag: visit

tag: site

value: KEMRI

tag: rin

value: IVB

value: nonLD

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

tag: yeasts

value: Nobs

tag: maritalstatus

value: Married

value: Primary school, some or complete

value: Yes

value: Unchecked


title: Midgut, 2 hours after feeding, replicate 1

tag: tissue

value: midgut

tag: genotype

value: WT

tag: treatment

value: 2 hours after feeding


title: Midgut, 10 minutes after feeding, replicate 6

value: 10 minutes after feeding


title: duizhao: syngeneic groups

city: Harbin

first: zhong

middle: hua

last: tong

state: Heilongjiang Province

address: 194 Xuefu Road, Nangang District

institute: The Second Affiliated Hospital of Harbin Medical University

data_processing:
The Cell Ranger software pipeline (version 2.2.0) provided by 10×Genomics was used to demultiplex cellular barcodes, map reads to the genome and transcriptome using the STAR aligner.
the unique molecular identifier (UMI) count matrix using the R package Seurat(version 2.3.4)
Library size normalization was performed with NormalizeData function in Seurat to obtain the normalized count. Specifically, the global-scaling normalization method “LogNormalize” normalized the gene expression measurements for each cell by the total expression, multiplied by a scaling factor (10,000 by default), and the results were logtransformed.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw gene counts for every gene and every cell

source_name: one sample from lymph nodes of syngeneic cardiac transplanted mice

extract_protocol:
Single cells were suspended in calcium- and magnesium-free PBS containing 0.04% weight/volume BSA. Cells were added to each channel. After generation of GEMs, reverse transcription reactions were engaged barcoded full-length cDNA followed by the disruption of emulsions using the recovery agent and cDNA clean up with DynaBeads Myone Silane Beads (Thermo Fisher Scientific). cDNA was then amplified by PCR with appropriate cycles which depend on the recovery cells. Subsequently, the amplified cDNA was fragmented, end-repaired, A-tailed, and index adaptor ligated and library amplification. Then these libraries were sequenced on the Illumina sequencing platform and 150 bp paired-end reads were generated.
RNA libraries  were prepared with Chromium Single cell 3’ Reagent v3 Kits according to the manufacturer’s protocol.

value: Lymph nodes

tag: strain

value: donor:Balb/c; recipient :Balb/c

tag: age

value: 6-8 weeks

tag: cell type

value: immune cells


title: yizhi: allogeneic group

source_name: one sample from lymph nodes of allogeneic cardiac transplanted mice

value: donor:C57BL/6; recipient :Balb/c


title: Midgut, 10 minutes after feeding, replicate 5


title: Midgut, 10 minutes after feeding, replicate 3


title: 401_Batch6_42_560233966601_S122_L008

value: baseline

value: KEMRI

value: IVD

value: nonLD

value: TRUE


title: 385_Batch6_26_5616_S106_L007

value: Emavundleni

value: IVB

value: Negative

value: Abs

value: Nobs

value: Married

value: Secondary school, some or complete


title: 376_Batch6_17_2000_S97_L007

value: IB

value: LD

value: Obs

value: Never married

value: No

value: Unchecked


title: Midgut, 10 minutes after feeding, replicate 4

value: midgut

value: WT

value: 10 minutes after feeding


title: Midgut, 10 minutes after feeding, replicate 2


title: 375_Batch6_16_272_S96_L007

value: baseline

value: IVD

value: nonLD

value: TRUE


title: WT, replicate 1, scRNAseq

description: 10x Genomics

value: immune cells

value: totoal colon

value: 8-10 weeks old


title: 355_Batch5_68_560244716601_S76_L005

value: KEMRI

value: IIIA

value: Negative

value: Abs

value: Nobs

value: Married

value: Primary school, some or complete

value: Yes


title: 354_Batch5_67_560240696601_S75_L005

value: BV

value: Unchecked


title: 343_Batch5_56_KAA2PQRW-01_S64_L005

value: WRHI

value: IVA

value: Never married

value: Secondary school, some or complete

value: No


title: Midgut, 10 minutes after feeding, replicate 1

value: midgut

value: WT

value: 10 minutes after feeding


title: 342_Batch5_55_HAA2P3NV-01_S63_L005

value: baseline

value: nonLD

value: TRUE

value: Obs


title: 339_Batch5_52_FAA2PFBK-01_S60_L004

value: IVD

value: Negative

value: Abs

value: Nobs


title: Donor 4

city: Stanford

first: Kristina

last: Maas-Bauer

address: 269 Campus Drive

department: Blood and Marrow Transplantation

institute: Stanford University

data_processing:
Sample demultiplexing, barcode processing, alignment to the GRCh38 assembly of the human genome, and single-cell 3′ gene counting were performed using the Cell Ranger Suite version 6.1.2.
A total of  1217 cells were sequenced, with 404267 mean reads per cell and 1250  (984-1949) median genes per cell. The detailed metrics per sample are provided in Supplemental Table 1. Cells with unique gene counts <100 or >2500, as well as cells with >10% of mitochondrial genes were excluded from the analysis.
scRNA-seq analysis was performed using the Seurat R package, version 4
Pseudotime analysis was performed using the Monocle3 package.
Supplementary files format and content: mm10
Supplementary files format and content: for all processed files: tab-separated values files and matrix files

source_name: thymus

extract_protocol:
Thymocytes were thawed at room temperature in RPMI 1640 containing FCS 30%, Penicillin-Streptomycin 1%, DNase I (10 ug/ml, Sigma), and heparin 20 U/ml. After washing, FACS surface staining was performed on ice, after FC blockage, using the following antibodies: Vα24 (FITC, Beckman Coulter), Vβ11 (APC, Beckman Coulter), CD3 (BV605, Biolegend), CD14 (APC Cy7, Biolegend), CD19 (APC Cy7, Biolegend), LIVE/DEAD™ Fixable Aqua Dead Cell Stain Kit (Invitrogen). CD3+, Vα24+, Vβ11+, CD14-, CD19- live cells were FACS-sorted on a FACS Aria-III (BD Biosciences).
Single-cell libraries were generated from FACS-sorted human thymic iNKT cells using the Chromium Controller Single-Cell Instrument and Chromium X instrument and Chromium Single 3′ Library & Gel Bead Kit v3 (10x Genomics).

