title: EV.day3.4_S19

description: 1x75 bp format

source_name: Emty vector control (EV)

value: Empty vector


title: MDS26

status: Public on Feb 07 2024

type: SRA

city: Singapore

first: Qiaoyang

last: Sun

address: 20 College Rd

department: Neurology

country: Singapore

institute: National Neuroscience Institute

library_source: genomic

data_processing:
The sequencing quality of the fastq files of MeDIP-seq was assessed before mapping to the hg19 using BWA. PCR duplicates were removed if both ends were at the same positions. Total number of mapped reads, mapping quality and fragment size were evaluated. For samples passing quality cut-offs, we proceeded to identification of differential methylation using both QSEA package in the R BioConductor and MACS2 and obtained the union of the two results as tentative candidates for downstream analysis. For each identified candidate, methylation level was quantified using featureCounts and normalized to Reads Per Million mapped reads (RPM). These normalized RPM counts cross different samples were further employed to extract the DMRs between two groups, e.g. pre-AML/MDS cases and controls or pre-AML and pre-MDS.
Assembly: hg19
Supplementary files format and content: log2 normalized counts (10 bg)

molecule: genomic DNA

organism: Homo sapiens

source_name: Peripheral blood

growth_protocol: whole blood

extract_protocol:
Total genomic DNA was extracted from 0.5 ml of whole blood using Qiagen DNeasy Blood & Tissue Kits.
The total genomic DNA was ultrasonic fragmented to 150-300 bp using Covaris M220 machine, following by end-repair and A-tailing using Kapa HyperPrep Kit (Kapa Biosystems). The A-tailed DNA were then ligated with the NEBNext adaptor, purified with AMPure XP beads (Beckman Coulter) and then digested with USER enzyme (New England BioLabs) to release the dU loop structure of the adapter. The products were further purified using Qiagen MinElute PCR Purification Kit. Subsequently, MeDIP immunoprecipitation using MagMeDIP kit (Diagenode) was performed following previously described protocols. An average of 100ng of fragmented DNA were used for the MeDIP immunoprecipitation

treatment_protocol: whole blood

tag: tissue

value: Peripheral blood

tag: cell type

value: Blood

tag: genotype

tag: chip antibody

value: 5-methylcytosine (5-mC) Antibody


title: EV.day3.3_S18

city: Sydney, Chippendale

first: Matthias

last: Windhagauer

state: NSW

address: 745 Harris St

country: Australia

institute: University of Technology Sydney

description: 1x75 bp format

library_source: transcriptomic

data_processing:
Trimgalore! was used to to trim Fastq files using default parameters.
FastQC was used to for quality control of fastq files pre- and post trimming. Reports were compiled by MultiQC v1.11.
Subsequently the reads were pseudo-aligned to the Phaeodactylum-tricornutum.ASM15095v2 transcriptome using kallisto v0.44.0 to give gene-level counts. Counts were combined for multiple transcripts.
Genes were filtered as follows: at least 10 counts in at least 3 out of 4 replicates.
Assembly: ASM15095v2
Supplementary files format and content: All presented counts are voom-transformed.

molecule: total RNA

organism: Phaeodactylum tricornutum CCAP 1055/1

extract_protocol:
A volume relative to 10^8 cells was added to 0.9% NaCl solution (-4°C) and centrifuged for 3 min. Total RNA extraction was done using Trizol aget following the protocol of the RNAeasy mini purification kit (Quiagen).
Samples were converted into libraries using the Illumina stranded mRNA library kit.

tag: time

value: Day 3 post induction

value: diatom

tag: treatment

value: P-limitation (standard condition)


title: MDS23


title: MDS14


title: MDS20


title: L2792

city: Leiden

first: Debora

last: Meijer

address: Albinusdreef 2

department: Pathology

country: Netherlands

institute: Leiden University Medical Center

data_processing:
Raw RNA-seq data was processed by the RNA-seq BioWDL pipeline using default settings, developed by the SASC (https://biowdl.github.io/, LUMC, Leiden, the Netherlands)
Reads were aligned against hg38 with STAR and expression quantification was performed using HTseq-count
Assembly: hg38
Supplementary files format and content: Tab-delimited tsv file with raw counts for each sample

source_name: tumor

extract_protocol:
RNA was isolated from tissue sections (thickness = 20 µm) in TRIzol (15596018, Ambion) according to manufacturer’s instructions. RNA purification was performed using RNaesy mini kit (74104, Qaigen) and included DNAse treatment according to manufacturer’s instructions
The NEBNext Ultra II Directional RNA Library Prep Kit for Illumina was used to process the samples.

tag: disease

value: Osteosarcoma

value: tumor

tag: patient id

tag: progression status

value: recurrence


title: EV.day3.1_S16

description: 1x75 bp format


title: MDS11


title: EV.day3.2_S17

description: 1x75 bp format


title: L2559

value: primary


title: MDS08


title: L2377


title: MDS02


title: MDS34


title: MDS05


title: EV.day1.4_S3

description: 1x75 bp format

value: Day 1 post induction


title: HUVECs with HG+Mg2+medium-3

city: chengdu

first: linfeng

last: liu

address: wuhou

country: China

institute: sichuan university

data_processing:
Clean reads were aligned to the mouse genome  by HISAT2.
Read counts were calculated by featureCounts.
Differential analysis were performed using R package DESeq2.
Assembly: hg38
Supplementary files format and content: raw counts

growth_protocol: Human Umbilical Vein Endothelial Cells (HUVEC) provided by State Key Laboratory of Biotherapy, West China Second University Hospital, Sichuan University, were cultured in Dulbecco’s modified Eagle medium (DMEM) (Hyclone, Laboratories, Logan, UT, USA) containing 10% fetal bovine serum (Gibco, Grand Island, NY, USA), 100 U/mL penicillin (Hyclone, Cytiva, Marlborough, MA, USA) and 100μg/mL streptomycin (Hyclone, Cytiva, Marlborough, MA, USA).

extract_protocol:
Total RNA was extracted with Trizol reagent (Invitrogen, Carlsbad, CA, USA) and RNA integrity and quantity were measured using the Agilent 2100/4200 system.
RNA library for RNA-seq was prepared as fllows: mRNA was purified from total RNA using polyT and then fragmented into 300~350 bp fragments, the first strand cDNA was reverse-transcribed using fragmented RNA and dNTPs (dATP, dTTP, dCTP and dGTP) and second strand cDNA synthesis was subsequently performed. Remaining overhangs of double-strand cDNA were converted into blunt ends via exonuclease/polymerase activities. After adenylation of 3’ ends of DNA fragments, sequencing adaptors were ligated to the cDNA and the library fragments were purified. The template was enriched by PCR, and the PCR product was purified to obtain the final library.

treatment_protocol: HUVEC were cultured in three different conditions:  high glucose (HG, 35mM), and HG+Mg2+ (MgSO4, MACKLIN).

tag: cell line

value: high glucose+Mg2+


title: EV.day1.3_S9

description: 1x75 bp format


title: MDS37


title: EV.day1.2_S2

description: 1x75 bp format


title: HUVECs with HG+Mg2+medium-2

source_name: Human Umbilical Vein Endothelial Cells (HUVEC)


title: MDS22


title: HUVECs with HG medium-3

value: Human Umbilical Vein Endothelial Cells (HUVEC)

value: high glucose


title: EV.day1.1_S1

description: 1x75 bp format


title: HUVECs with HG medium-2


title: MDS16


title: BACI358, Resistant, Time 60 minutes, Replicate B

city: Frederick

first: Christopher

middle: Patrick

last: Stefan

state: MD

address: 1425 Porter Street

country: USA

institute: USAMRIID

data_processing:
FASTQ files were imported into CLC Genomics workbench and analyzed using the RNA-Seq Analysis workflow. Reads were mapped using mapping setting: mismatch cost (2), insertion cost (2), deletion cost (3), length fraction (0.8), and similarity fraction (0.8). Paired reads were counted as two when calculating transcripts per million (TPM).
Assembly: GCF_000008445.1, GCF_000222975.1
Supplementary files format and content: Excel file containing raw TPM counts from CLC genomics workbench

organism: Bacillus anthracis

source_name: culture

growth_protocol: Glycerol stocks were plated on sheep’s blood agar plates, grown overnight at 37°C, and selected for recovery the following day in tryptic soy broth (TSB). Cells were recovered in TSB for approximately 3 hours then diluted to a McFarland standard of 0.5 using the DensiChek Plus

extract_protocol:
2 volumes of RNAprotect Bacteria Reagent was added to each tube and incubated at room temperature for 5 minutes at indicated time points. For all reactions tubes were centrifuged at 5000 x g for 10 minutes. The supernatant was decanted, and pellets were extracted or stored at -80°C until processing. Pellets were resuspended in 100µl 1xTE containing 15 mg/ml lysozyme and 10 µl Proteinase K. Suspended pellets were incubated at room temperature for 10 minutes. Then, 700 µl of buffer RLT was added to suspended pellets along with approximately 100 µl of 0.5 mM glass beads and cells were incubated at 95°C for 5 minutes, bead beaten for 10 minutes, then centrifuged at max speed for 30 seconds. 760 µl of supernatant was added to new 2 ml Eppendorf tubes containing 590 µl of 80% ethanol. Samples were then extracted utilizing the RNeasy kit protocol and an on-column DNase treatment according to manufacturer’s protocols
Extracted RNA was quantified using the Qubit 2.0 Fluorometer and Qubit RNA HS assay. RNA was spiked with the ERCC control, an external RNA control, and input into the QIAseq FastSelect – 5s/16s/23s kit to remove bacterial ribosomal RNA prior to sequencing. Sequencing libraries were prepared using the QIAseq Stranded total RNA library kit according to manufacturer’s instructions. Libraries were quantified using the High Sensitivity D1000 kit on the 4200 Tapestation System. Four barcoded libraries were combined and diluted to a 4 nM library pool, denatured with NaOH, and further diluted to a final library concentration of 12 pM prior to sequencing. Pooled libraries were sequenced using the MiSeq Instrument and MiSeq reagent kit version 3–150 cycles.

treatment_protocol: One milliliter of diluted cells were treated with indicated concentrations of ciprofloxacin and incubated at 37°C for 60 minutes (or indicated time) in 5 ml Eppendorf tubes (Thermo Fisher Scientific) with constant agitation.

value: 60 minutes

tag: strain

tag: resistance

value: Ciprofloxacin resistant

value: 0.25 ng/ul Ciprofloxacin


title: MDS31

value: Peripheral blood


title: HUVECs with HG medium-1


title: BACI358, Resistant, Time 60 minutes, Replicate A


title: MDS13

value: Blood


title: MDS07

value: 5-methylcytosine (5-mC) Antibody


title: BACI358, Resistant, Time 40 minutes, Replicate C

value: 40 minutes


title: AML26


title: C1D1_22

city: Boston

first: Kornelia

last: Polyak

state: MA

address: 450 Brookline Ave

department: Medical Oncology

institute: Dana-Farber Cancer Institute

description: patient sample

data_processing:
RNA-seq datasets were aligned to the human reference genome hg38. VIPER pipeline was used for data processing, and genes with constant 0 counts across all samples were filtered out.
Assembly: hg38
Supplementary files format and content: csv file include raw counts of each sample

source_name: human breast cancer tissue

extract_protocol:
RNA were extarcted from FFPE sections of each samples using Qiagen AllPrep DNA/RNA FFPE Kit.
Library was constructed using TruSeq RNA Exome kit using total RNA samples following the manufactured protocol.
Library was seuqneced using 40M 150bp read pairs on an Illumina NovaSeq.