treatment_protocol: Thymi were obtained after being removed from 3 newborn/infant donors undergoing cardiac surgery between 5 days and 13

value: thymus

value: 3 month old

value: natural killer t cells

tag: Sex

value: male


title: Donor 5

value: 5 month old


title: 338_Batch5_51_KAA2P3NH-01_S59_L004

tag: visit

value: WRHI

value: IVA

value: BV

value: Never married

value: Secondary school, some or complete

value: No

value: Unchecked


title: 363_Batch6_4_560241046601_S84_L006

tag: site

value: KEMRI

value: IVB

value: nonLD

value: TRUE

value: Intermediate

value: Married

value: Yes


title: OE33-KCNQ3_Treated-Lino_3

city: London

first: David

last: Shorthouse

address: 29-39 Brunswick Square

department: School of Pharmacy

country: United Kingdom

institute: UCL

description: Replicate 3

data_processing:
Quality control of raw sequencing reads was performed using FastQC v0.11.7. Reads were aligned to GRCh37 using STAR v2.6.1d. Read counts were generated within R 3.6.1 summarizeOverlaps.
Assembly: GRCh37
Supplementary files format and content: Processed data files contain RPKM and TPM

source_name: Oesophageal Adenocarcinoma

growth_protocol: OE33 was cultured in RPMI (Roswell Park Memorial Institute) 1640 medium supplied with 10% FBS (fetal bovine serum)

extract_protocol: Total RNA was extracted from fresh cells or mouse tissues using Qiagen RNeasy Mini Kit. RNA-seq libraries were prepared using Lexogen CORALL mRNA-seq kit (098.96 and 157.96) according to the manufacture’s protocol. 3 μg and 700 ng of total RNA input were used for cell line and mouse tissue RNA-seq, respectively. The libraries were sequenced in Illumina NovaSeq platform using SR100. For cell lines, three replicates were sequenced for each cell type or drug treatment condition.

treatment_protocol: Linopirdine (L134-10MG, MW 391.46, Sigma) was prepared in absolute ethanol for 100 mM stock. A final concentration of 50 μM was used to treat cells. Amitriptyline hydrochloride (A8404-10G, MW 313.86, Sigma), was prepared in absolute ethanol for 60 mM stock. A final concentration of 30 μM was used to treat cells. Culture medium was refreshed every 3 days.

value: Oesophageal Adenocarcinoma

tag: cell line

value: Cancer

value: KCNQ3 overexpression

value: Linopirdine


title: 337_Batch5_50_6384_S58_L004

value: Emavundleni

tag: rin

value: IVA

tag: bmi

value: Abs

value: Nobs

value: Post-secondary school


title: OE33-KCNQ3_Treated-Lino_2

description: Replicate 2


title: 336_Batch5_49_3600_S57_L004

value: baseline

tag: ngonorrhoeae

tag: chlamydiatrachomatis

value: BV

value: Never married

value: No

value: Unchecked


title: OE33-KCNQ3_Treated-Lino_1

description: Replicate 1


title: P253_08_HP

city: Giessen

first: Sarah

middle: Maria

last: Grundmann

state: Hesse

address: Heinrich-Buff-Ring 26-32

department: Institute of Animal Nutrition and Nutrition Physiology

country: Germany

institute: Justus Liebig University Giessen

description: gene expression data from adult male mice fed a high phosphorus group (P1.2) diet

hyb_protocol: 3.8 µg of the fragmented and labeled ss cDNA were hybridized to Applied Biosystems GeneChip Clariom S mouse arrays for 16 hours at 45°C and 60 rpm in an Applied Biosys-tems GeneChip hybridization oven 640. The hybridized arrays were washed and stained in an Applied Biosystems GeneChip Fluidics Station FS450.

scan_protocol: Fluorescence signals were measured using an Applied Biosystems GeneChip Scanner 3000 7G system. Fluidics and scanning functions were controlled using Applied Biosystems GeneChip Command Console v4.3.3 software.

data_processing: Summarized probe set signals at log2 scale were calculated using the GCCN-SST-RMA algorithm with Applied Biosystems GeneChip Expression Console v1.4 software.

label: Biotin

source_name: M. gastrocnemius, diet P1.2

label_protocol: The cRNA was labeled with biotin using the Affymetrix GeneChip labeling kit.

growth_protocol: The animal experiment was carried out according to the German animal welfare law and had been declared to the Animal Welfare Officer of the University (Registration No.: M_721). The animal housing facility was licensed by the local authorities (Az: FD 62 §11 JLU Stoffwl.). The methods used for humane euthanasia of the animals were in accord-ance with the recommendations of the AVMA guidelines for euthanasia of animals.  The experiment included 24 male, 19-week-old C57BL/6J mice purchased from Charles River (Sulzfeld, Germany). Animals were maintained in groups of two under controlled conditions (12 h light: 12 h dark, 22 ± 1°C ambient temperature, 50-60 % relative humidity).

extract_protocol: Total RNA from muscle aliquots (30 mg) of six male mice each of the P0.3 group and the P1.2 group was extracted using TRIzol reagent (Invitrogen, Karlsruhe, Germany) according to the manufacturer’s protocol. For microarray hybridization, RNA samples were sent on dry-ice to the Center of Excellence for Fluorescent Bioanalytics (Regensburg, Germany). After checking RNA quality using an Agilent 2100 Bioanalyzer (A260:A280 ratios and RNA integrity number (RIN) values were 1.84 ± 0.07 (mean ± SD) and 7.48 ± 0.31, respectively) the samples were processed using an Affymetrix GeneChip Clariom S mouse array.

treatment_protocol: After a one-week acclimation period, mice were randomly assigned to two groups (with adequate phosphorus (P0.3) and with high phosphorus (P1.2)) of 12 mice each. All groups received the same basal diet except for the phosphorus components, which corresponded to the maintenance requirement of mice according to the National Research Council (NRC) [28]. Mice were fed a diet with adequate (0.3%; P0.3) or high (1.2%; P1.2) phosphorus concentration for a period of 6 weeks. From each group, 6 mice were randomly selected for gene array analysis, at the end of the experiment.

tag: gender

value: male

tag: condition

value: 6.5 month

value: gastrocnemius


title: P253_12_HP


title: P253_04_HP


title: P253_06_HP


title: P253_10_HP


title: 331_Batch5_44_BAA2PK1N-01_S52_L004

value: WRHI

value: IB

value: LD

value: TRUE

value: Negative

tag: lactobacilli

tag: mobilincus

tag: yeasts

tag: maritalstatus

value: Secondary school, some or complete


title: Aspergillus flavus, treatment,rep3

data_processing:
The library  was  sequenced on Illumina sequencing platform.
Low quality reads were trimmed by using Trimmomatic (version 0.38)(parameter settings :HEADCROP:8 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36).
Quality control of raw reads was performed using FastQC (version 0.11.5).
Assembly: GCF_013267435.1,GCF_000002545.3,GCA_001576635.1
Supplementary files format and content: tab-delimited text file includes raw counts for each Sample
Supplementary files format and content: tab-delimited text files include RPKM values for each Sample

organism: Aspergillus flavus

source_name: Aspergillus flavus

growth_protocol: Bacterial suspension culture at 37℃;Fungus suspension culture at 28℃

extract_protocol:
RNA was extracted using Invitrogen TRIzol® Reagent. 1 ug of total RNA was used for the construction of sequencing libraries.
The fragmented mRNA was reverse transcripted with SuperScript II and then converted to double-stranded cDNA using RNaseH and DNA Pol I by random priming. After purification, the double-stranded cDNA was subjected to blunt-ending, dA addition to 3’-end and adapter ligation. Finally, PCR was carried out to enrich the adapter ligated cDNA and the libraries were analyzed by Agilent Bioanalyzer 2100 and quantified by qPCR before sequenced by the Illumina sequencing platform.

treatment_protocol: Microorganisms in logarithmic growth phase were cultured for 4 hours after adding MIC values essential oil or not.

value: Aspergillus flavus

tag: treatment

value: treated with Neolamarckia cadamba essential oil for four hours


title: 330_Batch5_43_BAA2P7VR-01_S51_L004

value: Abs

value: Nobs


title: OE33-KCNQ3_Treated-Ami_3

description: Replicate 3

tag: tissue

value: Oesophageal Adenocarcinoma

value: Cancer

tag: genotype

value: KCNQ3 overexpression

value: Amitriptyline


title: Aspergillus flavus, treatment,rep1

tag: cell type


title: P253_07_NP

description: gene expression data from adult male mice fed an adequate phosphorus diet (P0.3)