value: human breast cancer tissue

value: breast cabcer cancer cells

value: ruxolitinib+paclitaxel


title: HUVECs with HG+Mg2+medium-1


title: MDS04


title: MDS28


title: MDS01


title: BACI358, Resistant, Time 40 minutes, Replicate B


title: MDS19


title: AML22


title: BACI358, Resistant, Time 40 minutes, Replicate A


title: C1D1_19

description: patient sample

value: ruxolitinib


title: AML18


title: Baseline_19

description: patient sample

value: untreated


title: BACI358, Resistant, Time 20 mintues, Replicate C

value: 20 minutes


title: BACI358, Resistant, Time 20 mintues, Replicate B


title: AML16


title: Baseline_22

description: patient sample


title: AML14


title: AML20


title: Baseline_18

description: patient sample


title: AML28


title: MDS10


title: BACI358, Resistant, Time 0 minutes, Replicate C

value: 0 minutes

value: 0 ng/ul Ciprofloxacin


title: AML12


title: BACI358, Resistant, Time 20 mintues, Replicate A


title: AML10


title: AML08


title: Baseline_17

description: patient sample


title: CKdgd

city: guiyang

first: Tang

last: wenkun

address: Xibei Street

institute: Guizhou University

data_processing:
Raw sequencing reads were obtained using Illumina’s software to remove adaptors and low quality reads.
The extracted sequencing reads were then used to identify potentially cleaved targets by the CleaveLand pipeline.
The degradome reads were matched to transcriptome to generate the degradome density file. In addition, the targeted mRNA sequences of the miRNAs were predicted using TargetFinder software (http://targetfinder.org/). The overlapped mRNAs of the predicted target mRNAs and the mRNAs in degradome density file were considered as the target genes of the miRNAs.
Assembly: ftp://ftp.ensemblgenomes.org/pub/release-44/plants/fasta/hordeum_vulgare/dna
Supplementary files format and content: excel,expression profiles
Library strategy: Degradome sequencing

organism: Solanum lycopersicum

source_name: stem apex

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen, CA, USA) following the manufacturer's procedure
Poly(A) RNA is purified from plant total RNA(20ug) using poly-T oligo-attached magnetic beads using two rounds of purification. Because of the 3′ cleavage product of the mRNA contains a 5′-monophosphate，the 5' adapters were ligated to the 5' end of the 3′ cleavage product of the mRNA by the RNA ligase. The next step is reverse transcription to make the first strand of cDNA with a 3′-adapter random primer. and size selection was performed with AMPureXP beads.Then the cDNA were amplified with PCR by the following conditions: initial denaturation at 95℃ for 3 min; 15cycles of denaturation at 98℃ for 15 sec, annealing at 60℃ for 15 sec, and extension at 72℃ for 30 sec; and then final extension at 72℃ for 5 min. The average insert size for the final cDNA library was 200-400 bp. At last, we performed the 50bp single-end sequencing on an Illumina Hiseq 2500 (LC Bio, China) following the vendor's recommended protocol.

treatment_protocol: The two-leaf-old seedlings were subjected to K treatments consisting of two levels, 0.01mM (low K) and 1mM (normally used as control).

tag: cultivar

value: Ailsa Craig

value: stem apex

value: healthy control


title: AML24


title: Hdgd

value: infected with Hop stunt viroid (HSVd )


title: C1D1_18

description: patient sample


title: HSVd-infected tomato seedlings 3

description: HSVd-infected tomato

data_processing:
Subsequently, unique sequences with length in 18~25 nucleotide were mapped to specific species precursors in miRBase 22.0 by BLAST search to identify known miRNAs and novel 3p- and 5p- derived miRNAs. Length variation at both 3' and 5' ends and one mismatch inside of the sequence were allowed in the alignment.
The unique sequences mapping to specific species mature miRNAs in hairpin arms were identified as known miRNAs. The unique sequences mapping to the other arm of known specific species precursor hairpin opposite to the annotated mature miRNA-containing arm were considered to be novel 5p- or 3p-derived miRNA candidates. The remaining sequences were mapped to other selected species precursors (with the exclusion of specific species) in miRBase 22.0 by BLAST search, and the mapped pre-miRNAs were further BLASTed against the specific species genomes to determine their genomic locations.
The above two we defined as known miRNAs. The unmapped sequences were BLASTed against the genomes, and the hairpin RNA structures containing sequences were predicated from the flank 120 nt sequences using RNAfold software (http://rna.tbi.univie.ac. at/cgi-bin/RNAfold.cgi). The criteria for secondary structure prediction were: (1) number of nucleotides in one bulge in stem (≤12) (2) number of base pairs in the stem region of the predicted hairpin (≥16) (3) cutoff of free energy (kCal/mol ≤-15) (4) length of hairpin (up and down stems + terminal loop ≥50) (5) length of hairpin loop (≤200). (6) number of nucleotides in one bulge in mature region (≤4) (7) number of biased errors in one bulge in mature region (≤2) (8) number of biased bulges in mature region (≤2) (9) number of errors in mature region (≤4) (10) number of base pairs in the mature region of the predicted hairpin (≥12) (11) percent of mature in stem (≥80).
Assembly: ftp://ftp.ensemblgenomes.org/pub/release-54/plants/fasta/solanum_lycopersicum/dna/
Supplementary files format and content: excel,expression profiles

extract_protocol:
Total RNA was extracted using Trizol reagent (thermofisher, 15596018) following the manufacturer's procedure. The total RNA quantity and purity were analysis of Bioanalyzer 2100 and RNA 6000 Nano LabChip Kit (Agilent, CA, USA, 5067-1511) , high-quality RNA samples with RIN number > 7.0 were used to construct sequencing library.
Approximately 5 µg of total RNA were used to prepare nine small RNA librariesaccording to the protocol of TruSeq Small RNA Sample Prep Kits (Illumina, San Diego, CA, USA). And then the libraries were sequenced by Illumina Hiseq 2500 at the LC-BIO following the vendor’s recommended protocol. Raw reads were subjected to an in-house program, ACGT101-miR (v4.2) to remove adapter dimers, junk, low complexity, common RNA families (rRNA, tRNA, snRNA, snoRNA) and repeats.

value: HSVd-infected


title: BACI355, Suceptable, Time 60 minutes, Replicate C

value: 60 minutes

value: Ciprofloxacin suceptable

value: 0.25 ng/ul Ciprofloxacin


title: C1D1_9

description: patient sample


title: MDS25

value: Peripheral blood

value: Blood

value: 5-methylcytosine (5-mC) Antibody


title: AML06


title: BACI358, Resistant, Time 0 minutes, Replicate A

value: Ciprofloxacin resistant


title: HSVd-infected tomato seedlings 2

description: HSVd-infected tomato


title: AML04


title: AML02


title: C1D1_10

description: patient sample

value: human breast cancer tissue

value: breast cabcer cancer cells

value: ruxolitinib


title: C1D1_4

description: patient sample

value: ruxolitinib+paclitaxel


title: HSVd-infected tomato seedlings 1

description: HSVd-infected tomato


title: BACI355, Suceptable, Time 60 minutes, Replicate A


title: C1D1_17

description: patient sample


title: AML23


title: BACI355, Suceptable, Time 40 minutes, Replicate B

value: 40 minutes


title: Healthy control tomato seedlings 1

description: Healthy  tomato

value: Ailsa Craig

value: Healthy control


title: AML21


title: BACI358, Resistant, Time 0 minutes, Replicate B

value: 0 minutes

value: 0 ng/ul Ciprofloxacin


title: Baseline_10

description: patient sample

value: untreated


title: Baseline_3

description: patient sample


title: Baseline_9

description: patient sample


title: AML27


title: Healthy control tomato seedlings 3

description: Healthy  tomato

value: stem apex


title: Baseline_4

description: patient sample


title: ish2-CD73-3-No-Dox

city: Dallas

first: Lei

last: Guo

state: TX

address: 5323 Harry Hines Blvd

department: Department of Population and Data Sciences

institute: University of Texas Southwestern Medical Center

data_processing:
Adaptors were trimmed using Trim Galore (v0.6.4). The trimmed reads were then aligned to the human genome (GRCH38) using STAR (2.7.3a). The subsequent mapped reads were quantified by featureCounts of the Subread (v1.6.3) package.
Assembly: GRCH38
Supplementary files format and content: gene.count.txt

source_name: RD cells

growth_protocol: 5x10^5 cells were seeded in a 6-well plate with 2ml of 10% TET system media and allowed to attach for 24hr.

extract_protocol:
Cells were collected in 500µl of TRIzol. Chloroform extraction was performed. Then the aqueous phase was mixed with an equal volume of 75% ethanol and further purified using a RNeasy Mini Kit (QIAGEN, 74104) according to the manufacturer’s protocol. An Agilent 2100 TapeStation was used for RNA quality analysis.
Stranded mRNA-Seq libraries were generated using a KAPA mRNA HyperPrep Kit (Roche, KK8581) following manufacturer’s protocol. Sequencing was performed on an Illumina NextSeq 550 system using a 75-bp, high-output sequencing kit for paired-end sequencing.

treatment_protocol: The cells were treated with or without 10ng/mL of doxycycline. Untreated cells were used as control. The cells were incubated in the treatment for 96hr prior to RNA extraction.

value: No-Dox

value: Control

value: RD

value: Rhabdomyosarcoma cell


title: Healthy control tomato seedlings 2

description: Healthy  tomato


title: BACI355, Suceptable, Time 40 minutes, Replicate A

value: Ciprofloxacin suceptable

value: 0.25 ng/ul Ciprofloxacin


title: C1D1_2

description: patient sample

value: human breast cancer tissue


title: ish2-CD73-2No-Dox


title: AML19

value: Peripheral blood

value: Blood

value: 5-methylcytosine (5-mC) Antibody


title: AML17


title: BACI355, Suceptable, Time 60 minutes, Replicate B

value: 60 minutes


title: Baseline_2

description: patient sample

value: breast cabcer cancer cells


title: BACI355, Suceptable, Time 20 mintues, Replicate B

value: 20 minutes


title: BACI355, Suceptable, Time 40 minutes, Replicate C

value: 40 minutes


title: BACI355, Suceptable, Time 20 mintues, Replicate C


title: AML15


title: AML25


title: ish2-CD73-1-No-Dox


title: ish2-CD73-3-Dox

value: Dox treatment

value: CD73 Knockdown


title: AML13


title: siYap Taz XMUc

city: NEW YORK

first: Ana Maria

last: Low Calle

state: NY

address: 1212 Amsterdam Avenue

department: Biological Sciencies

institute: Columbia University

data_processing:
Firstly, Cutadapt and perl scripts in house were used to remove the reads that contained adaptor contamination, low quality bases and undetermined bases.
Then sequence quality was verified using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/).
We used HISAT2 to map reads to the genome of https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/. The mapped reads of each sample were assembled using StringTie.
Then, all transcriptomes were merged to reconstruct a comprehensive transcriptome using perl scripts and gffcompare.
After the ﬁnal transcriptome was generated, StringTie and edgeR was used to estimate the expression levels of all transcripts.
Assembly: We used HISAT2 to map reads to the genome of https://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/000/001/405/GCF_000001405.39_GRCh38.p13/. The mapped reads of each sample were assembled using StringTie.
Supplementary files format and content: StringTie was used to perform expression level for mRNAs by calculating FPKM. The differentially expressed mRNAs were selected with log2 (fold change) >1 or log2 (fold change) <-1 and with statistical significance (p value < 0.05) by R package edgeR [4].
Supplementary files format and content: tab-delimited text files include FPKM values for each Sample

molecule: polyA RNA

growth_protocol: MCF10A cells were maintained in DMEM/F12 with 5% horse serum, penicillin-streptomycin, 10 µg/mL insulin, 0.5 µg/mL hydrocortisone and 20 ng/mL Epidermal Growth Factor in humidified atmosphere with 5% CO2 at 37C

extract_protocol:
Total RNA was isolated using TRIzol reagent (Thermofisher, 15596026) following the manufacturer’s instructions.
Poly(A) RNA sequencing library was prepared following Illumina’s TruSeq-stranded-mRNA sample preparation protocol. RNA integrity was checked with Agilent Technologies 2100 Bioanalyzer. Poly(A) tail-containing mRNAs were purified using oligo-(dT) magnetic beads with two rounds of purification. After purification, poly(A) RNA was fragmented using divalent cation buffer in elevated temperature. The DNA library construction is shown in the following workflow. Quality control analysis and quantification of the sequencing library were performed using Agilent Technologies 2100 Bioanalyzer High Sensitivity DNA Chip. Paired-ended sequencing was performed on Illumina’s NovaSeq 6000 sequencing system.

treatment_protocol: MCF10A cells (3x105 cells per well) were transfected with 11 nM of two different siRNAs sets against YAP and TAZ or 22 nM of control siRNA wi RNAi Max; 48 h post transfection fresh media with DMSO or 5 µM of XMU-MP1 (MST1/2 inhibitor) was added and cells were harvested 6 h later.

value: Immortalized mammary epithelial cell

value: WT

value: siYap/Taz 5uM XMU-MP1


title: ish2-CD73-2-Dox

value: RD


title: BACI355, Suceptable, Time 20 mintues, Replicate A


title: siYap Taz XMUa


title: AML11


title: ish2-CD73-1-Dox

value: Rhabdomyosarcoma cell


title: siYap Taz XMUb


title: siYap Taz DMSOc

value: siYap/Taz DMSO


title: ish-CD73-3-No-Dox

value: No-Dox

value: Control


title: BACI355, Suceptable, Time 0 minutes, Replicate C

value: 0 minutes

value: Ciprofloxacin suceptable

value: 0 ng/ul Ciprofloxacin


title: AML09

value: Peripheral blood

value: Blood

value: 5-methylcytosine (5-mC) Antibody


title: AML05


title: zebrafish_8hour_wt_75mM_s4u_r3

city: Kansas City

first: Ariel

middle: Alejandro

last: Bazzini

state: Missouri

institute: Stowers Institute for Medical Research

data_processing:
Slamdunk 0.4.3.
Adapter sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
Reads that contain at least 2 T>C conversions were deemed labeled.
Assembly: danRer11
Supplementary files format and content: Comma-separated values, <.csv>; Total raw read and labeled read counts for all experiments and samples, including spike-ins. Rows represent different 3'UTR isoforms (for coding genes) or full-length transcript (non-coding genes). Columns represent: Ensembl gene IDs by itself (non-coding transcripts) + 3'UTR isoforms (coding transcripts), or ERCC IDs (spike ins);  Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature;

organism: Danio rerio

source_name: Embryos at 8 hours post-fertilization

growth_protocol: Zebrafish embryos were collected from natural breeding, with random mating parents, embryos were kept at 28.5 C in 0.5x Embryo Media.