source_name: M. gastrocnemius, diet P0.3

value: male

tag: strain

tag: age


title: 329_Batch5_42_1568_S50_L004

tag: visit

tag: site

value: Emavundleni

value: IVA

value: nonLD

value: BV

value: Never married

value: No

value: Unchecked


title: OE33-KCNQ3_Treated-Ami_2

description: Replicate 2

tag: cell line


title: Aspergillus flavus, control,rep3

value: control


title: 328_Batch5_41_433_S49_L004

value: baseline

tag: rin

value: TRUE

tag: bmi

tag: ngonorrhoeae

value: Negative

value: Secondary school, some or complete


title: P253_03_NP

tag: gender

tag: condition

value: 6.5 month

value: gastrocnemius


title: P253_02_HP


title: OE33-KCNQ3_Treated-Ami_1

description: Replicate 1

value: Oesophageal Adenocarcinoma

value: Cancer

value: KCNQ3 overexpression


title: P253_01_NP

value: male


title: P253_09_NP


title: Aspergillus flavus, control,rep1

value: Aspergillus flavus


title: Aspergillus flavus, control,rep2


title: P253_11_NP


title: P253_05_NP


title: 325_Batch5_38_EAA2P4ZZ-01_S46_L003

value: WRHI

value: IVB

value: nonLD

tag: chlamydiatrachomatis

tag: lactobacilli

value: Abs

tag: mobilincus

value: Nobs

value: Post-secondary school


title: OE33-KCNQ3_Treated-Ctr_3

description: Replicate 3

tag: treatment


title: Sp_5dpf_2_scRNAseq

city: Napoli

first: Maria Ina

last: Arnone

address: Villa Comunale 1

department: Biology and Evolution of Marine Organisms

country: Italy

institute: Stazione Zoologica Anton Dohrn

data_processing:
Fastq reads were aligned to S. purpuratus genome version 3.1 using Cell Ranger 3.0.2 (10x Genomics).
Cell Ranger output files for the two biological replicates were used in Seurat v4.0.5 R package.
Genes transcribed in less than three cells and cells with less than  250 transcribed genes were excluded.
Datasets were normalized and variable genes were found using vst method with maximum 2000 variable features.
Data was integration was performded using anchors between the two different objects.
Data was scaled and principal component (PCA) analysis was performed. Sharing Nearest Neighbor (SNN) was computed with 36 dimensions (resolution 1.0). UMAP was used to perform clustering dimensionality reduction..
Cluster markers were found using the genes that are detected in at least 0.01 fraction of min.pct cells in the two clusters.
The 3 dpf scRNA-seq and 5 dpf datasets were merged using the harmony package (v0.1.0._and 30 dimensions).
Subsetting analysis was performed by selecting all the cells present in neurons and immune cells that express Opsin3.2 and Opsin2 respectively, through the Seurat Subset function.
Assembly: S. purpuratus genome 3.1
Supplementary files format and content: R Seurat object

organism: Strongylocentrotus purpuratus

source_name: dissociated 5dpf pluteus larvae

growth_protocol: AdultStrongylocentrotus purpuratus were kept in circulating seawater aquaria at Stazione Zoologica Anton Dohrn in Naples. Spawning was induced by vigorous shaking of adult animals. Embryos and larvae were raised at 15°C in filtered 9:1 diluted Mediterranean Sea water (FSW) at 12/12h light/dark cycle.  Half of the water was exchanged 2 times per week. After the 3 days post fertilization (dpf)  larvae were fed 3 times per week 1000 cells/mL Dunaliella sp..

extract_protocol:
Larvae were collected, seawater was removed, and larvae were resuspended in Ca2+ Mg2+-free artificial sea water and then passed to dissociation buffer containing 1 M glycine and 0.02 M EDTA in Ca2+ Mg2+-free artificial sea water. Larvae were incubated for 10 min on ice and dissociated gently into cells via pipette aspiration.
Single cell cDNA libraries were prepared using the Chromium Single Cell 3’ Reagent Kit, Chemistry v3.
Libraries were indexed, multiplexed and sequenced on Illumina NextSeq 500 to generate paired end reads.

value: 5dpf pluteus cells

tag: developmental stage

value: 5dpf pluteus larva


title: Sp_5dpf_1_scRNAseq


title: 324_Batch5_37_BAA2NY5G-01_S45_L003

value: baseline

value: IIIA

value: LD

value: TRUE

value: Negative

tag: yeasts

value: Obs

tag: maritalstatus

value: Never married

value: No

value: Unchecked


title: MDAMB231, 3D, Day 7, Biol rep 3

city: Stockholm

first: Caterina

last: Collodet

state: Stockholm

address: Roslagstullsbacken 21

department: Protein technology

country: Sweden

institute: KTH

data_processing:
Illumina bcl2fastq (v2.20.0) was used for basecalling and demultiplexing.
Read quality was checked for each sample using FastQC (v0.11.8).
Reads were aligned to Ensemble GRCh38 reference genome using STAR (v2.6.1d).
Read summarization to gene counts was performed using featureCounts (v1.5.1).
Normalized counts were generated using DESeq2 (v1.28.1).
Assembly: GRCh38/hg38.
Supplementary files format and content: Tab-delimited text file includes raw counts for each sample.

source_name: Breast cancer

extract_protocol:
RNeasy microkit (74034, QIAGEN)
200 ng of total RNA was used to generate stranded mRNA libraries with the mRNA prep ligation kit according to manufacturer's instructions (#20040534, Illumina, USA). The concentration and quality of the cDNA libraries were assessed by Qubit (Life Technologies, USA) and TapeStation, respectively.
Illumina RNA-seq (Nextseq 2000, P2 flowcell, Paired End, dual index).

tag: tissue

value: Breast cancer

tag: cell type

value: Epithelial cells

tag: culture protocol

value: 3D FN-silk

tag: time point

value: Day 7


title: ID080UST

city: Bethesda

first: Niki

last: Moutsopoulos

address: 30 convent Dr

institute: NIDCR

data_processing:
Basecalls performed using Illumina’s RTA  2.0.12
Sample demultiplexing, alignment and gene counts were performed using the 10X Genomics CellRanger pipeline v2.0.0 (GM136, GM143, GM183, GM184a, PD134) or v3.0.1 ( BM150, BM152, BM156, BM157, BM158, BM165, BM168, BM169, GM144, GM147, GM148, GM238, GM241, GM242, GM169, GM283, GM289, PD153, PD161, PD161b, PD164, PD164b, PD164c, PD170, ID080UST) using default settings.
Secondary analysis was performed using Seurat v3 and nichenetr R packages.
Assembly: GRCh38
Supplementary files format and content: CellRanger v3.0.1 gene counts matrices.
Supplementary files format and content: Raw counts expression matrix.

source_name: Gingiva

extract_protocol:
To prepare single cell suspensions biopsies were minced and digested using Collagenase II (Worthington Biochemical Corporation) and DNase (Sigma) and processed through the gentleMACS Dissociator (Miltenyl) utilizing a nasal mucosa protocol for processing36. Following tissue dissociation, cells were passed through a 70μm filter (Falcon, Corning), washed, and counted with a Cellometer Auto 2000 (Nexcelom).
Single-cell suspensions were loaded onto a 10X Chromium Controller (10X Genomics) and library preparation was performed according to the manufacturer’s instructions for the 10X Chromium Next GEM Single Cell Library kit v3 (10X Genomics). Libraries were then pooled in groups of 4 and sequenced on 4 lanes on a NextSeq500 sequencer (Illumina) using 10X Genomics recommended reads configuration.

tag: disease state

value: Gingiva


title: OE33-KCNQ3_Treated-Ctr_1

description: Replicate 1

value: Oesophageal Adenocarcinoma

tag: cell line

value: Cancer

tag: genotype

value: KCNQ3 overexpression


title: MDAMB231, 3D, Day 7, Biol rep 2


title: 319_Batch5_32_4576_S40_L003

tag: visit

tag: site

value: Emavundleni

tag: rin

value: IVA

value: nonLD

tag: bmi

tag: ngonorrhoeae

value: Abs

value: BV

value: Nobs

value: Post-secondary school

value: Yes


title: OE33-KCNQ3_Treated-Ctr_2

description: Replicate 2


title: MDAMB231, 2D, Day 7, Biol rep 2

extract_protocol:
RNeasy minikit (74104, QIAGEN)
200 ng of total RNA was used to generate stranded mRNA libraries with the mRNA prep ligation kit according to manufacturer's instructions (#20040534, Illumina, USA). The concentration and quality of the cDNA libraries were assessed by Qubit (Life Technologies, USA) and TapeStation, respectively.
Illumina RNA-seq (Nextseq 2000, P2 flowcell, Paired End, dual index).

value: 2D tissue culture treated well


title: OE33-Ctr_Treated-Lino_3

description: Replicate 3

value: WT

value: Linopirdine


title: MDAMB231, Flask, Day 0, Biol rep 3

value: Breast cancer

value: Epithelial cells

value: 2D tissue culture treated flask

value: Day 0


title: MDAMB231, 2D, Day 7, Biol rep 1

value: Day 7


title: MDAMB231, 2D, Day 7, Biol rep 3


title: 307_Batch5_20_560238726601_S28_L002

value: KEMRI

value: IB

value: LD

value: TRUE

value: Negative

tag: chlamydiatrachomatis

tag: lactobacilli

tag: mobilincus

value: Married

value: Secondary school, some or complete

value: Unchecked


title: 306_Batch5_19_560234156601_S27_L002

value: baseline

value: Abs

tag: yeasts

value: Nobs

value: Yes


title: MDAMB231, 3D, Day 7, Biol rep 1

value: Breast cancer

value: 3D FN-silk


title: MCF7, 3D, Day 7, Biol rep 3

value: Epithelial cells


title: OE33-Ctr_Treated-Lino_2

description: Replicate 2

value: Oesophageal Adenocarcinoma

value: Cancer

value: WT

tag: treatment

value: Linopirdine


title: OE33-Ctr_Treated-Lino_1

description: Replicate 1

tag: tissue


title: MDAMB231, Flask, Day 0, Biol rep 1

tag: cell type

value: 2D tissue culture treated flask

value: Day 0


title: 302_Batch5_15_EAA2NSXB-01_S23_L002

value: WRHI

value: IIIA

value: LD

value: TRUE

value: Negative

tag: maritalstatus

value: No


title: MDAMB231, Flask, Day 0, Biol rep 2

tag: culture protocol

tag: time point


title: OE33-Ctr_Treated-Ami_3

description: Replicate 3

tag: cell line

value: Amitriptyline


title: OE33-Ctr_Treated-Ami_2

description: Replicate 2

tag: genotype


title: MCF7, 3D, Day 7, Biol rep 1

value: Day 7


title: MCF7, 2D, Day 7, Biol rep 3

value: Breast cancer

value: 2D tissue culture treated well


title: 300_Batch5_13_HAA2NJT2-01_S21_L002

tag: visit

value: baseline

value: Abs

value: Nobs

value: Never married

value: Secondary school, some or complete

value: Yes

value: Unchecked


title: OE33-Ctr_Treated-Ami_1

description: Replicate 1

value: Oesophageal Adenocarcinoma

value: Cancer

value: WT


title: 287_Batch4_72_560236936601_S8_L001

tag: site

value: KEMRI

value: IIIA

value: LD

value: TRUE

value: Married

value: Checked


title: MCF7, 2D, Day 7, Biol rep 1

value: Breast cancer

value: Epithelial cells

value: 2D tissue culture treated well

value: Day 7


title: OE33-Ctr_Treated-Ctr_2

description: Replicate 2


title: MCF7, Flask, Day 0, Biol rep 1

value: 2D tissue culture treated flask

value: Day 0


title: MCF7, Flask, Day 0, Biol rep 2


title: 286_Batch4_71_560232636601_S7_L001

value: baseline

tag: rin

value: IVD

value: nonLD

value: Negative

value: Abs

value: BV

value: Nobs

value: Secondary school, some or complete

value: Yes


title: MCF7, 2D, Day 7, Biol rep 2


title: CRC organoid, asparaginase

city: Hannover

first: Laura

last: Hinze

state: Niedersachsen

address: Carl-Neuberg-Straße 1

institute: Hannover Medical School

data_processing:
Initial quality control of transcriptomics data was performed using FastQC version 0.11.9
“filter by tile” function of BBMap was used to discard low-quality reads
trimming with trimmomatic version 0.39 using specifications: ILLUMINACLIP:TruSeq3-PE.fa:2:30:10:2:True HEADCROP:14 LEADING:3 TRAILING:3 SLIDINGWINDOW:4:15 MINLEN:36
preprocessed reads were mapped using kallisto version 0.46.1 with a transcriptome index of Mus musculus GRCm38.p6
Assembly: Mus musculus NCBI:GCA_000001635.8
Supplementary files format and content: table in tab-separated values formating including kallisto estcount and  TPM, as well as log2FC for the samples

source_name: organoid

growth_protocol:
Organoids were resuspended in Matrigel composed of 25% advanced DMEM/F12 (Gibco) and 75% Matrigel (Corning)
After the Matrigel polymerized, organoids were cultured in complete small-intestinal organoid growth medium consisting of organoid basal medium supplemented with murine Noggin (50 ng/mL), murine EGF (R&D Systems, 50 ng/mL), and human RSPO1 (R&D Systems).