extract_protocol:
Trizol™
QuantSeq 3′ mRNA-Seq Library Prep Kit for Illumina UDI Bundle (FWD, Lexogen GmbH, cat. no. 144.96)

treatment_protocol: Embryos were injected with ~1000pL of 75mM s4-UTP.

value: Embryos

tag: Stage

value: 8 hours post-fertilization

value: Offspring of [AB-TU]x[TL-TLF]


title: AML07


title: siYap Taz DMSOa

value: Immortalized mammary epithelial cell


title: BACI355, Suceptable, Time 0 minutes, Replicate B


title: BACI355, Suceptable, Time 0 minutes, Replicate A


title: zebrafish_8hour_wt_75mM_s4u_r2


title: ish-CD73-2No-Dox


title: ish-CD73-1-No-Dox


title: siC XMUc

value: WT

value: si Negative Control 5uM XMU-MP1


title: AML01


title: ish-CD73-2-Dox

value: Dox treatment

value: CD73 Knockdown

value: RD


title: AML03


title: zebrafish_7hour_wt_75mM_s4u_r3

source_name: Embryos at 7 hours post-fertilization

value: 7 hours post-fertilization


title: ish-CD73-3-Dox

value: Rhabdomyosarcoma cell


title: ish-CD73-1-Dox


title: siC XMUa


title: zebrafish_7hour_wt_75mM_s4u_r2


title: HE-RNA-2

city: Blacksburg

first: Chang

last: Lu

state: VA

address: 235 Goodwin Hall, 635 Prices Fork Road, Virginia Tech

department: Chemical Engineering

institute: Virginia Tech

data_processing:
RNA-seq data were quantified using Salmon (1.10.2) against the hg38 transcriptome using a full decoy.
Differential gene expression analysis was performed using DESeq2, where genes with a fold change > = 2 and FDR < 0.05 were considered as significantly differentially expressed.
Gene ontology analysis of differentially expressed genes was analyzed for gene ontologies with clusterProfiler (4.8.3).
GSVA analysis: Gene set variation analysis (GSVA)66  (1.48.3) was conducted using the GSVA package on MsigDB Hallmark gene sets. GSVA enrichment scores of each condition were calculated. Differential analysis of enrichment scores between NN-HN, NN-NF, NN-HF, NN-NE and NN-HE were performed using the limma R package (3.56.2). The GSVA heatmaps were plotted using the pheatmap package (1.0.12).
Assembly: hg38
Supplementary files format and content: RNA-seq: Raw counts of sequencing reads (.sf) were generated by Salmon.

source_name: HCT116 cells

extract_protocol:
Cell preparation: Cell culture medium was removed by centrifuging at 300g for 5 minutes at 4°C. Cells were washed twice with 1 mL cold PBS and suspended in 60 μL PBS supplemented with 0.6 μL PIC and 0.6 μL PMSF solution. Cells were then stored on ice until used for ChIP-seq or RNA-seq.
RNA-seq library construction: Each RNA-seq library was prepared using 25,000 cells. We prepared two technical replicates for each condition. Total RNA was extracted using the RNeasy Mini Kit (74104, Qiagen) and RNase-Free DNase Set (79254, Qiagen). The extracted total RNA was suspended in 30 μL RNase-free water and concentrated by ethanol precipitation. Total RNA was resuspended in 4.6 μL of RNase-free water supplemented with 5% RNase inhibitor (40 U/μL). SMART-seq2 protocol (Picelli et al., Nature Protocols 9 (2014) 171–181.) with minor alterations (Zhu et al., Cell Reports 37 (2021) 109836, Naler et al., Commun Biol 5 (2022) ) was then used for reverse transcription to produce cDNA. 2 μL of oligo-dT primer (10 μM), 2 μL of dNTP mix (10 mM) and 4.3 μL of total RNA solution were first mixed well. This mixture (8.3 μL) was denatured at 72°C for 3 minutes and immediately stored on ice. Next, 11.7 μL of reverse transcription mix (1μL of SuperScript II reverse transcriptase (200 U/μL), 0.5μL of RNase inhibitor (40 U/μl), 4μL of Superscript II first-strand buffer, 1 μL of DTT (100 mM), 4 μL of 5 M Betaine, 0.12 μL of 1 M MgCl2, 0.2 μL of TSO (100 μM), 0.88 μL of nuclease-free water) was added to the 8.3μl mixture. The total reverse transcription reaction mix was incubated in a thermal cycler at 42°C for 90 minutes, followed by 10 cycles of (50°C for 2 minutes and 42°C for 2 minutes), and finally inactivated at 70°C for 15 minutes. The reverse transcription reaction mix was then mixed with 30 μL of PCR mix (25 μL KAPA HiFi HotStart ReadyMix, 0.5μL IS PCR primers (10 μM), 2.5μL Evagreen dye, and 2μL nuclease-free water) and amplified with the program: 98°C for 1 minute, 9–11 cycles of (98 °C for 15 seconds, 67 °C for 30 seconds, 72 °C for 6 minutes). Finally, the cDNA was purified using 40 μL of SPRIselect beads and resuspended in ~7 μL of low-EDTA TE buffer.   The RNA-seq library was made using Tn5-tagmentation. Tn5 transposase (14-17 mg/ml) was produced following a published protocol (Picelli et al., Genome Res 24 (2014) 2033–2040.). Tn5 transposase and T5/T7 transposons were assembled to form Tn5 transposome using a published protocol (Amini et al., Nat. Genet. 46 (2014) 1343-1349). Briefly, 1.5 μl of 100 μM T5 transposon (IDT) was mixed with 1.5 μl of 100 μM pMENTS (a 5'-phosphorylated 19-bp mosaic end complementary oligonucleotide, IDT), while 1.5 μl of 100 μM T7 transposon (IDT) was mixed with 1.5 μl of 100 μM pMENTS. 3 μl of T5-pMENTS solution and 3 μl of T7-pMENTS solution were separately incubated at 95°C for 5 min followed by a slow ramp to 25°C at -0.1°C/sec. 2.5 μl of T5-pMENTS solution was then mixed with 2.5 μl of Tn5 transposase (14-17 mg/ml), while 2.5 μl of T7-pMENTS solution was mixed with 2.5 μl of Tn5 transposase. T5-Tn5 solution and T7-Tn5 solution were separately incubated at 37°C for 1 h to form T5-Tn5 transposome and T7-Tn5 transposome, respectively. 4 μl of T5-Tn5 transposome and 4 μl of T7-Tn5 transposome were mixed to form 8 μl of assembled Tn5 transposome before it was mixed with 1 μl cDNA (containing ~500 pg cDNA) and 1 μl reaction buffer (TNP92110, Lucigen). The reaction mixture was incubated at 37 °C for 1 h. 1 μl of 10× stop solution (TNP92110, Lucigen) was added to the reaction mixture to stop tagmentation. Two rounds of 1× SPRIselect beads cleanup were performed to purify tagmented cDNA. The tagmented cDNA was then eluted in 10 μl low EDTA TE buffer. 25 μl KAPA HiFi HotStart ReadyMix was activated at 98 °C for 30 sec and then mixed with 9.5 μl tagmented cDNA and 10 μl Nuclease-free water, followed by incubation at 72 °C for 5 min. 1.5 μl of 25 μM P5 primer, 1.5 μl of 25 μM P7 primer and 2.5 μl 20x Evagreen were then added. The following amplification program was used to achieve a 300-400 RFU increase: 98 °C for 30 s; 11-12 cycles of (98 °C for 10 seconds, 63 °C for 30 seconds, 72 °C for 30 seconds) and 72 °C for 1 minute. Amplified library was purified with 0.8× SPRIselect beads and eluted in 8 μl low EDTA TE buffer. Libraries were sequenced with Illumina HiSeq 4000 with single-end 50 nt read length.

value: HCT116 cells

value: Hypoxia - infection with E. coli (HE)


title: zebrafish_7hour_wt_75mM_s4u_r1


title: HEC1B siPRMT6-2 48hr RNA

city: Tokyo

first: Kohei

last: Kumegawa

address: 3-8-31 Ariake, Koto-ku

country: Japan

institute: Japanese Foundation for Cancer Research

data_processing:
The row reads were trimmed to remove adaptor sequences using Skewer (v0.2.2).
The reads were mapped to the hg38 genome using STAR (v.2.7.8a).
The mapped reads were then counted using featureCounts (v.2.0.10).
Assembly: hg38
Supplementary files format and content: tab-delimited text files include counts for each Sample

extract_protocol:
RNA was harvested using Rneasy mini plus kit (Qiagen).
RNA-seq libraries were prepared with 10 ng of total RNA using a SMARTer Stranded Total RNA-Seq Kit v2-Pico Input Mammalian (Takara)

value: endometrial cancer

value: PRMT6 knockdown


title: siYap Taz DMSOb

value: siYap/Taz DMSO


title: HF-RNA-2

value: Hypoxia - infection with Fnn (HF)


title: zebrafish_8hour_wt_75mM_s4u_r1

value: Embryos


title: siC DMSOc

value: si Negative Control DMSO


title: HEC1B siPRMT6-1 48hr RNA


title: HE-RNA-1


title: zebrafish_6hour_wt_75mM_s4u_r2

source_name: Embryos at 6 hours post-fertilization

value: 6 hours post-fertilization

value: Offspring of [AB-TU]x[TL-TLF]


title: zebrafish_6hour_wt_75mM_s4u_r3


title: HF-RNA-1


title: zebrafish_5hour_wt_75mM_s4u_r3

source_name: Embryos at 5 hours post-fertilization

value: 5 hours post-fertilization


title: HN-RNA-2

value: Hypoxia - No Bacteria


title: HEC1B siNC 48hr RNA

value: WT


title: HN-RNA-1


title: siC XMUb

value: Immortalized mammary epithelial cell

value: si Negative Control 5uM XMU-MP1


title: HEC1B siPRMT6-2 48hr H3K27ac

data_processing:
The sequenced reads were mapped to the hg38 genome using bowtie2 (v.2.4.2).
Multi-mapped reads and PCR duplicates were removed using Picard (v.2.25.3).
Overlapping reads according to the ENCODE blacklist were filtered out using bedtools (2.30.0).
MACS2 (v.2.2.7.1) was used for calling peaks with the ”--keep-dup auto -q 0.1” parameter.
Assembly: hg38
Supplementary files format and content: peak summit files

extract_protocol:
Cells were fixed with 0.5% formaldehyde for 10 min at room temperature, quenched with 1.25 M glycine, washed, and lysed. The chromatin was sheared using S220 Focused-ultrasonicator (Covaris).
ChIP-seq libraries were prepared using ThruPLEX DNA-seq Kit (Takara)

value: H3K27ac (Cell Signaling Technology, 8173S)


title: OV_PAX3_18d_18days3

city: Changsha

first: sijun

last: li

state: Hunan

address: 87 Xiangya Road

department: ENT

institute: Xiangya Hospital, Central South University

data_processing:
The image data measured by the high-throughput sequencer are convertedintosequence data (reads) by CASAVA base recognition.
Raw data (rawreads) of fastqformat were firstly processed through in-house perl scripts. In this step, cleandata(clean reads) were obtained by removing reads containing adapter, reads containingNbase and low quality reads from raw data. At the same time, Q20, Q30 andGCcontent the clean data were calculated. All the downstream analyses were basedonthe clean data with high quality.
Clean reads were mapped to hg38 using hisat2 with default parameters. Index of the reference genome was built using Hisat2(v2.0.5) and paired-end clean reads were aligned to the reference genome using Hisat2. featureCounts (v1.5.0-p3) was used to count the reads numbers mapped to eachgene. And then FPKM of each gene was calculated based on the length of the geneand reads count mapped to this gene. (v2.0.5).
Differential expression analysis  was performed usingtheDESeq2 R package (1.20.0).
Gene Ontology (GO) enrichment analysis of differentially expressed genes wasimplemented by the clusterProfiler R package (3.8.1),We usedclusterProfiler R package (3.8.1) to test the statistical enrichment of differential  expression genes in KEGG pathways.
Assembly: hg38
Supplementary files format and content: tab-delimited text files include TPM values for each Sample

source_name: OV_PAX3_18days, gene mutation

extract_protocol:
Total RNA was extracted using Trizol reagent (Invitrogen,15596018)
the library fragments were purified with AMPure XP system(BeckmanCoulter, Beverly, USA). Then PCR amplification, the PCR product was purifiedbyAMPure XP beads, and the library was finally obtained.

value: inner ear organoids

tag: disease state

value: patient

value: Differentiated from iPSCs


title: zebrafish_5hour_wt_75mM_s4u_r2


title: OV_PAX3_18d_18days2


title: HEC1B siPRMT6-2 36hr H3K27ac

value: endometrial cancer


title: NF-RNA-2

value: HCT116 cells

value: Normoxia - infection with Fnn (NF)


title: OV_PAX3_18d_18days1


title: HEC1B siPRMT6-2 24hr H3K27ac

value: PRMT6 knockdown


title: zebrafish_5hour_wt_75mM_s4u_r1

value: Embryos


title: NF-RNA-1


title: HEC1B siPRMT6-1 48hr H3K27ac


title: siC DMSOb

value: si Negative Control DMSO


title: zebrafish_4hour_wt_75mM_s4u_r3

source_name: Embryos at 4 hours post-fertilization

value: 4 hours post-fertilization


title: HEC1B siPRMT6-1 36hr H3K27ac


title: NE-RNA-2

value: Normoxia - infection with E. coli (NE)


title: OV_Control_18day2

source_name: OV_Control_18days ,healthy control

value: healthy control


title: siC DMSOa


title: OV_Control_18day1


title: NE-RNA-1


title: zebrafish_4hour_wt_75mM_s4u_r2

value: Offspring of [AB-TU]x[TL-TLF]


title: BACI358, Resistant, Time 60 minutes, Replicate C

value: 60 minutes

value: Ciprofloxacin resistant

value: 0.25 ng/ul Ciprofloxacin


title: zebrafish_4hour_wt_75mM_s4u_r1


title: NN-RNA-2

value: Normoxia - No Bacteria (NN)


title: iPSCs_PAX3_0days3

source_name: iPSCs_PAX3,gene mutation

value: iPSCs

value: induced from PBMC


title: HEC1B siNC 48hr H3K27ac

value: WT

value: H3K27ac (Cell Signaling Technology, 8173S)


title: HEC1B siPRMT6-1 24hr H3K27ac

value: endometrial cancer


title: NN-RNA-1

value: HCT116 cells


title: iPSCs_PAX3_0days2

value: patient


title: zebrafish_3hour_wt_75mM_s4u_r3

source_name: Embryos at 3 hours post-fertilization

value: Embryos

value: 3 hours post-fertilization


title: iPSCs_PAX3_0days1


title: zebrafish_3hour_wt_75mM_s4u_r1


title: HEC1B siNC 24hr H3K27ac


title: OV_Control_18day3

value: inner ear organoids

value: Differentiated from iPSCs


title: HF-input

data_processing:
Sequencing reads were trimmed by trim galore v0.6.6 with default parameters. Samples with more than 25 million reads were randomly downsampled to 25 million reads using seqtk1.3.
Trimmed ChIP-seq reads were mapped to the hg38 genome with bowtie2 v2.4.2. Peaks were called using MACS2 v2.2.7.1 (q < 0.05). Mapped reads from ChIP and input samples were extended by 100 bp on either side (250 bp total) and a normalized signal was calculated. For visualization in IGV v2.8.12 (Broad Institute), the signal was calculated in 100bp windows over the entire genome and output as a bigWig file.
Enhancer predicting and differential analysis: We predicted enhancer regions by identifying H3K27ac high regions that did not intersect with promoter regions (TSS ± 2000 bp). First, consensus H3K27ac peak sets were generated for each of the experimental conditions (NN, NE, NF, HN, HE, HF) with Diffbind (3.10.1). Peaks were expanded 500bp on each side around the summit, forming a 1000 bp long peak width. H3K27ac peak regions that intersected with a promoter region were removed and the remaining regions were designated as enhancers. Differential enhancers between any two experimental conditions were identified using the bioconductor DESeq2 package (1.40.2) with Benjamini-Hochberg method (FDR < 0.05).
GO analysis: Gene ontology analysis of differential enhancers was performed using GREAT (4.0.4) with default settings.
Transcription factor binding motif analysis: Transcription factor binding motif analysis was conducted to locate enriched transcription factor binding motifs across the enhancer regions using Homer v4.11 (with options –size 200 –p 16, and q-value < 0.01).
Assembly: hg38
Supplementary files format and content: ChIP-seq: bigwig files (.bw) were generated by wigToBigWig.

extract_protocol:
Cell preparation: Cell culture medium was removed by centrifuging at 300g for 5 minutes at 4°C. Cells were washed twice with 1 mL cold PBS and suspended in 60 μL PBS supplemented with 0.6 μL PIC and 0.6 μL PMSF solution. Cells were then stored on ice until used for ChIP-seq or RNA-seq.
ChIP-seq library construction: MNase-digested chromatin samples of ~10,000 cells per library were used in MOWChIP-seq to profile H3K27ac. We prepared two ChIP-seq libraries and one input library for each condition. The protocol of MOWChIP-seq has been detailed previously (Zhu et al., Nature Protocols 14 (2019) 3366-3394.). ChIP DNA bound to the beads was collected by phenol-chloroform extraction. The Accel-NGS 2S Plus DNA Library Kit (Swift Biosciences Cat# 21024) was used to prepare sequencing libraries.

value: Hypoxia - infection with Fnn (HF)


title: iPSCs_Control_0day3

source_name: iPSCs_Control ,healthy control

value: healthy control


title: HE-input

value: Hypoxia - infection with E. coli (HE)


city: Oxford

first: Maricris

last: Zaidem

state: Oxfordshire

address: South Parks Rd

department: Department of Biology

country: United Kingdom

institute: University of Oxford

data_processing:
Sequenced reads were mapped to the Zea Mays B73 RefGen V4 genome (https://phytozome-next.jgi.doe.gov/info/Zmays_RefGen_V4) using STAR, transcript quantification was done with Salmon and differential gene expression was determined using DESEq2.
Assembly: Zea Mays B73 RefGen V4 genome (https://phytozome-next.jgi.doe.gov/info/Zmays_RefGen_V4)
Supplementary files format and content: tab-delimited file includes raw counts, abundance and length of each gene assayed per sample
Supplementary files format and content: tab-delimited file includes transcript-based differential expression relative to the WT samples at padj <0.05

organism: Zea mays

source_name: pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)

growth_protocol: Maize seeds were germinated in vermiculite for 7 days. Germinated seedlings were dissected to isolate the SAM, P0 - P5 primordia  (including the leaf sheath) and to excise the root, embryo and coleoptile tissue. All isolated samples were immediately kept in RNAse-later prior to further processing.

extract_protocol:
Total RNA was extracted from three individual shoot apices, per genotype (mutant and wild-type) pool, using the Qiagen RNeasy Plant Mini Kit (Cat. No. 74904). Subsequent DNase treatment was done using the Ambion® TURBO DNA-free™ Kit (Cat. No. AM1907). RNA quantity was checked and normalized using a Qubit™ RNA HS Assay Kit (Cat. No. Q32852). RNA quality was assessed with an Agilent RNA 6000 Nano Kit (5067-1511) ensuring that all RNA used for library preparation had a RIN value of 9.0.
Strand-specific RNA sequencing library preparation and sequencing was conducted by the Oxford Genomics Centre at the Wellcome Centre for Human Genetics (funded by Wellcome Trust grant reference 203141/A/16/Z)
RNA-Seq was performed on an Illumina NovaSeq 6000 with paired-end 150-bp reads

treatment_protocol: CRISPR/Cas9 gene editing was emploted to generate tml1;tml2 knock-outs. Seeds were genotyped by seed chipping to select segregating wild-type and homozygous tml1;tml2 prior to germination.

value: MT4, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 4, sample C3 [WTCHG_960489_73685344] [WTCHG_960489_73685344]

value: B104 tml1;tml2

value: CRISPR/Cas9 homozygous tml1;tml2 mutant


title: NF-input

value: Normoxia - infection with Fnn (NF)


title: zebrafish_2hour_wt_75mM_s4u_r1

source_name: Embryos at 2 hours post-fertilization

value: 2 hours post-fertilization

value: Offspring of [AB-TU]x[TL-TLF]


title: zebrafish_2hour_wt_75mM_s4u_r2


title: iPSCs_Control_0day1

value: iPSCs

value: induced from PBMC


title: HN-input

value: HCT116 cells

value: Hypoxia - No Bacteria (HN)


title: iPSCs_Control_0day2


value: pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)

value: MT3, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 3, sample D6 [WTCHG_960489_73675343] [WTCHG_960489_73675343]


value: MT2, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 2, sample A2 [WTCHG_960489_73625338] [WTCHG_960489_73625338]


title: zebrafish_1hour_wt_75mM_s4u_r3

source_name: Embryos at 1 hour post-fertilization

value: Embryos

value: 1 hour post-fertilization


value: WT4, maize inbred line B104, segregating wild-type 4, sample H6 [WTCHG_960489_73705346] [WTCHG_960489_73705346]

value: CRISPR/Cas9 segregating TML wild-type


title: NN-input

value: Normoxia - No Bacteria (NN)


title: zebrafish_3hour_wt_75mM_s4u_r2

value: 3 hours post-fertilization


title: zebrafish_1hour_wt_75mM_s4u_r2


title: PNIBD55_I, ileal tissue

city: Chapel Hill

first: Terrence

last: Furey

state: NC

address: 7320 Medical Biomolecular Research Building, CB# 7032, 111 Mason Farm Road

department: Center for Gastrointestinal Biology and Disease

institute: University of North Carolina at Chapel Hill

data_processing:
Transcript expression was quantified using Salmon with default parameters.
Supplementary files format and content: Processed files are comma-separated, rows representing raw counts for genes (as gene symbols or as Ensembl ID's if no gene symbol available)

source_name: ileum

extract_protocol:
Macroscopically uninflamed mucosal samples from the ascending colon and terminal ileum were obtained at the time of initial iagnosis, before therapy was started. These samples were preserved as fresh frozen paraffin-embedded (FFPE) tissue. RNA was isolated from FFPE tissue using the Quick-RNA FFPE MiniPrep (Zymo Research, Irvine, CA). Total RNA was then purified using the MagMAX kit in the KingFisher system (ThermoFisher, Carlsbad, CA).
RNA-seq libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero (Illumina, San Diego, CA). Paired-end (50bp) sequencing was processed on the NovaSeq 6000 platform using default parameters (Illumina, San Diego, CA).

value: ileum

tag: Sex

value: F

tag: status

value: nonIBD

tag: diagnosis age

tag: location montreal

tag: batch

tag: b montreal

tag: perianal disease

tag: rectosigmoid involvement

tag: family history

tag: surgery

tag: remission


title: PNIBD56_I, ileal tissue

tag: tissue


title: zebrafish_1hour_wt_75mM_s4u_r1

tag: genotype

value: Offspring of [AB-TU]x[TL-TLF]


title: HEC1B siNC 36hr H3K27ac

tag: cell line

tag: cell type

value: endometrial cancer

value: WT

tag: chip antibody

value: H3K27ac (Cell Signaling Technology, 8173S)


title: PNIBD54_I, ileal tissue

value: M


title: HF-H3K27ac-2

value: HCT116 cells

tag: treatment

value: Hypoxia - infection with Fnn (HF)


title: PNIBD53_I, ileal tissue

tag: Sex


value: pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)

value: WT3, maize inbred line B104, segregating wild-type 3, sample B3 [WTCHG_960489_73635339] [WTCHG_960489_73635339]


title: zebrafish_shield_20µM_lnamir430_50mM_s4u_r6

source_name: Embryos at shield stage

treatment_protocol: Embryos were injected with ~1000pL of 50mM s4-UTP plus 20µM of either locked nucleic acid against miR-430 seed or a mismatch oligo.