extract_protocol:
Total RNA was isolated at indicated time points using the RNeasy kit (Qiagen) according to the manufacturer’s protocols.
Library preparation was performed by eurofins genomics

treatment_protocol:
On day 1, 100 U/L asparaginase or vehicle (PBS) were added to organoids, which were cultured in basal medium without growth factor supplementation.
Subsequently, organoids were split every 48h and treatment pressure was maintained by continuously adding asparaginase or vehicle to achieve outgrowth of resistant organoids.
On day 13, RNA was isolated for sequencing.

value: organoid

value: Rspo3 fusion positive CRC organoids

value: colorectal cancer cells

value: vehicle


title: CRC organoid, vehicle

value: asparaginase


title: OE33-Ctr_Treated-Ctr_1

description: Replicate 1

value: Oesophageal Adenocarcinoma

value: Cancer

value: WT


title: 284_Batch4_69_560236326601_S5_L001

value: baseline

value: KEMRI

value: IVB

value: TRUE

tag: bmi

value: Married

value: Unchecked


title: 285_Batch4_70_560241776601_S6_L001

value: nonLD

tag: ngonorrhoeae

value: Negative

value: Abs

value: BV

value: Nobs


title: 120_20180727_12_sample6_IL13

city: Bunkyo-ku

first: Yoshitaka

address: Hongo 7-3-1

institute: The University of Tokyo

description: 3' mRNA library: read1 file contains transcript; read2 file contains cell barcord

data_processing:
After library demultiplexing (SMART-Seq DE3 Demultiplexer; Clontech) and adaptor trimming (by deleting 7 bases from the end), read 1 sequences were aligned to reference sequences (human: GRCh38.90) using TopHat2, and the read counts were calculated using HTSeq3.
Single-cell libraries stochastically lose information on low copy number transcripts in a quantity-dependent manner in the starting resource. Note should be taken of the correction for counts to avoid cell-to-cell bias.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files

source_name: Silent, index: IL13

extract_protocol:
We obtained pooled mesentery from 20 wildtype C57BL/6 mice. Lineage-negative cells were selected by negative selection using MicroBeads and AutoMACS (Miltenyi Biotec GmbH). Then, c-Kit+Sca-1+ cells were sorted as ILC2s using a FACSAria flow cytometer (BD Bioscience).
cDNA libraries were prepared using SMART-Seq v4 3’-DE Kits (Clontech) according to the manufacturer’s instructions, with some modifications. A total of 3,892 copies of ERCC spike-in RNA were added to each sample as a mixture of quantitative internal controls. The cDNA was purified using Agencourt AMPure XP magnetic beads (Beckman Coulter). Library quality check was performed using an Agilent 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA, USA) and Agilent High Sensitivity DNA Kits (5067-4626). Degraded or low-yield samples were removed. Qubit High Sensitivity assays (Thermo Fisher Scientific) were performed to quantify the cDNA in each library, and 5 or 6 libraries with different indexed primers were evenly pooled. Pooled cDNA (400 pg) was tagmented using Nextera XT DNA Library Prep Kits (Illumina, San Diego, CA, USA), as described in the protocol. Library size and cDNA amount were quantified using an Agilent High Sensitivity DNA Kit and Qubit High Sensitivity assays, respectively.

value: fat tissues

value: incubated with IL-2/IL-33


title: MCF7, 3D, Day 7, Biol rep 2

value: Breast cancer

value: Epithelial cells

value: 3D FN-silk

value: Day 7


title: Aspergillus flavus, treatment,rep2

value: Aspergillus flavus

value: treated with Neolamarckia cadamba essential oil for four hours


title: MCF7, Flask, Day 0, Biol rep 3

value: 2D tissue culture treated flask

value: Day 0


title: 318_Batch5_31_3040_S39_L003

value: baseline

value: Emavundleni

value: IVB

value: TRUE

tag: chlamydiatrachomatis

value: Never married

value: Post-secondary school

value: Yes


title: OE33-KCNQ3.S1_3

description: Replicate 3

value: Oesophageal Adenocarcinoma

value: Cancer

value: KCNQ3 overexpression


title: 119_20180727_11_sample6_IL13

value: fat tissues

value: incubated with IL-2/IL-33


title: 283_Batch4_68_560238886601_S4_L001

value: KEMRI

value: IB

value: LD

value: Negative

tag: lactobacilli

value: Abs

value: Nobs

value: Married

value: Secondary school, some or complete

value: Unchecked


title: 118_20180727_10_sample6_IL13


title: 117_20180727_9_sample6_IL13


title: Pool_B2

type: genomic

city: Eiheiji-cho, Yoshida-gun

first: Shota

last: Nishitani

state: Fukui

address: 23-3 Matsuoka-Shimoaizuki

department: Research Center for Child Mental Development

institute: University of Fukui

hyb_protocol: Bisulfite-converted DNA was amplified, fragmented and hybridised to Illumina Infinium Human MethylationEPIC Beadchip using standard Illumina protocol