value: Embryos

tag: Stage

value: shield stage

value: 1000pL of 20µM lna against miR-430 seed and 50mM s4UTP injection


value: MT4, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 4, sample C3 [WTCHG_960488_73685344] [WTCHG_960488_73685344]

value: B104 tml1;tml2

value: CRISPR/Cas9 homozygous tml1;tml2 mutant


title: zebrafish_shield_20µM_lnamir430_50mM_s4u_r5


title: HE-H3K27ac-2

value: Hypoxia - infection with E. coli (HE)


title: HF-H3K27ac-1


title: PNIBD50_I, ileal tissue

value: ileum

value: F

tag: status

value: nonIBD

tag: diagnosis age


value: MT3, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 3, sample D6 [WTCHG_960488_73675343] [WTCHG_960488_73675343]


title: NE-input

value: Normoxia - infection with E. coli (NE)


title: PNIBD49_I, ileal tissue

value: M

tag: location montreal

tag: batch


title: zebrafish_shield_20µM_lnamir430_50mM_s4u_r3

value: Offspring of [AB-TU]x[TL-TLF]


title: zebrafish_shield_20µM_lnamir430_50mM_s4u_r4


title: HE-H3K27ac-1

value: HCT116 cells


value: pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)

value: MT2, maize inbred line B104, tml1;tml2 HMZ CRISPR-Cas mutant 2, sample A2 [WTCHG_960488_73625338] [WTCHG_960488_73625338]


title: PNIBD46_I, ileal tissue

tag: b montreal

tag: perianal disease


title: zebrafish_shield_20µM_lnamir430_50mM_s4u_r2

value: Embryos


title: HN-H3K27ac-2

value: Hypoxia - No Bacteria (HN)


title: PNIBD45_I, ileal tissue

tag: rectosigmoid involvement

tag: family history


value: WT4, maize inbred line B104, segregating wild-type 4, sample H6 [WTCHG_960488_73705346] [WTCHG_960488_73705346]

value: CRISPR/Cas9 segregating TML wild-type


title: HN-H3K27ac-1


value: WT3, maize inbred line B104, segregating wild-type 3, sample B3 [WTCHG_960488_73635339] [WTCHG_960488_73635339]


value: WT2, maize inbred line B104, segregating wild-type 2, sample A6 [WTCHG_960489_73595335] [WTCHG_960489_73595335]


title: PNIBD44_I, ileal tissue

tag: surgery

tag: remission


title: zebrafish_shield_20µM_lnacontrol_50mM_s4u_r6

tag: tissue

value: shield stage

tag: genotype

value: 1000pL of 20µM lnacontrol and 50mM s4UTP injection


title: PNIBD43_I, ileal tissue

value: ileum

value: F


title: NF-H3K27ac-1

tag: cell line

value: Normoxia - infection with Fnn (NF)


title: head, old, male, H3.3BK36R, rep3

first: Gregory

last: Matera

state: North Carolina

address: Genome Science Building

description:
Sample_MATA_LB_JB_93
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

data_processing:
Reads were aligned with STAR (v2.7.7a) to the DM6 genome build.
Aligned reads were counted using featureCounts (Subread v2.0.3). Strand orientation specified as forward.
Differential expression analysis was performed with DESeq2 (v1.34.0)
Assembly: DM6
Supplementary files format and content: DESeq2 matrix of normalized counts (.csv)

organism: Drosophila melanogaster

source_name: whole head

extract_protocol:
Heads were removed from the rest of the carcass and total RNA was extracted. Briefly, 10-25 flies were anesthetized and placed in a 15 mL tube. The tube was submerged in liquid nitrogen for 5-10 seconds and then vortexed for 5-10 seconds to separate heads from carcasses. This process was repeated for a total of 5 times before pouring the contents of the tube into a set of stacked sieves. Fly heads were crushed in TRIzol reagent (Thermo Fisher) and RNA was purified with the RNA clean & concentrator-5 kit (Zymo research).
Total (Ribo-minus) RNA-seq libraries, three replicates per genotype, were prepared using a Universal RNA-seq library preparation kit with NuQuant (Tecan). Sequencing was performed on a NovaSeq 6000SP (Illumina) producing 100 nt, paired-end reads.

value: whole head

tag: developmental stage

value: adult

value: male

tag: age

value: old


title: PNIBD41_I, ileal tissue

tag: Sex

value: nonIBD


title: NE-H3K27ac-2

value: HCT116 cells

tag: treatment

value: Normoxia - infection with E. coli (NE)


title: head, old, female, H3.3BK36R, rep3

description:
Sample_MATA_LB_JB_92
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: female


title: zebrafish_shield_20µM_lnacontrol_50mM_s4u_r4

value: Embryos

tag: Stage

value: Offspring of [AB-TU]x[TL-TLF]


title: NE-H3K27ac-1


title: head, young, male, H3.3BK36R, rep3

description:
Sample_MATA_LB_JB_91
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: young


title: zebrafish_shield_20µM_lnacontrol_50mM_s4u_r3


title: head, young, female, H3.3BK36R, rep3

description:
Sample_MATA_LB_JB_90
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv


title: PNIBD39_I, ileal tissue

value: M

tag: status

tag: diagnosis age


title: NN-H3K27ac-1

value: Normoxia - No Bacteria (NN)


title: PNIBD38_I, ileal tissue

tag: location montreal

tag: batch


title: zebrafish_shield_20µM_lnacontrol_50mM_s4u_r1

value: shield stage

value: 1000pL of 20µM lnacontrol and 50mM s4UTP injection


title: NF-H3K27ac-2


value: pooled leaf primordia (SAM, plastochron 0 to plastochron 5, leaf sheath)

tag: cell type

value: WT2, maize inbred line B104, segregating wild-type 2, sample A6 [WTCHG_960488_73595335] [WTCHG_960488_73595335]

value: CRISPR/Cas9 segregating TML wild-type


title: zebrafish_shield_20µM_lnamir430_50mM_s4u_r1

value: 1000pL of 20µM lna against miR-430 seed and 50mM s4UTP injection


title: PNIBD37_I, ileal tissue

value: ileum

value: F

tag: b montreal

tag: perianal disease

tag: rectosigmoid involvement


title: 12_CC_CPH1EFG1_III

city: Jena

first: Sascha

last: Schäuble

address: Beutenbergstraße 11a

country: Germany

institute: Leibniz Institute for Natural Product Research and Infection Biology

description:
Single-RNAseq
wt_vs_mut_Hsapiens_counts.xls
wt_vs_mut_Hsapiens_counts_mrn.xls

data_processing:
quality control using multiQC (v1.7)
quality trimming of raw data using trimmomatic (v0.36)
mapping using HiSat2 (v2.1.0)
read counts using featureCounts (v1.28.0)
Assembly: Homo sapiens: Ensembl_GRCh38; C_albicans_SC5314_version_A22
Supplementary files format and content: *counts.xls

source_name: IECs (C2BBe1)

growth_protocol: The intestinal epithelial Caco-2 brush border expressing 1 cell line (C2BBe1; ATCC, CRL2102)  was cultivated and differentiated in Dulbecco’s Modified Eagle’s Medium (DMEM) supplemented with 10% fetal bovine serum , 10µg/ml Holotransferrin , and 1% non-essential amino acids at 37°C with 5% CO2 for 12 d in collagen-coated 6-well plates (5×10^5 cells/well). Candida albicans overnight cultures were cultured for 16 h in YPD broth (1% yeast extract, 2% peptone, 2% ᴅ-glucose) at 30°C with shaking at 180 rpm.

extract_protocol:
At each respective time point, the medium was removed, unadhered Candida cells were washed away, and 650 µl of RLT buffer (RNeasy Minikit; Qiagen) was added to each well. The plates were frozen with liquid nitrogen and thawed at room temperature (RT). Each well was scraped and the suspensions were centrifuged for 8 min (20,000×g) to pellet the Candida cells. The supernatant was removed and the host RNA was isolated using the RNeasy Minikit (Qiagen) according to the manufacturer’s instructions.
After poly(A) enrichment, mRNA was fragmented and random-primed cDNA synthesis was performed followed by adaptor ligation and adaptor-specific PCR amplification. Single sequence reads of 50 bp were produced.

treatment_protocol: Differentiated intestinal epithelial cells (IECs) were infected with 2×10^6 Candida cells/well and incubated at 37°C and 5% CO2 in DMEM medium for 0.75, 3, 6, 12, or 24 h. In parallel, C2BBe1 and C. albicans cells were cultured individually in 6-well plates in DMEM medium. Prior to infection, individual C. albicans and C2BBe1 samples were harvested (0h).

tag: strain

value: IECs (C2BBe1)

value: C.alb. + C2BBe1 co-incubation (infection)

tag: time

tag: oxygen condition

value: normoxic


title: 12_CC_CPH1EFG1_II

tag: cell line


title: zebrafish_shield_20µM_lnacontrol_50mM_s4u_r5

tag: tissue

tag: genotype


title: head, young, male, H3.3Adelta, rep3

description:
Sample_MATA_LB_JB_87
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: whole head

tag: developmental stage

value: adult

tag: Sex

value: male

tag: age


title: PNIBD36_I, ileal tissue

tag: status

value: nonIBD

tag: family history

tag: surgery

tag: remission


title: head, old, female, H3.3Adelta, rep3

description:
Sample_MATA_LB_JB_88
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: female

value: old


title: PNIBD34_I, ileal tissue

value: M

tag: diagnosis age

tag: location montreal

tag: batch


title: PNIBD40_I, ileal tissue

tag: b montreal

tag: perianal disease

tag: rectosigmoid involvement


title: 12_CC_CPH1EFG1_I

tag: strain

tag: treatment

tag: time

tag: oxygen condition


title: head, young, female, H3.3Adelta, rep3

description:
Sample_MATA_LB_JB_86
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: tissue

tag: developmental stage

value: young

tag: genotype


title: PNIBD33_I, ileal tissue

tag: Sex

tag: status


title: 12_CC_SC5314_III

tag: cell line


title: head, old, male, H3.3BK36R, rep2

description:
Sample_MATA_LB_JB_85
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: age


title: 12_CC_SC5314_II


title: PNIBD31_I, ileal tissue

tag: diagnosis age

tag: family history

tag: surgery

tag: remission


title: head, old, female, H3.3BK36R, rep2

description:
Sample_MATA_LB_JB_84
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv


title: 12_CC_SC5314_I


title: NN-H3K27ac-2

value: HCT116 cells

value: Normoxia - No Bacteria (NN)


title: PNIBD30_I, ileal tissue

tag: location montreal

tag: batch

tag: b montreal

tag: perianal disease


title: head, old, male, H3.3Adelta, rep3

description:
Sample_MATA_LB_JB_89
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv


title: zebrafish_shield_20µM_lnacontrol_50mM_s4u_r2

value: Embryos

tag: Stage

value: shield stage

value: Offspring of [AB-TU]x[TL-TLF]

tag: treatment

value: 1000pL of 20µM lnacontrol and 50mM s4UTP injection


title: MuscleC_Cattle

city: Beijing

first: Siqian

last: Chen

address: 2rd, Yuanmingyuan West Road

department: College of Animal Science and Technology

institute: China Agricultural University

data_processing:
FastQC v 0.11.2 and Trim Galore v 0.4.0 was used to assess the quality of the sequence data and filter low-quality reads (q < 30), respectively. The cleaned data were then mapped to the sscrofa11.1 genomes using bowtie2 under the Bismark software (0.14.5) with default parameters
Duplicated reads were removed using deduplicate_bismark
symmetric-cpgs was employed to obtain methyl CpG site information using methpipe software
Assembly: ARS-UCD1.2, Oar_rambouillet_v1.0, ARS1
Supplementary files format and content: CpG report files

organism: Bos taurus

source_name: muscle

extract_protocol:
DNA was extracted according to the TIANamp Genomic DNA Kit protocol
DNA libraries were prepared for sequencing using standard Illumina protocols

tag: tissue

value: muscle


title: 12_CC_ECE1_III

tag: strain

value: IECs (C2BBe1)

value: C.alb. + C2BBe1 co-incubation (infection)

tag: time

tag: oxygen condition


title: PNIBD28_I, ileal tissue

value: ileum

tag: Sex

tag: status

tag: rectosigmoid involvement


title: PNIBD29_I, ileal tissue

value: F

tag: diagnosis age


title: head, old, male, H3.3Adelta, rep2

description:
Sample_MATA_LB_JB_81
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: whole head

tag: developmental stage

value: adult

value: male

tag: age

tag: genotype


title: 12_CC_ECE1_II

tag: cell line

value: normoxic


title: MuscleB_Cattle


title: head, young, female, H3.3BK36R, rep2

description:
Sample_MATA_LB_JB_82
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: female


title: 12_CC_ECE1_I


title: MuscleA_Cattle


title: PNIBD27_I, ileal tissue

value: M

value: nonIBD

tag: location montreal

tag: batch

tag: family history

tag: surgery

tag: remission


title: PNIBD26_I, ileal tissue

tag: tissue

tag: b montreal

tag: perianal disease


title: PNIBD25_I, ileal tissue


title: 12_CC_BWP17_II

tag: strain

tag: treatment

tag: time

tag: oxygen condition


title: head, young, male, H3.3Adelta, rep2

description:
Sample_MATA_LB_JB_79
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: Sex

value: young


title: BrainC_Cattle

source_name: brain

value: brain

tag: developmental stage


title: head, old, female, H3.3Adelta, rep2

description:
Sample_MATA_LB_JB_80
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: age

value: old


title: 12_CC_BWP17_III


title: BrainB_Cattle


title: 12_CC_BWP17_I


title: head, young, female, H3.3Adelta, rep2

description:
Sample_MATA_LB_JB_78
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: genotype


title: head, old, male, H3.3BK36R, rep1

description:
Sample_MATA_LB_JB_77
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv


title: PNIBD24_I, ileal tissue

tag: status

tag: diagnosis age

tag: rectosigmoid involvement


title: BrainA_Cattle


title: head, old, female, H3.3BK36R, rep1

description:
Sample_MATA_LB_JB_76
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv


title: head, young, male, H3.3BK36R, rep2

description:
Sample_MATA_LB_JB_83
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv


title: 12_C2_II

tag: cell line

value: C2BBe1 alone


title: PNIBD23_I, ileal tissue

tag: location montreal

tag: batch

tag: family history

tag: surgery


title: 12_C2_III


title: S225K_3

first: Ling

last: Li

address: 20th Dong Street, Fengtai District

institute: Beijing Institute of Biotechnology

data_processing:
Illumina Casava 1.8 software used for basecalling
Raw data (raw reads) of fastp format were firstly processed through in-house perl scripts. In this step, clean data (clean reads) were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. At the same time, Q20, Q30 and GC content the clean data were calculated. All the downstream analyses were based on the clean data with high quality.
Reference genome and gene model annotation files were downloaded from genome website directly. Index of the reference genome was built using Hisat2 v2.0.5 and paired-end clean reads were aligned to the reference genome using Hisat2 v2.0.5.
featureCounts v1.5.0-p3 was used to count the reads numbers mapped to each gene.
Differential expression analysis of two conditions/groups (two biological replicates per condition) was performed using the DESeq2 R package (1.20.0).
Assembly: mm10
Supplementary files format and content: tab-delimited text files include FPKM values and gene count for each Sample

organism: Mus musculus

source_name: liver tumor

extract_protocol:
Total RNA was isolated using TRIzol (Tiangen) according to the manufacturer’s instructions.
RNA libraries for RNA-seq were prepared using NEBNext® Ultra™ RNA Library Prep Kit for Illumina® following manufacturer's protocols.

tag: tissue

value: liver tumor

tag: cell type

value: mice liver tumor cell

value: Alb-Cre; SIX1 S225Kfl/fl

value: DEN induce


title: 12_C2_I

value: IECs (C2BBe1)

tag: treatment


title: S225K_2


title: PNIBD21_I, ileal tissue

value: ileum

value: F

tag: b montreal

tag: perianal disease

tag: remission


title: head, young, female, H3.3BK36R, rep1

description:
Sample_MATA_LB_JB_74
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: whole head

tag: developmental stage

value: adult

tag: Sex


title: 0_C2_III

tag: time

value: 0 h

tag: oxygen condition

value: normoxic


title: S225K_1

tag: genotype


title: head, young, male, H3.3BK36R, rep1

description:
Sample_MATA_LB_JB_75
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

value: male

tag: age


title: PNIBD20_I, ileal tissue

tag: status

value: nonIBD

tag: diagnosis age

tag: rectosigmoid involvement


title: ctrl_3

value: SIX1 S225Kfl/fl


title: head, old, male, H3.3Adelta, rep1

description:
Sample_MATA_LB_JB_73
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv


title: PNIBD19_I, ileal tissue

tag: location montreal

tag: batch

tag: family history


title: 0_C2_II

description:
Single-RNAseq
wt_vs_mut_Hsapiens_counts.xls
wt_vs_mut_Hsapiens_counts_mrn.xls

tag: cell line


title: PNIBD18_I, ileal tissue

tag: tissue

value: M

tag: surgery


title: PNIBD17_I, ileal tissue

tag: b montreal

tag: perianal disease


title: head, old, female, H3.3Adelta, rep1

description:
Sample_MATA_LB_JB_72
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: developmental stage

value: female

value: old


title: ctrl_1

value: liver tumor

tag: cell type

tag: treatment


title: ctrl_2

value: mice liver tumor cell


title: head, young, male, H3.3Adelta, rep1

description:
Sample_MATA_LB_JB_71
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: Sex

value: young


title: progeny from hybrid chimera, replicate 4

city: Vodnany

first: Rigolin

last: Nayak

state: South Bohemia

address: Zátiší 728/II

department: Faculty of Fisheries and Protection of Waters

country: Czech Republic

institute: University of South Bohemia in Ceske Budejovice

data_processing:
The Trimmomatic is used for Trimming, the implemented trimming steps are as follows. (1) Scan the read with a 4-base wide sliding window, cutting when the average quality per base drops below 15 (Parameters: SLIDINGWINDOW:4:15) (2) Remove leading low quality and trailing low quality. (Parameters: LEADING:3，TRAILING:3) (3) Remove Illumina adapters. Initially Trimmomatic will look for seed matches reach a score of 7 (around 12 bases) allowing maximally 2 mismatches. These seeds will be extended and clipped if in the case of paired end reads reach a score of 30. (Parameters: ILLUMINACLIP:adapter.fa:2:30:7:1:true) (4) Drop reads which are less than 36 bases long after these steps. (5) Drop reads which cannot match with pairs after these steps. (6) For single cell methylation libraries and low initial methylation libraries, cut the specified number of bases from the start of the read. (Parameters: HEADCROP:10)  Summary of parameters: SLIDINGWINDOW:4:15, LEADING:3, TRAILING:3, mismatch 2, ILLUMINACLIP:adapter.fa:2:30:7
Bismark software (version 0.16.3; Krueger F, 2011) was used to perform alignments of bisulfite-treated reads to a reference genome (-X 700 --dovetail). The reference genome was firstly transformed into bisulfite-converted version (C-to-T and G-to-A converted) and then indexed using bowtie2 (Langmead B, 2012). Sequence reads were also transformed into fully bisulfite-converted versions (C-to-T and G-to-A converted) before they are aligned to similarly converted versions of the genome in a directional manner. Sequence reads that produce a unique best alignment from the two alignment processes (original top and bottom strand) are then compared to the normal genomic sequence and the methylation state of all cytosine positions in the read is inferred. The same reads that aligned to the same regions of genome were regarded as duplicated ones. The sequencing depth and coverage were summarized using deduplicated reads. The results of methylation extractor (bismark_methylation_extractor, -- no_overlap) were transformed into bigWig format for visualization using IGV browser. The sodium bisulfite non-coversion rate was calculated as the percentage of cytosine sequenced at cytosine reference positions in the lambda genome
Assembly: GRCz11 (genome ID: ensembl_danio_rerio_grcz11_gca_000002035_4)

source_name: whole larvae

growth_protocol: The sperm was collected from the males separately for each group by hand stripping followed by fertilization with the oocyte from the control females

extract_protocol:
genomic DNA was extracted using  PureLink™ Genomic DNA Kit (ThermoFisher)
Accel-NGS Methyl-Seq DNA Library Kit was used for WGBS library preparation

value: whole larvae

tag: genotype


title: PNIBD16_I, ileal tissue

tag: remission


title: head, young, female, H3.3Adelta, rep1

description:
Sample_MATA_LB_JB_70
DESeq2_20230929_dm6_forStrand_noINT_wOUT_normCounts.csv

tag: age


title: 0_C2_I

value: IECs (C2BBe1)

value: C2BBe1 alone

tag: time

tag: oxygen condition


title: PNIBD15_I, ileal tissue

value: ileum

value: F

tag: status

tag: diagnosis age

tag: location montreal

tag: rectosigmoid involvement


title: progeny from hybrid chimera, replicate 2

tag: tissue


title: Placenta Ethanol 9 mRNA-Seq

city: Montreal

first: Serge

last: McGraw

state: Qc

address: 3175 Côte Sainte-Catherine, office 5.17.005

country: Canada

institute: CHU Ste-Justine Research Center/Université de Montréal

data_processing:
Sequence reads were trimmed using Trimmomatic (v0.36)
Gene counts matrix and differentially expressed genes (DEGs) were obtained using the R package DESeq2 (v1.24.0)
Assembly: mm10
Supplementary files format and content: tab-delimited text files including raw counts

source_name: Placenta

extract_protocol:
RNA was extracted using Qiagen Rneasy Mini kit (Qiagen) following manufacturer's recommendations
Libraries were performed using NEBNext Ultra II Directional RNA Library Prep Kit following manufacturer's protocol

value: Placenta

tag: strain

value: Ethanol


title: Placenta Ethanol 10 mRNA-Seq


title: PNIBD13_I, ileal tissue

tag: batch

tag: b montreal

tag: family history

tag: surgery


title: Placenta Ethanol 8 mRNA-Seq

tag: treatment


title: PNIBD12_I, ileal tissue

tag: Sex

tag: perianal disease


title: Placenta Ethanol 7 mRNA-Seq


title: PNIBD11_I, ileal tissue

tag: remission


title: progeny from morpholino treated chimera, replicate 4

tag: genotype


title: progeny from morpholino treated chimera, replicate 3


title: Placenta Ethanol 6 mRNA-Seq


title: Placenta Ethanol 5 mRNA-Seq


title: progeny from morpholino treated chimera, replicate 2


title: PNIBD09_I, ileal tissue


title: PNIBD08_I, ileal tissue


title: progeny from morpholino treated chimera, replicate 1


title: zebrafish_7hours_aamanitin_75mM_s4u_r2

data_processing:
Slamdunk 0.4.3.
Reads that contain at least 2 T>C conversions were deemed labeled.
Assembly: danRer11
Supplementary files format and content: Comma-separated values, <.csv>; Total raw read and labeled read counts for all experiments and samples, including spike-ins. Rows represent different 3'UTR isoforms (for coding genes) or full-length transcript (non-coding genes). Columns represent: Ensembl gene IDs by itself (non-coding transcripts) + 3'UTR isoforms (coding transcripts), or ERCC IDs (spike ins);  Chromosome name; Genomic start of feature; Genomic end of feature; DNA strand of feature; Number of Ts within feature;

extract_protocol:
Trizol™
QuantSeq 3′ mRNA‐Seq Library Prep Kit for Illumina (FWD) with 24 reactions (Lexogen GmbH, cat. no. 015.24), Lexogen i7 6-nt Index Set.

treatment_protocol: Embryos were dechorionated and either non-injected or injected at single cell stage with ~1000pL of 25/50/75mM s4-UTP by itself or the highest dose with 200mg/mL Alpha Amanitin

value: Embryos

tag: Stage

value: shield stage

value: Offspring of [AB-TU]x[TL-TLF]


title: Placenta Ethanol 3 mRNA-Seq


title: progeny from hybrid chimera, replicate 3


title: progeny from hybrid chimera, replicate 1


title: PNIBD14_I, ileal tissue

value: nonIBD


title: Placenta Ethanol 4 mRNA-Seq


title: zebrafish_7hours_aamanitin_75mM_s4u_r1


title: progeny from donor, replicate 4


title: PNIBD06_I, ileal tissue

value: M


title: Placenta Ethanol 2 mRNA-Seq


title: PNIBD05_I, ileal tissue


title: PNIBD03_I, ileal tissue


title: Hepa1-6 tumor endothelial cell

type: RNA

city: Kurume

first: Hideki

last: Iwamoto

state: Fukuoka

address: 67 Asahimachi

department: Division of Gastroenterology, Department of Medicine

institute: Kurume University School of Medicine

description: Gene expression

hyb_protocol: cRNA was hybridized to a 60K 60-mer oligomicroarray (SurePrint G3 Mouse Gene Expression Microarray 8x60K v2 ; Agilent Technologies) according to the manufacturer's instructions.

scan_protocol: The hybridized microarray slides were scanned using an Agilent scanner. The relative hybridization intensities and background hybridization values were calculated using Feature Extraction Software version 9.5.1.1 (Agilent Technologies).

data_processing: The scanned images were analyzed with Feature Extraction Software 9.5.1.1 (Agilent) using default parameters to obtain background subtracted and spatially detrended Processed Signal intensities. The raw signal intensities and flags for each probe were calculated from the hybridization intensities and spot information according to the procedures recommended by Agilent Technologies using the Flag criteria in the GeneSpring Software. The raw signal intensities of all samples were  normalized by the quantile algorithm with the Bioconductor.

source_name: Tumor endothelial cell isolated from hepatoma

label_protocol: cRNA was amplified and labelled using a Low input Quick Amp Labelling Kit (Agilent Technologies).

extract_protocol: The total RNA was isolated from cells using TRIzol Reagent (nitrogen) and purified using SV Total RNA Isolation System (Promega) according to the manufacturer's instructions.