scan_protocol: Arrays were imaged using BeadArray Reader using standard recommended Illumina scanner setting

data_processing: GenomeStudio Software v2.0.5

label: Cy5 and Cy3

label_protocol: Standard Illumina Protocol

extract_protocol: Whole blood samples were collected in EDTA tubes and immediately preserved in RNAlater® (whole blood : RNAlater® = 5 : 13). They were stored overnight at 4 °C, then at −20 °C for long-term storage. Although this preprocessing was originally for RNA extraction, we followed the instructions in the RiboPure RNA Purification Kit (Thermo Fisher Scientific, Inc., MA, US) for preprocessing for DNA extraction using RNAlater® preserved blood samples. In brief, the RNAlater® preserved blood samples (720 uL) were centrifuged for 1 min at 16 000 ×g, and the supernatant was removed. Then, 200 uL of PBS was pipetted in and mixed, and centrifugation and supernatant removal were repeated. Finally, 200 uL of PBS was added and pipetted together before being used for DNA extraction. QIAamp DNA Mini kit (QIAGEN, Hilden, Germany) was used to extract DNA, and the protocols for each tissue type were followed.

tag: sample type

value: blood (pooled from 11 subjects)

tag: gender

value: male

tag: age

tag: group

value: typically developing

tag: race

value: Japanese


title: OE33-KCNQ3.S1_1

description: Replicate 1

tag: tissue

value: Oesophageal Adenocarcinoma

tag: cell type

value: Cancer

tag: treatment


title: 115_20180727_7_sample6_IL13

last: Shirasaki

value: fat tissues


title: OE33-Ctr_Treated-Ctr_3

description: Replicate 3

tag: cell line

value: WT


title: 282_Batch4_67_560234856601_S3_L001

value: baseline

value: KEMRI

value: TRUE

tag: mobilincus

tag: yeasts

tag: maritalstatus

value: Yes


title: 114_20180727_12_sample5_IL13

source_name: Activated, index: IL13

value: incubated with IL-2/IL-33


title: 271_Batch4_56_7696_S114_L008

tag: visit

tag: site

value: Emavundleni

tag: rin

value: IVD

value: nonLD

value: Negative

value: Abs

value: BV

value: Nobs

value: Never married


title: 116_20180727_8_sample6_IL13


title: OE33-Ctr50_3

description: Replicate 3

value: Oesophageal Adenocarcinoma

tag: genotype


title: 111_20180727_9_sample5_IL13


title: 113_20180727_11_sample5_IL13


title: Pool_A2

value: blood (pooled from 11 subjects)

value: male

value: child maltreatment

value: Japanese


title: 269_Batch4_54_AAA2PK9P-01_S112_L008

value: WRHI

value: IIIA

value: LD

tag: bmi

tag: ngonorrhoeae

tag: chlamydiatrachomatis

tag: lactobacilli

value: Obs

value: Secondary school, some or complete

value: No

value: Unchecked


title: 110_20180727_8_sample5_IL13

value: fat tissues

value: incubated with IL-2/IL-33


title: 270_Batch4_55_6048_S113_L008

value: baseline

value: Emavundleni

value: IVD

value: nonLD

value: TRUE

value: Negative

value: Abs

value: BV


title: OE33-Ctr50_2

description: Replicate 2

value: Oesophageal Adenocarcinoma

value: Cancer

value: WT


title: 112_20180727_10_sample5_IL13


title: 109_20180727_7_sample5_IL13


title: OE33-KCNQ3.S1_2

description: Replicate 2

value: KCNQ3 overexpression


title: 257_Batch4_42_AAA2P38Q-01_S100_L007

value: WRHI

value: IIIA

value: LD

value: Nobs

value: Never married

value: Secondary school, some or complete


title: OE33-Ctr50_1

description: Replicate 1


title: 108_20180727_12_sample4_IL13

source_name: Transition state (90min), index: IL13

value: fat tissues

value: incubated with IL-2/IL-33


title: Pool_B1

tag: sample type

value: blood (pooled from 11 subjects)