value: liver


title: zebrafish_7hours_wt_75mM_s4u_r2


title: Hepa 1-6 cancer

description: Gene expression

source_name: culture cell

tag: cell strain

value: Hepa 1-6


title: KYN2 tumor endothelial cell

description: Gene expression


title: progeny from donor, replicate 1


title: zebrafish_7hours_wt_75mM_s4u_r1


title: PNIBD02_I, ileal tissue

tag: status


title: HAK1B tumor endothelial cell

description: Gene expression


title: PNIBD07_I, ileal tissue

tag: diagnosis age


title: Hybrid chimera sperm, replicate 4

source_name: sperm

value: sperm


title: zebrafish_7hours_wt_50mM_s4u_r3


title: zebrafish_7hours_aamanitin_75mM_s4u_r3


title: Hybrid chimera sperm, replicate 3


title: Placenta Ctrl 5 mRNA-Seq

value: Saline


title: PB319_I, ileal tissue

value: CD

tag: location montreal


title: progeny from donor, replicate 3

value: whole larvae


title: Placenta Ctrl 3 mRNA-Seq


title: zebrafish_7hours_wt_50mM_s4u_r2


title: PB318_I, ileal tissue

tag: rectosigmoid involvement


title: Hybrid chimera sperm, replicate 2

tag: tissue


title: Placenta Ctrl 2 mRNA-Seq

tag: strain


title: zebrafish_7hours_wt_75mM_s4u_r3


title: Liver Sinusoidal endothelial cell

description: Gene expression

source_name: Liver sinusoidal endothelial cell isolated from mouse liver


title: zebrafish_7hours_wt_50mM_s4u_r1


title: Placenta Ethanol 1 mRNA-Seq


title: PB317_I, ileal tissue

tag: batch


title: PB314_I, ileal tissue


title: Morpholino treated chimera sperm, replicate 4


title: progeny from donor, replicate 2


title: zebrafish_7hours_wt_25mM_s4u_r2


title: zebrafish_7hours_wt_25mM_s4u_r3


title: Placenta Ctrl 6 mRNA-Seq


title: zebrafish_7hours_wt_25mM_s4u_r1


title: Placenta Ctrl 4 mRNA-Seq


title: Morpholino treated chimera sperm, replicate 3


title: Morpholino treated chimera sperm, replicate 2


title: PB306_I, ileal tissue


title: Placenta Ctrl 1 mRNA-Seq


title: zebrafish_7hours_wt_non_injected_r3


title: PB311_I, ileal tissue


title: Placenta Ethanol 8 Capture

data_processing:
Sequence reads were trimmed using Trimmomatic (v0.36)
Alignment and methylation counts were performed with Bismark (v0.18.1)
Assembly: mm10
Supplementary files format and content: tab-delimited files including CpG sites coordinate, coverage, methylation values
Supplementary files format and content: Input files for the methylKit package

extract_protocol:
Genomic DNA was extracted using QIAamp DNA Micro Kit (Qiagen) following manufacturer's recommendations
Libraries were performed using SureSelectXT Methyl-Seq mouse Target Enrichment System (Agilent) following manufacturer's protocol


title: Placenta Ethanol 10 Capture


title: PB303_I, ileal tissue


title: Morpholino treated chimera sperm, replicate 1


title: Placenta Ethanol 7 Capture


title: PB227_I, ileal tissue


title: zebrafish_7hours_wt_non_injected_r1


title: Placenta Ethanol 6 Capture


title: Hybrid chimera sperm, replicate 1


title: Donor sperm, replicate 3


title: PHBC endothelial cells 30 hpf, wnt7aa MO 4

city: bad nauheim

first: Stefan

last: Günther

address: ludwigtr. 43

institute: MPI for heart and lung research

data_processing:
The resulting raw reads were assessed for quality, adapter content, and duplication rates with FastQC. Trimmomatic version 0.33 was employed to trim reads after a quality drop below a mean of Q20 in a window of 10 nucleotides82. Only reads between 30 and 150 nucleotides were cleared for further analyses.
Trimmed and filtered reads were aligned versus the Zebrafish genome version DanRer10 (GRCz10.87) using STAR 2.4.0a with the parameter “—outFilterMismatchNoverLmax 0.1” to increase the maximum ratio of mismatches to mapped length to 10%.
The number of reads aligning to genes was counted with featureCounts 1.5.1 tool from the Subread package84. Only reads mapping at least partially inside exons were admitted and aggregated per gene. Reads overlapping multiple genes or aligning to multiple regions were excluded.
The Ensemble annotation was enriched with UniProt data (release 06.06.2014) based on Ensembl gene identifiers (activities at the Universal Protein Resource (UniProt)).
Assembly: DanRer10
Supplementary files format and content: library-size normlized counts

source_name: Vascular endothelium

extract_protocol:
RNA was isolated from FACS sorted zebrafish CtAs ECs cells using the miRNeasy micro Kit (Qiagen) combined with on-column DNase digestion (DNase-Free DNase Set, Qiagen) to avoid contamination by genomic DNA.
RNA amount was adjusted on number of isolated cells by FACS and ~250–500 pg total RNA was used as input for SMART-Seq® v4 Ultra® Low Input RNA Kit (Takara Bio) for cDNA pre-amplification. Obtained full-length cDNA was checked on LabChip and fragmented by Ultrasonication by E220 machine (Covaris). Final Library Preparation was performed by Low Input Library Prep Kit v2 (Takara Bio).

value: Vascular endothelium

tag: cell line

value: PHBC endothelial cells

value: 30 hpf

tag: cell type

value: Endothelial cells

tag: transgene

value: wnt7aa MO

value: photoconverted


title: PB213_I, ileal tissue

value: ileum

tag: family history

tag: surgery


title: PHBC endothelial cells 30 hpf, wnt7aa MO 3

tag: treatment


title: Placenta Ethanol 5 Capture

value: Placenta

value: Ethanol


title: PB212_I, ileal tissue

tag: Sex

value: F

tag: perianal disease

tag: remission


title: Placenta Ethanol 4 Capture


title: Donor sperm, replicate 2

tag: genotype


title: PB216_I, ileal tissue

value: M

tag: status


title: Placenta Ethanol 9 Capture


title: Donor sperm, replicate 1


title: PB211_I, ileal tissue

tag: diagnosis age


title: Donor sperm, replicate 4


title: PHBC endothelial cells 30 hpf, wnt7aa MO 1

tag: Stage


title: RIAILs_Batch9_QX572

city: Lausanne

first: Gaby

last: El Alam

state: Vaud

address: Station 15

department: SV LISP

country: Switzerland

institute: École polytechnique fédérale de Lausanne

data_processing:
FastQC (default parameters) was used to verify the quality of the reads. No low-quality reads were present and no trimming was needed.
Alignment was performed against worm genome (WBcel235 sm-toplevel) following the STAR (version 2.73a) manual guidelines
Counts for each sample features (outputed by STAR) where read into R
The STAR gene-counts for each alignment were analyzed for differentially expressed genes using the R package DESeq2
Assembly: WBcel235 sm-toplevel
Supplementary files format and content: tab-delimited text files include raw mapped read counts per feature (generated by STAR - per strand and combined strands)

organism: Caenorhabditis elegans

growth_protocol: Worms of each strain were cultured on plates seeded with E. coli OP50, then eggs were obtained by alkaline hypochlorite treatment of gravid adults. A synchronized L1 population was obtained by incubating the egg suspension in M9 butter overnight at room temperature. Approximately 2000 L1 worms were transferred onto plates seeded with E. coli HT115. L4 worms were harvested after 50 h by three times of washing with M9 buffer. Tubes containing worm pellets were immediately submerged in liquid nitrogen for snap freezing and stored at -80ºC until use.

extract_protocol:
On the day of the extraction, 1 mL of TriPure Isolation Reagent was added to each tube. The samples were then frozen and thawed quickly eight times with liquid nitrogen and 37ºC water bath to rupture cell membranes. RNA was then extracted by using a column-based kit from Macherey-Nagel.
BGISeq-500 library construction Protocol

treatment_protocol: Synchronized worms from each strain were few with E. coli HT115

value: Cntrl


title: Placenta Ethanol 3 Capture


title: PHBC endothelial cells 30 hpf, wnt7aa MO 2


title: PHBC endothelial cells 30 hpf, reck MO 4

value: reck MO


title: RIAILs_Batch9_QX568


title: PHBC endothelial cells 30 hpf, reck MO 3


title: zebrafish_7hours_wt_non_injected_r2

value: Embryos

value: shield stage

value: Offspring of [AB-TU]x[TL-TLF]


title: PB210_I, ileal tissue

value: CD

tag: location montreal

tag: rectosigmoid involvement


title: Placenta Ctrl 6 Capture

tag: tissue

tag: strain

value: Saline


title: Placenta Ethanol 1 Capture


title: RIAILs_Batch9_QX537


title: PB209_I, ileal tissue

tag: batch


title: RIAILs_Batch9_QX515


title: PB207_I, ileal tissue


title: Placenta Ctrl 3 Capture


title: RIAILs_Batch9_QX503


title: PHBC endothelial cells 30 hpf, TF MO 3

value: Vascular endothelium

tag: cell line

value: PHBC endothelial cells

tag: cell type

value: TF MO


title: RIAILs_Batch9_QX519


title: Placenta Ctrl 1 Capture


title: PB208_I, ileal tissue

tag: family history


title: PHBC endothelial cells 30 hpf, TF MO 2

value: 30 hpf

value: Endothelial cells

tag: transgene


title: PB148_I, ileal tissue

value: ileum

tag: surgery


title: PHBC endothelial cells 30 hpf, reck MO 2

tag: treatment

value: photoconverted


title: Placenta Ctrl 5 Capture

value: Placenta


title: MD2

city: Fort Collins

first: Devin

last: Wahl

state: Colorado

address: 1582 Campus Delivery, Moby Reception

institute: Colorado State University

description: rTg4510 treated

data_processing:
Adapters trimmed & file QC by Fastp
Reads aligned with STAR
Differential expression analyzed with DESeq2
Assembly: mm10 Mus musculus
Supplementary files format and content: Raw counts for each sample in excel matrix

source_name: Hippocampus

extract_protocol:
RNA for RNA-seq extracted using Trizol and Zymo spin columns.
Libraries were prepared according to manufacturer's instructions using the Illumina TruSeq kit

value: Hippocampus

value: Nanoligomer


title: PHBC endothelial cells 30 hpf, reck MO 1


title: RIAILs_Batch9_QX496

value: Cntrl


title: PB146_I, ileal tissue

tag: Sex

value: M

tag: perianal disease


title: PB206_I, ileal tissue

tag: remission


title: RIAILs_Batch9_QX508


title: PHBC endothelial cells 30 hpf, TF MO 4

tag: genotype


title: PB204_I, ileal tissue

tag: status

tag: diagnosis age


title: Placenta Ctrl 2 Capture


title: Placenta Ethanol 2 Capture

value: Ethanol


title: PB202_I, ileal tissue

tag: location montreal


title: RIAILs_Batch9_QX501


title: RIAILs_Batch9_QX494


title: PB144_I, ileal tissue

value: F

tag: rectosigmoid involvement


title: M2

tag: tissue

value: Control


title: RIAILs_Batch9_QX492

tag: strain


title: RIAILs_Batch9_QX498


title: LMM2

description: Littermate Controls

value: Littermate control


title: PHBC endothelial cells 30 hpf, TF MO 1

tag: Stage


title: MD3

description: rTg4510 treated


title: PB147_I, ileal tissue

value: CD

tag: batch


title: RIAILs_Batch9_QX497


title: PHBC endothelial cells 30 hpf, gpr124 MO 4

value: Vascular endothelium

tag: cell line

tag: cell type

value: gpr124 MO


title: Placenta Ctrl 4 Capture

value: Saline


title: PB143_I, ileal tissue

tag: family history


title: PHBC endothelial cells 30 hpf, WT 4

value: PHBC endothelial cells

value: 30 hpf

tag: transgene

value: WT


title: PHBC endothelial cells 30 hpf, gpr124 MO 3

value: Endothelial cells

tag: treatment

value: photoconverted


title: PB142_I, ileal tissue

value: ileum

tag: Sex

tag: surgery


title: PHBC endothelial cells 30 hpf, gpr124 MO 2


title: M3

value: Hippocampus


title: LMF3

description: Littermate Controls


title: RIAILs_Batch9_CB4856

value: Cntrl


title: LMM1

description: Littermate Controls


title: LMF2

description: Littermate Controls


title: RIAILs_Batch9_QX491


title: PHBC endothelial cells 30 hpf, gpr124 MO 1


title: PB140_I, ileal tissue

tag: perianal disease

tag: remission


title: PHBC endothelial cells 30 hpf, WT 3

tag: genotype


title: RIAILs_Batch9_N2


title: FD2

description: rTg4510 treated

value: Nanoligomer


title: PB145_I, ileal tissue

value: M

tag: status

tag: diagnosis age


title: PB141_I, ileal tissue

value: F

tag: location montreal

tag: rectosigmoid involvement


title: RIAILs_Batch8_QX598

tag: strain


title: FD1

description: rTg4510 treated

tag: tissue


title: PHBC endothelial cells 30 hpf, WT 2

tag: Stage


title: PHBC endothelial cells 30 hpf, WT 1

tag: cell line


title: PB139_I, ileal tissue

tag: batch


title: RIAILs_Batch8_QX595


title: Endothelial cells 30 hpf, negative 1

tag: cell type

value: Non photoconverted


title: RIAILs_Batch8_QX596


title: Endothelial cells 30 hpf, negative 3

tag: transgene


title: RIAILs_Batch8_QX597

tag: treatment


title: Endothelial cells 30 hpf, negative 2


title: PB136_I, ileal tissue

tag: Sex

tag: family history


title: F1

value: Control


title: F3


title: PB137_I, ileal tissue

value: CD

tag: perianal disease

tag: surgery


title: P5

city: Tianjin

first: Kui

last: Wang

address: Weijin Road 94

department: School of Statistics and Data Science

institute: Nankai University

description: LGH

library_source: transcriptomic single cell

data_processing:
The sequencing reads were processed using the pipeline of Drop-Seq and mapped to human genome with STAR2.6.0a
Assembly: GRCh38
Supplementary files format and content: anndata with raw counts of RNA expression

source_name: interventricular septum

extract_protocol:
Tissue fragments from HCM patients were transfered to the oxygenated Ca2+ free solution and filtered into a conical flask containing enzymatic buffer (275 u/ml collagenase II and 1.2 u/ml protease XXIV). Discard the supernatant once the supernatant become obscure and incubate the fragments in a fresh enzyme solution without protease. Remove the supernatant and re-suspend pelleted myocytes in resuspension buffer. Freshly collected cardiocytes from HCM patients were washed with PBS, picked using piptides under a microscope and then processed for library construction.
cDNA libraries were prepared based on the STRT-seq protocol. Briefly, cardiocytes were resuspended in the lysis buffer. 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 barcodes.  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. The pooled barcoded cDNA was then amplified by PCR and fragmented using Tn5 transpose. The apropiated sized fragments were selected with Ampure XP beads

value: CM cells

value: interventricular septum

tag: age


title: PB135_I, ileal tissue

tag: status

tag: remission


title: RIAILs_Batch8_QX587


title: YM4

description: Young Control

tag: genotype

value: wildtype


title: PB133_I, ileal tissue

tag: diagnosis age

tag: location montreal

tag: rectosigmoid involvement


title: P4

description: SCL

tag: tissue


title: P3

description: GCZ


title: PB134_I, ileal tissue


title: YF4

description: Young Control

tag: strain


title: YM1

description: Young Control


title: PB132_I, ileal tissue

tag: batch


title: RIAILs_Batch8_QX586


title: P2

description: ZZW

tag: cell type


title: RIAILs_Batch8_QX584


title: YF2

description: Young Control


title: P1

description: CZQ


title: RIAILs_Batch8_QX591


title: PB130_I, ileal tissue


title: DM2

description: Old Treated


title: RIAILs_Batch8_QX580


title: DF2

description: Old Treated


title: PB129_I, ileal tissue


title: RIAILs_Batch8_QX579


title: PB128_I, ileal tissue


title: Day3-N3

city: Kisarazu

first: Toshio

last: Kanno

state: Chiba

address: 2-6-7 Kazusa-kamatari

institute: KAZUSA DNA Research Institute

data_processing:
For RNA-sequence, read sequences (75 bp) were aligned to the mm10 mouse reference genome (University of California, Santa Cruz (UCSC) December 2011) using STAR (version 2.7.9a).
Fragments per kilobase of transcripts for each gene were calculated using Subread (version 2.0.1, 13 ).
Assembly: mm10
Supplementary files format and content: Text files include TPM values for each Sample

source_name: Spleen

growth_protocol: See "Materials and Methods".

extract_protocol:
Total cellular RNA was extracted with TRIzol reagent (Invitrogen).
QuantSeq 3' mRNA-Seq Library Prep Kit FWD (LEXOGEN) was used for library constraction according to the manufacturer's protocol.

treatment_protocol: See "Materials and Methods".

value: Spleen

value: Gr1+ cell

value: Gr-1+ cells on day 3 after P/A immunization.ヤクザイショリ オオマカナ


title: Day3-N2

value: WT


title: DF1

description: Old Treated


title: Day1-N3

value: Gr-1+ cells on day 1 after P/A immunization.


title: RIAILs_Batch8_QX565


title: RIAILs_Batch8_QX585


title: Day3-N1


title: PB126_I, ileal tissue

source_name: ileum

value: ileum


title: RIAILs_Batch8_QX567


title: PB124_I, ileal tissue


title: RIAILs_Batch8_QX561


title: Day1-N2


title: RIAILs_Batch8_QX545


title: PB131_I, ileal tissue


title: CM1

description: Old Control

value: Hippocampus


title: Day1-N1


title: RIAILs_Batch8_QX534

value: Cntrl


title: CF3

description: Old Control


title: DM5

description: Old Treated

value: Nanoligomer


title: PB121_I, ileal tissue

value: M


title: Day0-N3

value: Non treatment


title: PB123_I, ileal tissue

value: F


title: CF2

description: Old Control

value: Control


title: PB120_I, ileal tissue

value: CD


title: RIAILs_Batch8_QX533


title: PB114_I, ileal tissue


title: Day0-N2


title: CM3

description: Old Control


title: Day0-N1


title: Heart, aged, hashtag oligos

city: Charleston

first: Stefano

last: Berto

state: SC

address: 68 President Street

department: Neuroscience

institute: Medical University of South Carolina

data_processing:
Raw sequencing data were processed with Cell Ranger (v7.0.0). Cellranger mkfastq command was used to demultiplex the different samples and cellranger multi command was used to generate gene – cell expression, ADT - cell expression, and HTO - cell expression matrices. Ambient RNA contamination was inferred and removed using CellBender (v0.232) with standard parameters. Mouse genome mm10 was used for the alignment and gencode vM10 (GRCm38.p4)was used for gene annotation and coordinates. We used the R package Seurat (v4.1.0) and customized R scripts for data analyses Data from different samples (young and aged) were merged into a unique single cell object. Nuclei with > 250 genes, < 20000 UMIs, and < 20% mitochondrial transcripts were retained for downstream analysis. Genes located in the mitochondrial genome were removed. Doublets were removed using scDblFinder (v1.8.0) for a resultant expression matrix with 16,418 genes and 15,826 cells. The SCTransform workflow was used for count normalization and data integration using 30 principal components and resolution of 0.6 for Louvain clustering and UMAP. Cluster marker genes were identified using FindAllMarkers using Wilcoxon Rank Sum test with the standard parameters. After removing 4 clusters showing high expression of glutamatergic neuronal markers and subsequent re-clustering, we identified 20 final distinct clusters. Cell annotation was manually curated using markers from literature. To identify differentially expressed genes between conditions (young vs aged) in each defined cell types, the R package LIBRA with option MAST was used to perform zero-inflated regression analysis. Genes were defined as significantly differentially expressed at Benjamini–Hochberg correction FDR < 0.05 and abs(log2(Fold Change)) > 0.2.
Assembly: Mus musculus mm10
Supplementary files format and content: HDF5 Feature-Barcode Matrix

source_name: heart

extract_protocol:
Myocardial infarction as induced in C57Bl6/J female mice by permanent occlusion of the left anterior descending artery ligation. At post-MI Day 5, cells were isolated from the infarct zone of young (3-5 months) and old (15-17 months old) and run for scRNA sequencing.
Droplet-based snRNA-seq libraries were prepared using the Chromium Single Cell 3’ v3.1 according to the manufacturer’s protocol. Libraries and sequencing were performed at the Translational Sequencing Core at MUSC. Antibody-derived tag (ADT) libraries were constructed using TotalSeq-A anti-mouse for CD8a, CD44, CD62L, NK1.1, TCRgd, and CD3. Three biological replicates were used for each category (young and aged); these replicates were each tagged with TotalSeq B anti-mouse hashtags 2, 3, and 4 and multiplexed.

value: heart

value: old (15-17 months)


title: RIAILs_Batch8_QX532


title: Heart, young, hashtag oligos

value: young (3-5 months)


title: RIAILs_Batch8_N2


title: PB113_I, ileal tissue


title: RIAILs_Batch8_QX527


title: Anti-IL-27-N3

value: Spleen

value: NKT cell

value: NKT cells on day 3 after P/A immunization treated with anti-IL-27 antibody.ヤクザイショリ オオマカナ


title: PB112_I, ileal tissue


title: RIAILs_Batch8_CB4856


title: PB111_I, ileal tissue


title: Heart, aged, antibody-derived tags


title: Anti-IL-27-N1

value: WT


title: RIAILs_Batch7_QX577


title: Heart, aged, gene expression


title: Anti-IL-27-N2


title: Isotype-N3

value: NKT cells on day 3 after P/A immunization treated with isotype control.オオマカナ


title: Heart, young, gene expression


title: PB109_I, ileal tissue

value: ileum


title: RIAILs_Batch7_QX576


title: Isotype-N2


title: Yumm3.3_ActA_IFNy_12H_R4

first: Giovanna

last: Ambrosini

address: Station 19

institute: EPFL

data_processing:
Sequencing data were demultiplexed using the BRB-seq tools suite from Deplancke Lab (https://github.com/DeplanckeLab/BRB-seqTools)
Raw reads were aligned to the mouse (GRCm39) genome using STAR (2.7.10b)
Gene counts were generated using FeatureCounts and differential expression analysis was performed with the DESeq2 (v.1.36.0) package from Bioconductor (v3.15)
Assembly: mm39
Supplementary files format and content: raw_counts.txt

source_name: skin

growth_protocol: YUMM3.3 mouse melanoma cells were maintained in DMEM/F12 (Gibco) medium supplemented with 10% fetal bovine serum, 50 µg/mL gentamicin (Gibco, Thermo Fisher Scientific, Waltham, MA, USA), and 1% GlutaMAX (Gibco).

extract_protocol:
Total RNA was extracted using Quant-iT™ RiboGreen™ RNA Assay Kit from Invitrogen R11490
Transcriptomes were prepared using MERCURIUS BRB-seq kit library

treatment_protocol: YUMM3.3 cells were seeded in 6 well plates in quadruplicates at density of 0.5x106 and treated with 20 ng/ml IFN-γ and 40 ng/ml Activin-A individually or together for 4 or 12 hrs.

value: skin

tag: cell line

value: mouse melanoma cell line

tag: time


title: RIAILs_Batch7_QX575

tag: treatment

value: Cntrl


title: PB108_I, ileal tissue

data_processing:
Transcript expression was quantified using Salmon with default parameters.
Supplementary files format and content: Processed files are comma-separated, rows representing raw counts for genes (as gene symbols or as Ensembl ID's if no gene symbol available)

extract_protocol:
Macroscopically uninflamed mucosal samples from the ascending colon and terminal ileum were obtained at the time of initial iagnosis, before therapy was started. These samples were preserved as fresh frozen paraffin-embedded (FFPE) tissue. RNA was isolated from FFPE tissue using the Quick-RNA FFPE MiniPrep (Zymo Research, Irvine, CA). Total RNA was then purified using the MagMAX kit in the KingFisher system (ThermoFisher, Carlsbad, CA).
RNA-seq libraries were prepared using TruSeq Stranded Total RNA with Ribo-Zero (Illumina, San Diego, CA). Paired-end (50bp) sequencing was processed on the NovaSeq 6000 platform using default parameters (Illumina, San Diego, CA).

tag: Sex

tag: family history


title: PB107_I, ileal tissue

value: M

tag: perianal disease

tag: surgery


title: Isotype-N1


title: PB106_I, ileal tissue

tag: status


title: Naive-N3

value: Non treatment


title: RIAILs_Batch7_QX574


title: Yumm3.3_ActA_IFNy_12H_R2


title: Heart, young, antibody-derived tags

tag: age


title: RIAILs_Batch7_QX573


title: Naive-N2

tag: genotype


title: PB105_I, ileal tissue

tag: diagnosis age

tag: remission


title: PB102_I, ileal tissue

value: F

tag: location montreal

tag: rectosigmoid involvement


title: Yumm3.3_ActA_IFNy_12H_R1

tag: tissue


title: Yumm3.3_IFNy_12H_R4

value: IFN-gamma


title: Naive-N1

tag: strain


title: RIAILs_Batch7_QX570


title: cortical progenitors, siPhf6

city: Ottawa

first: Arezu

last: Jahani-Asl

state: Ontario

address: 451 Smyth Road

department: Department of Cellular and Molecular Medicine

institute: University of Ottawa

data_processing:
RNA-seq raw reads were mapped to mm10 genome usingHISAT2, followed by duplicate read removal usingsamtools.
Gene-level read counts were obtained byHTSeq, using gene annotations from GENCODE (release M9).
Bigwig files were created from BAM files using bamCoverage (version 3.5.1, --binSize 10).
Assembly: mm10
Supplementary files format and content: TAB delimited file with counts

source_name: brain cortex

extract_protocol:
Cortical progenitors were established from the cortex and were maintained in culture for 5 days to expand the homogeneous population prior to submitting samples for mRNA-Seq.
RNA-Seq libraries were constructedfrom total RNA with the TruSeq RNA v2 kit (Illumina).

value: brain cortex

value: progenitor cells

tag: cell type

value: cortical progenitors


title: RIAILs_Batch7_QX569


title: Yumm3.3_IFNy_12H_R3

tag: cell line


title: Yumm3.3_IFNy_12H_R1

tag: time


title: RIAILs_Batch7_QX493

tag: treatment


title: PNIBD56_C, colonic tissue

source_name: colon

value: colon

tag: Sex

value: nonIBD

tag: batch

tag: b montreal