tag: gender

value: male

tag: age

tag: group

value: typically developing

value: Japanese


title: Pool_A1

value: child maltreatment

tag: race


title: 256_Batch4_41_BAA2NVYS-01_S99_L007

value: baseline

value: TRUE

value: Negative

value: Abs

value: Unchecked


title: 107_20180727_11_sample4_IL13

tag: tissue

tag: cell type

tag: treatment


title: 106_20180727_10_sample4_IL13


title: 104_20180727_8_sample4_IL13


title: 255_Batch4_40_6016_S98_L007

value: Emavundleni

value: IVA

value: nonLD

tag: mobilincus

value: Intermediate

tag: yeasts

tag: maritalstatus

value: No


title: 254_Batch4_39_4160_S97_L007

tag: visit

tag: site

tag: rin

value: IIIA

value: LD

value: Nobs

value: Never married

value: Secondary school, some or complete


title: 100_20180727_10_sample3_IL13

source_name: Transition state (60min), index: IL13

value: fat tissues

value: incubated with IL-2/IL-33


title: 103_20180727_7_sample4_IL13


title: 102_20180727_12_sample3_IL13


title: AD patient, PBMC SNUBH-9-2

city: Seoul

first: Namphil

last: Kim

address: Gwanak-ro 1

department: Electrical and Computer Engineering

institute: Seoul National University

description: AD patient, PBMC

data_processing:
The raw NGS forward (R1) and reverse (R2) reads were merged, filtered based on Phred scores, and subclustered using UMI using paired-end read merger (PEAR), v0.9.10, and Clustal Omega, v1.2.4, with the default setting30,31. The sequence annotation process used the IMGT (International Immunogenetics Information System) constant gene database32 to obtain the isotype, and IgBLAST, v1.17.133 to obtain VJ genes, CDR1/2/3 sequences, and the number of mutations from the corresponding V genes as previously described16. To eliminate the possibility of contamination due to index swapping within Illumina flow cells between samples, reads with identical sequences including the UMI from different samples were excluded on the basis that such an event is highly unlikely without contamination34. The combined NGS throughput of each sample is listed in Extended table 2. Sequencing reads that have survived through the entire process is considered to be a productive BCR sequence.
Supplementary files format and content: sequence_id     duplicate_count frequency       sequence        sequence_aa     sequence_alignment      germline_alignment      v_call  j_call  c_call  junction        junction_aa      cdr1    cdr2    cdr3    cdr1_aa cdr2_aa cdr3_aa rev_comp        productive      v_cigar j_cigar v_alignment_length      v_alignment_mutation

source_name: PBMC

extract_protocol:
All peripheral blood samples were collected by EDTA tubes (BD Vacutainer K2EDTA tubes, 367525) at least 15 ml in total per a patient29. Peripheral blood mononuclear cells (PBMCs) and plasma were separated by density-gradient centrifugation using Ficoll (Cytiva Ficoll-Paque Plus, 17-1440-02) solution. After the PBMC suspension was resuspended in CELLBANKER (Amsbio CELLBANKER 2, 11914), the collected PBMCs were immediately cryopreserved and stored in a Freezing container (Nalgene Mr. Frosty, C1562) for a week. Total RNA was isolated by TRIzol Reagent (Invitrogen TRIzol Reagents, 15596026) following the manufacturer’s instructions.
For the NGS library preparation of BCR heavy chain sequence, genes encoding the variable region of the heavy chain (VH) at the 5 prime forward part and the first constant region of the heavy chain (CH1) domain at the 3 prime reverse part were amplified by specific PCR primers as reported previously16. All primer sequences are listed in Extended Table 2. In short, one microgram of total RNA was used as the input template for library preparation. Next, reverse transcription was conducted as following the manufacturer’s instructions using SuperScript IV First-Strand Synthesis System (Invitrogen, 18091050) with CH1 gene-specific primers for five immunoglobulin heavy chain isotypes containing UMI (unique molecular identifiers) barcodes that consist of 12 random nucleotides, 14 base pair in total; NNNNTNNNNTNNNN, and partial Illumina adapters (No. 1-8). After first-strand cDNA synthesis, it was purified with SPRI beads (Beckman Coulter AMPure XP Reagents, A63882) at a 1:1.8 ratio and second-strand cDNA was synthesized using a KAPA Biosystems kit (Roche KAPA HiFi Hotstart PCR kit, KK2502) with VH gene-specific primers (No. 9-14; 95°C for 3 min, 98°C for 30 s, 60°C for 45 s, and 72°C for 6 min). Double-stranded cDNA was purified through SPRI beads at a 1:1 ratio. Following that, it was amplified using KAPA Biosystems kit and double primers containing Illumina adapters and index sequences (No. 15, 16; 95°C for 3 min, 25 cycles of 98°C for 30 s, 60°C for 30 s, 72°C for 1 min, and 72°C for 5 min). The PCR products were subjected to electrophoresis on a 1.5% agarose gel to separate through the length of DNA and purified using QIAquick gel extraction kit (QIAGEN, 28704) following the manufacturer’s protocols. The final NGS libraries were obtained using SPRI beads at a 1:1 ratio and quantified with a 4200 TapeStation System (Agilent Technologies, G2991BA) for QC.
Libraries with a single peak of appropriate length were subjected to NGS analysis using the Illumina Nocaseq6000 platform.

value: PBMC

tag: cell line


title: 98_20180727_8_sample3_IL13


title: AD patient, PBMC SNUBH-7-2

description: AD patient, PBMC


title: 235_Batch4_20_560251056601_S78_L006

source_name: endocervical cells

value: KEMRI

value: IVD

value: TRUE

tag: bmi

tag: ngonorrhoeae

tag: chlamydiatrachomatis

value: BV

value: Married

value: Primary school, some or complete

value: Yes


title: AD patient, PBMC SNUBH-8-1

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-9-1

description: AD patient, PBMC


title: 99_20180727_9_sample3_IL13


title: 96_20180727_12_sample2_IL13

source_name: Transition state (30min), index: IL13


title: 227_Batch4_12_JAA2PBMB-01_S70_L005

value: WRHI

value: Negative

tag: lactobacilli

value: Abs

value: Unchecked


title: 234_Batch4_19_560243216601_S77_L006

value: baseline

value: nonLD

value: Intermediate

value: Obs


title: AD patient, PBMC SNUBH-7-1

description: AD patient, PBMC


title: 101_20180727_11_sample3_IL13

value: fat tissues

value: incubated with IL-2/IL-33


title: 95_20180727_11_sample2_IL13


title: 94_20180727_10_sample2_IL13


title: 93_20180727_9_sample2_IL13


title: AD patient, PBMC SNUBH-6-2

description: AD patient, PBMC

value: PBMC


title: AD patient, PBMC SNUBH-5-1

description: AD patient, PBMC


title: AD patient, PBMC SNUBH-6-1

description: AD patient, PBMC